RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4990
(130 letters)
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 173 bits (440), Expect = 1e-57
Identities = 66/80 (82%), Positives = 74/80 (92%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
V+D E+QEH+D F+EDVFVE E+KYGEIEEMNVCDNLGDHLVGNVY+KFRREEDAEKA
Sbjct: 25 VKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAEKA 84
Query: 64 VNDLNNRWFGGRPVYAELSP 83
VNDLNNRWF G+P+YAELSP
Sbjct: 85 VNDLNNRWFNGQPIYAELSP 104
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 126 bits (318), Expect = 6e-39
Identities = 48/77 (62%), Positives = 64/77 (83%), Gaps = 1/77 (1%)
Query: 7 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND 66
++EE+QEH+D F+EDVF+E ++GEIE++ VCDNLGDHL+GNVY+KF EEDAE A+
Sbjct: 27 SEEEIQEHFDEFYEDVFLELS-RFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQA 85
Query: 67 LNNRWFGGRPVYAELSP 83
LN R++ GRP+Y ELSP
Sbjct: 86 LNGRYYAGRPLYPELSP 102
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 111 bits (280), Expect = 3e-33
Identities = 42/79 (53%), Positives = 59/79 (74%), Gaps = 1/79 (1%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++ E+QEH+++F+ED+F E K+GE+E +NVCDNLGDH+VGNVY+KFR EE A A+
Sbjct: 26 SLDPRELQEHFEDFYEDIFEEL-SKFGEVEALNVCDNLGDHMVGNVYVKFRDEEHAAAAL 84
Query: 65 NDLNNRWFGGRPVYAELSP 83
L R++ GRP+ E SP
Sbjct: 85 KALQGRFYDGRPIIVEFSP 103
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 80.4 bits (199), Expect = 6e-21
Identities = 29/78 (37%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 6 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVN 65
+E++ ++ F++DV E E K+GE+ + VC N HL GNVY++++ EE+A A
Sbjct: 29 YDEEDLYSDFEEFYDDVLPEFE-KFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFK 87
Query: 66 DLNNRWFGGRPVYAELSP 83
N RW+ G+ + E SP
Sbjct: 88 MFNGRWYAGKQLTCEFSP 105
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 65.3 bits (160), Expect = 3e-15
Identities = 31/87 (35%), Positives = 44/87 (50%), Gaps = 9/87 (10%)
Query: 1 MIISNVTDEEMQEHYDNFF----EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRR 56
+I+ N+ D + D + EDV EC K+G +E + V N G VY+KF+
Sbjct: 4 VILKNMFDPAEETE-DEWDDEIKEDVLEECS-KFGPVEHIKVDKN---SPEGVVYVKFKT 58
Query: 57 EEDAEKAVNDLNNRWFGGRPVYAELSP 83
E A+K + LN RWF GR + AE
Sbjct: 59 VEAAQKCIQALNGRWFDGRQITAEYVD 85
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 62.0 bits (151), Expect = 4e-14
Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 4/70 (5%)
Query: 15 YDNFFEDVFVECEDKYGEIEEMN--VCDNLG--DHLVGNVYIKFRREEDAEKAVNDLNNR 70
D FE E E+ +GE+ ++N D++G +H GNVYI F R EDA +A+ DLN R
Sbjct: 1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGR 60
Query: 71 WFGGRPVYAE 80
+F GR V AE
Sbjct: 61 YFDGRLVKAE 70
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 55.6 bits (135), Expect = 2e-11
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 1 MIISNVTDEEM---QEHYDNFFEDVFVECEDKYGEIEEMNV----CDNLGDHLVGNVYIK 53
+ + N+ E E Y+ EDV EC KYG++ + + + + VG V+++
Sbjct: 4 LCLLNMVTPEELEDDEEYEEILEDVKEECG-KYGKVLSVVIPRPEAEGVDVPGVGKVFVE 62
Query: 54 FRREEDAEKAVNDLNNRWFGGRPV 77
F EDA+KA L R F GR V
Sbjct: 63 FADVEDAQKAQLALAGRKFDGRTV 86
>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 = 5e-10
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 12/76 (15%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ T+E+++E F K+GEIE + + + G +++F EDAEKA+
Sbjct: 9 DTTEEDLREL----FS--------KFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKAL 56
Query: 65 NDLNNRWFGGRPVYAE 80
LN + GR +
Sbjct: 57 EALNGKELDGRKLKVS 72
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 48.4 bits (116), Expect = 2e-08
Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 1 MIISNVTDEEMQEHYDNFF----EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRR 56
+I+ N+ E E +D+ ECE K+G+++++ V D H G +KF+
Sbjct: 4 VILKNLFSPEEFEEDPTLINELRDDLREECE-KFGQVKKVVVFD---RHPDGVASVKFKE 59
Query: 57 EEDAEKAVNDLNNRWFGGRPVYAEL-SPVTDF 87
E+A++ + LN RWF GR + AE TD+
Sbjct: 60 PEEADRCIEALNGRWFAGRQLEAERWDGKTDY 91
>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 = 46.4 bits (111), Expect = 4e-08
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
+G +E++ + G +++F EE AEKAV LN FGGRP+ + S
Sbjct: 7 PFGNVEKIKLLKKKP----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 48.7 bits (116), Expect = 9e-08
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 1 MIISNVTD--EEMQEHYDN-FFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 57
+++SN+ D E + ++DN +DV EC KYG + + V G +Y+KF
Sbjct: 365 LVLSNMFDPATEEEPNFDNEILDDVKEECS-KYGGVVHIYVDTKNSA---GKIYLKFSSV 420
Query: 58 EDAEKAVNDLNNRWFGGRPVYAELSPVTDFREAC 91
+ A A LN R+FGG+ + A + +C
Sbjct: 421 DAALAAFQALNGRYFGGKMITAAFVVNDVYDMSC 454
Score = 25.6 bits (56), Expect = 9.2
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 13/77 (16%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDA 60
+ N+T++E++ FE +G+IE++ + D G +I+F E+A
Sbjct: 194 LHFNITEQELR----QIFE--------PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEA 241
Query: 61 EKAVNDLNNRWFGGRPV 77
++A+ +N GRP+
Sbjct: 242 KEALEVMNGFELAGRPI 258
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 45.3 bits (108), Expect = 1e-07
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 13/75 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+ T+EE++E F K+G++E + + D G +++F EEDAEKA
Sbjct: 10 DTTEEELRE----LFS--------KFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA 57
Query: 64 VNDLNNRWFGGRPVY 78
+ LN + GRP+
Sbjct: 58 LEALNGKELDGRPLK 72
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 42.6 bits (101), Expect = 2e-06
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVCDN---LGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 72
++ +++ ECE KYG++ + V + D V ++++F ++A KAV LN R+F
Sbjct: 17 EDLKDEIEEECE-KYGKVLNVIVHEVASSEADDAV-RIFVEFSDADEAIKAVRALNGRFF 74
Query: 73 GGRPVYAELSP 83
GGR V A
Sbjct: 75 GGRKVTARFYD 85
>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 = 42.2 bits (100), Expect = 2e-06
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
K+G IE + + + G +++F EEDAEKA+ LN + GGR +
Sbjct: 21 KFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal
region, followed by a G-patch motif and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors a RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain)
and an Arg-Xaa-Phe sequence motif. SPF45 regulates
alternative splicing of the apoptosis regulatory gene
FAS (also known as CD95). It induces exon 6 skipping in
FAS pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 41.9 bits (99), Expect = 4e-06
Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 25 ECEDKYGEIEEMNVCDNLG---DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
EC KYG++ ++ + + G D ++++F R E A KAV DLN R+FGGR V A
Sbjct: 27 ECS-KYGKVTKVLIFEIPGASPDDEAVRIFVEFERVESAIKAVVDLNGRFFGGRTVKASF 85
Query: 82 SPVTDFR 88
FR
Sbjct: 86 YDEERFR 92
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. The research indicates that
PUF60 binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 98
Score = 40.1 bits (94), Expect = 3e-05
Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 15/93 (16%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIE------EMNVCDNLGDHLVGNVYIKF 54
M+ D++++ +V EC K+G + E + + +V ++++F
Sbjct: 9 MVGPEDLDDDLEG-------EVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIV-KIFVEF 59
Query: 55 RREEDAEKAVNDLNNRWFGGRPVYAELSPVTDF 87
+AEKA+ LN RWFGGR V AEL T F
Sbjct: 60 SLPSEAEKAIQALNGRWFGGRKVKAELYDQTKF 92
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 41.4 bits (97), Expect = 4e-05
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 6 VTDEEM--QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL----VGNVYIKFRREED 59
VT +++ E Y+ +EDV E KYG + + + GD VG V++++
Sbjct: 418 VTGDDLMDDEEYEEIYEDVKTEFS-KYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRS 476
Query: 60 AEKAVNDLNNRWFGGRPVYA 79
AEKA+ +N R F R V A
Sbjct: 477 AEKAMEGMNGRKFNDRVVVA 496
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an
N-terminal C4C4 type RING finger motif, followed by a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RING fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 39.1 bits (92), Expect = 6e-05
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 29 KYGEIE--EMNVCDNLGDHLVGN--VYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+YG+I+ +N + + Y+ + R+EDA + + ++ + GR + A
Sbjct: 31 QYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRLLKA 85
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 37.1 bits (87), Expect = 1e-04
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
YG++E + + N D G +++F EDAE A+ LN GR +
Sbjct: 21 PYGKVEGVRLVRN-KDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 36.7 bits (85), Expect = 3e-04
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
++ FR ++DAE A+N++N +W G RP+
Sbjct: 45 FVSFRSQQDAENAINEMNGKWLGSRPI 71
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 35.0 bits (81), Expect = 0.001
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 20 EDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
E+ E + +GEI E+++ D G ++ F E A KA ++L+ F GR ++
Sbjct: 13 EEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLH 72
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 36.2 bits (83), Expect = 0.002
Identities = 19/87 (21%), Positives = 43/87 (49%), Gaps = 10/87 (11%)
Query: 1 MIISNVTDEEMQEHYDNFFE-DVFVECEDKYGEIEEMNV-----CDNLGDHLVGNVYIKF 54
+++ N+ + D F E ++ EC K+G ++ + + + ++ ++++F
Sbjct: 517 IVLRNMVTPQ---DIDEFLEGEIREEC-GKFGVVDRVIINFEKQGEEEDAEIIVKIFVEF 572
Query: 55 RREEDAEKAVNDLNNRWFGGRPVYAEL 81
+ ++A L+ R+FGGR V AE
Sbjct: 573 SDSMEVDRAKAALDGRFFGGRTVVAEA 599
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 34.2 bits (79), Expect = 0.003
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
+G + E+ + G +++F + DAEKA+ +N + GRPV
Sbjct: 22 PFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPV 70
>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 = 34.1 bits (79), Expect = 0.003
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++ DE+++E F KYG+I V + G ++ F E A+KAV
Sbjct: 12 DMDDEKLKE----LFG--------KYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59
Query: 65 NDLNNRWFGGRPVYA 79
+LN + G+ +Y
Sbjct: 60 EELNGKEVNGKKLYV 74
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM1 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 33.7 bits (78), Expect = 0.003
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 13/79 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLV-GNVYIKFRREEDAEKA 63
+ TDE+++E FF +V G I+ V + G G Y+ F EEDA++A
Sbjct: 10 DTTDEQLEE----FFSEV--------GPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRA 57
Query: 64 VNDLNNRWFGGRPVYAELS 82
+ + FGGR ++ E +
Sbjct: 58 LEEKKKTKFGGRKIHVEFA 76
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 33.9 bits (78), Expect = 0.004
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
+ E ++ + F GEI + V D G ++ F ++EDAE A
Sbjct: 10 EIDTETLRAAFAPF------------GEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57
Query: 64 VNDLNNRWFGGRPV 77
+ +N +W GGR +
Sbjct: 58 IQSMNGQWLGGRAI 71
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 33.4 bits (77), Expect = 0.005
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 9/69 (13%)
Query: 17 NFFEDVFVECEDKYGEIEEMNV----CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 72
+ +F K+GE+E + + + G G ++ F+ AE A+ LN
Sbjct: 15 DDLRGIFS----KFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ-LNGTEL 69
Query: 73 GGRPVYAEL 81
GGR + L
Sbjct: 70 GGRKISVSL 78
>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 = 33.2 bits (76), Expect = 0.006
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
N+T +E++ + + GEIE + D + +G ++ + EDAEKA
Sbjct: 12 NMTQDEIRSLFSSI------------GEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59
Query: 64 VNDLN 68
+N LN
Sbjct: 60 INTLN 64
>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 = 34.4 bits (79), Expect = 0.010
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 74
ED E K+GEI V + G ++ F + EDA KAV ++N + G
Sbjct: 192 EDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 33.2 bits (76), Expect = 0.023
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 14/86 (16%)
Query: 6 VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAV 64
VTDE+++E + + GEI V D G G ++ F E+A +AV
Sbjct: 297 VTDEKLRELFS------------ECGEITSAKVMLDEKGVSR-GFGFVCFSNPEEANRAV 343
Query: 65 NDLNNRWFGGRPVYAELSPVTDFREA 90
+++ R GG+P+Y L+ + R A
Sbjct: 344 TEMHGRMLGGKPLYVALAQRKEQRRA 369
Score = 30.9 bits (70), Expect = 0.16
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 20 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
E + +G + + VC D++ +G Y+ F+ DAE+A+ +N + GG+P+
Sbjct: 14 EAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPI 72
Score = 27.1 bits (60), Expect = 2.9
Identities = 26/101 (25%), Positives = 40/101 (39%), Gaps = 3/101 (2%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
K+G I V + G ++ F +EE A+ A+ +N + VY R
Sbjct: 111 KFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHER 170
Query: 89 EACCRQYEMVLETKNADPVCTREKAKKKMGVYEISGVSTSA 129
EA + L KN DP +K ++ + G TSA
Sbjct: 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKF---GEITSA 208
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 32.3 bits (74), Expect = 0.011
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 40 DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
D G L G Y++F EEDA +A L+ + GR +
Sbjct: 35 DKTGKTL-GEAYVEFVSEEDAMRAE-RLHRKKLKGREIL 71
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 83
Score = 32.5 bits (74), Expect = 0.014
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
+YG++ E + G L G ++ ++ ++AE A+ + N GRPV
Sbjct: 24 RYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPV 72
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or
P-CIP2, is a serine/threonine protein kinase
functionally related to RNA metabolism and neurite
outgrowth. It contains an N-terminal kinase domain and
a C-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), with high homology to the corresponding motif
of the mammalian U2 small nuclear ribonucleoprotein
auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2).
UHMK1 targets two key regulators of cell proliferation
and migration, the cyclin-dependent kinase (CDK)
inhibitor p27Kip1 and the microtubule-destabilizing
protein stathmin. It plays a critical role during
vascular wound repair by preventing excessive vascular
smooth muscle cell (VSMC) migration into the vascular
lesion. Moreover, UHMK1 may control cell migration and
neurite outgrowth by interacting with and
phosphorylating the splicing factor SF1, thereby
probably contributing to the control of protein
expression. Furthermore, UHMK1 may be functionally
related to microtubule dynamics and axon development.
It localizes to RNA granules, interacts with three
proteins found in RNA granules (KIF3A, NonO, and
eEF1A), and further enhances the local translation.
UHMK1 is highly expressed in regions of the brain
implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 32.3 bits (73), Expect = 0.016
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 5 NVTDE---EMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 60
NV D+ + +E Y++ ED+ EC+ KYG + + + +N G G V++++ D+
Sbjct: 10 NVLDDAHLQNEEEYEDIIEDIKEECQ-KYGPVVSLLIPKENPGK---GQVFVEYANAGDS 65
Query: 61 EKAVNDLNNRWFGGRPVYAELSP 83
+ A L R F G+ V A P
Sbjct: 66 KAAQKLLTGRIFDGKFVVATFYP 88
>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 = 31.8 bits (73), Expect = 0.017
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+ T+E+++ +FF + + + I + + G Y++F EDA +A+
Sbjct: 10 SATEEDIR----DFFSGLDIPPDG----IHIVY---DDDGRPTGEAYVEFASPEDARRAL 58
Query: 65 NDLNNRWFGGRPVY 78
NN+ GGR +
Sbjct: 59 RKHNNK-MGGRYIE 71
>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 = 31.7 bits (73), Expect = 0.022
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
G + + VC D + +G Y+ F+ DAE+A++ LN G+P+
Sbjct: 22 PAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIR 72
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 31.9 bits (72), Expect = 0.022
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+ FED + +K G+I EM + + + G ++ F +++A+ A+ LNN
Sbjct: 12 DLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNN 64
>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 = 31.8 bits (73), Expect = 0.023
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 49 NVYIKFRREEDAEKAVNDLNNRWFGGR 75
N Y+ F+ EE AEKA+ LN F G
Sbjct: 61 NAYVVFKEEESAEKALK-LNGTEFEGH 86
>gnl|CDD|225494 COG2943, MdoH, Membrane glycosyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 736
Score = 33.2 bits (76), Expect = 0.024
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 7 TDEEMQE--HYDNFFEDVFVECEDKYGEI---EE---MNVCDNLGDHLVGNVYIKFRREE 58
T E + H ++F D FV + + +I E+ +C LG GN++ + RR
Sbjct: 167 TYESLAATGHAEHF--DFFVLSDSRDPDIALAEQKAWAELCRELGGE--GNIFYRRRRRN 222
Query: 59 DAEKAVN--DLNNRWFGG 74
KA N D RW
Sbjct: 223 VKRKAGNIADFCRRWGSA 240
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 31.5 bits (72), Expect = 0.028
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 29 KYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDAEKAVNDLNNRWFGGR 75
KYG+I++ + + L G ++ F +E+AEKA+ LN + G+
Sbjct: 22 KYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGK 72
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 31.5 bits (72), Expect = 0.031
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 20 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 76
ED E +GEI+++ V D G Y+KF + A +A+ ++N + GG
Sbjct: 16 EDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family
of histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes
Set1A and Set1B that are ubiquitously expressed
vertebrates histone methyltransferases exhibiting high
homology to yeast Set1. Set1A and Set1B proteins
exhibit a largely non-overlapping subnuclear
distribution in euchromatic nuclear speckles, strongly
suggesting that they bind to a unique set of target
genes and thus make non-redundant contributions to the
epigenetic control of chromatin structure and gene
expression. With the exception of the catalytic
component, the subunit composition of the Set1A and
Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The
genomic targeting of these complexes is determined by
the identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast
to Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 31.5 bits (72), Expect = 0.032
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 74
F +D C+ KYGE+EE+ + HL G + F + A++ V LN G
Sbjct: 17 GFLKD---MCK-KYGEVEEVKIYFHPKTNKHL-GLARVVFDSVKSAKRCVEKLNQTSVMG 71
Query: 75 RPVYAELSPVTDFREACCRQYE 96
+ + L P E R YE
Sbjct: 72 KIIKVFLDP---KGEIRKRLYE 90
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 30.8 bits (70), Expect = 0.040
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 31 GEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
G I+ + + N G G I F+R DA KA + N R G
Sbjct: 25 GPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGN 69
>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 = 32.2 bits (73), Expect = 0.047
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 31 GEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
GEIE V D + +G ++ + R EDAEKAVN LN
Sbjct: 28 GEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLN 66
Score = 26.8 bits (59), Expect = 3.9
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 30 YGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
+G+I + DN+ G +I+F + ++A++A+ LN
Sbjct: 113 FGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 32.3 bits (73), Expect = 0.051
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 29 KYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDAEKAVNDLNN 69
KYG+I + N+ L D L G +++F + E+A++A++ LNN
Sbjct: 216 KYGQIVQKNI---LRDKLTGTPRGVAFVRFNKREEAQEAISALNN 257
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe
CD corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 79
Score = 30.7 bits (70), Expect = 0.053
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
++ DE ++E + +G I V + G ++ F E+A KAV
Sbjct: 12 SIDDERLREEFS------------PFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAV 59
Query: 65 NDLNNRWFGGRPVYAEL 81
++N R GG+P+Y L
Sbjct: 60 TEMNGRIIGGKPLYVAL 76
>gnl|CDD|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear
membrane protein Man1 (Man1) and similar proteins.
This subfamily corresponds to the RRM of Man1, also
termed LEM domain-containing protein 3 (LEMD3), an
integral protein of the inner nuclear membrane that
binds to nuclear lamins and emerin, thus playing a role
in nuclear organization. It is part of a protein
complex essential for chromatin organization and cell
division. It also functions as an important negative
regulator for the transforming growth factor (TGF)
beta/activin/Nodal signaling pathway by directly
interacting with chromatin-associated proteins and
transcriptional regulators, including the R-Smads,
Smad1, Smad2, and Smad3. Moreover, Man1 is a unique
type of left-right (LR) signaling regulator that acts
on the inner nuclear membrane. Man1 plays a crucial
role in angiogenesis. The vascular remodeling can be
regulated at the inner nuclear membrane through the
interaction between Man1 and Smads. Man1 contains an
N-terminal LEM domain, two putative transmembrane
domains, a MAN1-Src1p C-terminal (MSC) domain, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The LEM domain interacts with the DNA and
chromatin-binding protein Barrier-to-Autointegration
Factor, and is also necessary for efficient
localization of MAN1 in the inner nuclear membrane.
Research has indicated that C-terminal nucleoplasmic
region of Man1 exhibits a DNA binding winged helix
domain and is responsible for both DNA- and
Smad-binding. .
Length = 92
Score = 30.7 bits (70), Expect = 0.053
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 80
G VYIK EDA KA L+ WF GR V +
Sbjct: 48 GCVYIKCSSPEDAGKAFKALHGWWFDGRLVTVK 80
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM2 of the sex-lethal protein (SXL)
which governs sexual differentiation and X chromosome
dosage compensation in Drosophila melanogaster. It
induces female-specific alternative splicing of the
transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 30.6 bits (69), Expect = 0.061
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 20 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
ED + + YG I + N+ D G ++++ + E+A+ A++ LN G
Sbjct: 14 EDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70
>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 = 30.4 bits (69), Expect = 0.077
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGR 75
G Y +F E AEK V DLN + F R
Sbjct: 47 GIAYAEFSSPEQAEKVVKDLNGKVFKNR 74
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B).
This subgroup corresponds to the RRM of Setd1B, also
termed SET domain-containing protein 1B (Set1B), or
lysine N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits
high homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone
H3 at Lys4. Set1B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. .
Length = 93
Score = 30.4 bits (68), Expect = 0.080
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVCDNLGD--HLVGNVYIKFRREEDAEKAVNDLNNRWFG 73
DN E+ + KYGE+EE+ + N + HL G + F + A+ AV L+N
Sbjct: 12 DNIRENFLTDMCKKYGEVEEVEILYNPKNKKHL-GIAKVVFATVKGAKDAVQHLHNTSVM 70
Query: 74 GRPVYAELSPVTDFREACCRQYEMVL 99
G ++ EL + R R YE+++
Sbjct: 71 GNIIHVELDTKGETRM---RFYELLV 93
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 30.1 bits (68), Expect = 0.082
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 19 FEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++F YG ++E+ + N +++F E A +A + ++ + P+Y
Sbjct: 16 IREIF----SPYGAVKEVKMISNFA-------FVEFESLESAIRAKDSVHGKVLNNNPLY 64
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 31.5 bits (70), Expect = 0.084
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 11/73 (15%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+VT+E+++E + F V + E +++F EE AEKA+
Sbjct: 126 DVTEEDLRELFKKFGPVKRV----RLVRDRETGKSRGFA-------FVEFESEESAEKAI 174
Query: 65 NDLNNRWFGGRPV 77
+LN + GRP+
Sbjct: 175 EELNGKELEGRPL 187
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 30.2 bits (69), Expect = 0.084
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+YG IEE+ + D G ++KF E+A+KA+ L+
Sbjct: 22 EYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 30.1 bits (68), Expect = 0.086
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAEKAVNDLNNRW-FGGRPV 77
++G + + V N Y +KF A +A N +W F G P+
Sbjct: 27 QFGLLYSVKVFPNAA-VATPGFYAFVKFYSARAASRAQKACNGKWLFQGSPL 77
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM2 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 80
Score = 29.9 bits (68), Expect = 0.10
Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+VTD +QE + + V + ++ V D + G +++F E++ ++A+
Sbjct: 12 DVTDYMLQETFRARYPSV------RGAKV----VMDPVTGRSKGYGFVRFGDEDERDRAL 61
Query: 65 NDLNNRWFGGRPVYAELSPVT 85
++N + RP+ +SP T
Sbjct: 62 TEMNGVYCSSRPM--RVSPAT 80
>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 = 29.5 bits (67), Expect = 0.12
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 17/76 (22%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
+ +T+EE+Q + F G IEE+ V + G +++F E A
Sbjct: 8 LPHGLTEEELQRTFSPF------------GAIEEVRVFKD-----KGYAFVRFDTHEAAA 50
Query: 62 KAVNDLNNRWFGGRPV 77
A+ +N G+ V
Sbjct: 51 TAIVAVNGTSINGQTV 66
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 29.5 bits (67), Expect = 0.16
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 47 VGNVYIKFRREEDAEKAVNDLNNRWFGGRP 76
G + F + EDAE+A+ N G+P
Sbjct: 41 EGTADVVFEKREDAERAIKQFNGVLLDGQP 70
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 29.3 bits (66), Expect = 0.16
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 19 FEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
E +F K+GE+ E++V D G Y+ F EDA KA +L+ + F GR
Sbjct: 19 LEKLF----SKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGR 72
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 29.2 bits (66), Expect = 0.18
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRPV 77
+ FR+ EDAEKA+ + F G +
Sbjct: 46 VFFRKPEDAEKALEVSKGKLFFGAEI 71
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 29.6 bits (66), Expect = 0.18
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREED 59
+ + N+ D+ E F +YG I ++ V D G Y++F D
Sbjct: 3 LFVRNIADDTRSEDLRREF--------GRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRD 54
Query: 60 AEKAVNDLNNRWFGGRPV 77
AE A+++L+ +W GR +
Sbjct: 55 AEDALHNLDRKWICGRQI 72
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and
similar proteins. This subfamily corresponds to the
RRM of Acinus, a caspase-3-activated nuclear factor
that induces apoptotic chromatin condensation after
cleavage by caspase-3 without inducing DNA
fragmentation. It is essential for apoptotic chromatin
condensation and may also participate in nuclear
structural changes occurring in normal cells. Acinus
contains a P-loop motif and an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which indicates Acinus
might have ATPase and DNA/RNA-binding activity. .
Length = 90
Score = 29.5 bits (67), Expect = 0.20
Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 51 YIKFRREEDAEKAVNDLNN-RW--FGGRPVYAELSPVTDFREA 90
Y+ + E+A L+ +W + + + P + EA
Sbjct: 43 YVTYSTVEEAVATREALHGLQWPSSNPKRLKVDFVPQEELEEA 85
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 29.2 bits (65), Expect = 0.21
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G YI+F DAE A+ +LN +W GR +
Sbjct: 43 GFAYIQFEDVRDAEDALYNLNRKWVCGRQI 72
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 29.3 bits (65), Expect = 0.22
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G ++ F + DAE A+ + +W GGR +
Sbjct: 44 GYGFVSFFNKWDAENAIQQMGGQWLGGRQI 73
>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 = 28.8 bits (65), Expect = 0.25
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
+VT EE+ E F ++G+I E+N+ +H +IKF RE+ A +AV
Sbjct: 14 DVTKEELNE----RFS--------RHGKILEVNLIKR-ANHTNAFAFIKFEREQAAARAV 60
Query: 65 NDLNNRWFGGRPVYAEL 81
N+ + ++ +
Sbjct: 61 ESENHSMLKNKTMHVQY 77
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 28.4 bits (64), Expect = 0.28
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 54 FRREEDAEKAVNDLNNRWFGGRPVYAEL 81
+ R++DA A++ NNR G+P+ +L
Sbjct: 42 YVRKDDALTAIDKYNNRELDGQPMKCKL 69
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 28.7 bits (65), Expect = 0.32
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 20 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 78
E +F K+G +EE+ + D G ++ F EDA+ A+ DLN + GR +
Sbjct: 19 EALF----SKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIK 74
Query: 79 AE 80
E
Sbjct: 75 VE 76
>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 = 28.4 bits (64), Expect = 0.32
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRP 76
+ +F E A A+ +LN F GR
Sbjct: 44 FCEFEDIETAASAIRNLNGYEFNGRA 69
>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 = 28.4 bits (64), Expect = 0.35
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRPV 77
++F +ED E+A+ L+ F GR V
Sbjct: 42 VEFTSQEDMERALRKLDGTEFRGRRV 67
>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 = 28.3 bits (64), Expect = 0.36
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 74
++GE++ + D L H G ++KF+ +E A+K + +N G
Sbjct: 23 QFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSG 69
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 28.3 bits (64), Expect = 0.36
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 13/77 (16%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL-VGNVYIKFRREEDAEKA 63
NV + ++E + N YG ++++++ + +L G Y++F EDAEKA
Sbjct: 9 NVNKDHLKEIFSN------------YGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56
Query: 64 VNDLNNRWFGGRPVYAE 80
+ ++ G+ V E
Sbjct: 57 IKHMDGGQIDGQEVTVE 73
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 28.1 bits (63), Expect = 0.38
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
ED+F KYG I+ +++ + +++F DAE AV + F G +
Sbjct: 17 EDLF----YKYGPIKAIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGRDGYDFDGYRLRV 70
Query: 80 EL 81
E
Sbjct: 71 EF 72
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 28.0 bits (63), Expect = 0.39
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 17/75 (22%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
VT++E++ + F E V+V+ G C +++F AE A
Sbjct: 11 PAVTEDELRSLFGPFGEIVYVKIPPGKG-------CG----------FVQFVHRAAAEAA 53
Query: 64 VNDLNNRWFGGRPVY 78
+ L GG +
Sbjct: 54 IQQLQGTIIGGSRIR 68
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the
RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. SRSF12, also
termed 35 kDa SR repressor protein (SRrp35), or
splicing factor, arginine/serine-rich 13B (SFRS13B), or
splicing factor, arginine/serine-rich 19 (SFRS19), is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice
site of the adenovirus E1A pre-mRNA in vivo. Both,
SRSF10 and SRSF12, contain a single N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a C-terminal RS domain rich in serine-arginine
dipeptides. .
Length = 84
Score = 28.5 bits (64), Expect = 0.41
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 29 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
KYG I ++ + D G Y++F DAE A+ L+ F GR +
Sbjct: 23 KYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREI 72
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the
RRM of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved
in termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
Its localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 28.0 bits (63), Expect = 0.44
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
ED F +KYG + + V N G +++F DAE AV L+ R G V
Sbjct: 17 EDEF----EKYGPLRSVWVARNPP----GFAFVEFEDPRDAEDAVRALDGRRICGNRVRV 68
Query: 80 ELS 82
ELS
Sbjct: 69 ELS 71
>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 = 27.9 bits (63), Expect = 0.46
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
Y++F E A AV LN + G + ++S
Sbjct: 45 YVQFTSPESAAAAVALLNGKLGEGYKLVVKIS 76
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 29.6 bits (66), Expect = 0.47
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+ +ED V +K G I E+ + + G ++ F +E+A++AV LNN
Sbjct: 69 DLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNN 121
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads and is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 83
Score = 28.2 bits (62), Expect = 0.50
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 25 ECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLN 68
E + +G I E+ C + D + G ++ + +DAEKA+N LN
Sbjct: 20 ELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 28.0 bits (63), Expect = 0.54
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 52 IKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 83
++F DA KA L + F P+Y E +P
Sbjct: 41 VEFLEPSDARKAFKSLAYKRFKHVPLYLEWAP 72
>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 = 28.0 bits (63), Expect = 0.55
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 63
NVT+E++++ F +GE+ V D G +++ E+A A
Sbjct: 10 NVTEEDLKD----LFGQ--------FGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57
Query: 64 VNDLNNRWFGGRPV 77
+ LN FGGR +
Sbjct: 58 IEKLNGTDFGGRTL 71
>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 = 28.1 bits (62), Expect = 0.56
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G ++ F + DAE A+ + +W GGR +
Sbjct: 44 GYGFVSFYNKLDAENAIVHMGGQWLGGRQI 73
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells, as well as the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 28.2 bits (62), Expect = 0.57
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREED 59
+I++ + QE + + F + GEIE V D + +G ++ + +D
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSI--------GEIESCKLVRDKITGQSLGYGFVNYIDPKD 56
Query: 60 AEKAVNDLN 68
AEKA+N LN
Sbjct: 57 AEKAINTLN 65
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1),
a ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response; it binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
Meanwhile, HuR also has pro-apoptotic function by
promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Like other Hu proteins, HuR contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 81
Score = 28.1 bits (62), Expect = 0.60
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 31 GEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 26 GEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLN 64
>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 = 27.5 bits (61), Expect = 0.63
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
++ R E A++A+ +LN R GR + E S
Sbjct: 38 FVHLRGEAAADRAIEELNGRELHGRKLVVEHS 69
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is ubiquitously expressed Hu family member. It has
a variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the
cytoplasm, Hu proteins recognize and bind to AU-rich
RNA elements (AREs) in the 3' untranslated regions
(UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. This family
also includes the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own
pre-mRNA and promotes female-specific alternative
splicing. It contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 77
Score = 27.7 bits (62), Expect = 0.65
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 29 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 70
G IE V D + +G ++ + E DA+KA+N LN
Sbjct: 23 AIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 27.6 bits (62), Expect = 0.67
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFG 73
++ F+ EEDA++AV N +
Sbjct: 45 FVGFKSEEDAQQAVKYFNKTFID 67
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 27.6 bits (62), Expect = 0.67
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 50 VYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
++ FR EE+ +KA+ L+ + GR + A L+
Sbjct: 45 AFVTFRSEEERQKALEILDGFKWKGRVLSARLA 77
>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 = 27.2 bits (61), Expect = 0.72
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 80
KYG + E +V N G ++ EEDAE A+ LN F G+ + E
Sbjct: 22 KYGTVTECDVVKNYG-------FVHMEEEEDAEDAIKALNGYEFMGKRINVE 66
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 27.5 bits (61), Expect = 0.74
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 44 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
D + ++ REE+A A+ LN + GR + EL
Sbjct: 31 DKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 27.2 bits (61), Expect = 0.74
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 29 KYGEIEEMNVCDNLGDHLV-GNVYIKFRREEDAEKAVNDLNNR 70
+G+I + + G ++ F E A KA+ LN R
Sbjct: 23 PFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 27.3 bits (61), Expect = 0.75
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
YG I E+N+ + G +++F DA+ AV +LN + G V E +
Sbjct: 22 GYGRIREINLKNGFG-------FVEFEDPRDADDAVYELNGKELCGERVIVEHA 68
>gnl|CDD|217006 pfam02382, RTX, RTX N-terminal domain. The RTX family of bacterial
toxins are a group of cytolysins and cytotoxins. This
Pfam family represents the N-terminal domain which is
found in association with a glycine-rich repeat domain
and hemolysinCabind pfam00353.
Length = 653
Score = 29.0 bits (65), Expect = 0.76
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 10/78 (12%)
Query: 2 IISNVTD---EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCD-----NLGDHLVGNVYIK 53
+IS + + + M EH N D VE E K+G+ N D L D+ +
Sbjct: 402 LISGILEASKQAMFEHVANKIADKIVEWEKKHGKNYFENGYDARHLAFLEDNF--KLLSN 459
Query: 54 FRREEDAEKAVNDLNNRW 71
+E E+ V RW
Sbjct: 460 LNKEYQVERVVAITQQRW 477
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 27.6 bits (61), Expect = 0.79
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+YG I + D L G +I+F + +AE+A+ LN
Sbjct: 23 QYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNG 64
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 27.3 bits (61), Expect = 0.83
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
Y++F +E A+ A++ L GRPV
Sbjct: 44 YVEFSSQEAAQAALDALGGTDLLGRPV 70
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 27.2 bits (61), Expect = 0.85
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 11/58 (18%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
E++F KYG+I +++ G +++F EEDA AV N R G+ +
Sbjct: 19 EEIF----SKYGKILGISLHKGYG-------FVQFDNEEDARAAVAGENGREIAGQKL 65
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 27.5 bits (61), Expect = 0.90
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 74
+ E VF KYG+I E+ V D G ++ F +DA+ A+ +N + G
Sbjct: 14 EQSLEQVF----SKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69
Query: 75 R 75
R
Sbjct: 70 R 70
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 27.2 bits (60), Expect = 0.94
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
G +++F EDA++A+N NN GR + E
Sbjct: 39 GYAFVEFESAEDAKEALNSCNNTEIEGRSIRLEF 72
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar
proteins. This subfamily corresponds to the RRM1 of
RBM19 and MRD1. RBM19, also termed RNA-binding domain-1
(RBD-1), is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 77
Score = 27.2 bits (61), Expect = 0.98
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 11/74 (14%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
+++T+ E++EH+ GEI ++ + +I ++ EE+A+KA
Sbjct: 10 ASLTEAELKEHFSK-----------HGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKA 58
Query: 64 VNDLNNRWFGGRPV 77
+ NN + +
Sbjct: 59 KDYFNNTYINTSKI 72
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers.
Moreover, hnRNP M is able to interact with early
spliceosomes, further influencing splicing patterns of
specific pre-mRNAs. hnRNP M functions as the receptor
of carcinoembryonic antigen (CEA) that contains the
penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 26.9 bits (59), Expect = 1.2
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G ++F+ EE +KAV LN GRP+
Sbjct: 42 GCAVVEFKMEESMKKAVEVLNKHVLNGRPL 71
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 26.9 bits (59), Expect = 1.3
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+ +ED V + G I EM + + G ++ + ++ +A++AV +LNN
Sbjct: 12 DVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELNN 64
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 26.7 bits (60), Expect = 1.5
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 28 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 70
YG +E++ + + ++F E AE A LN R
Sbjct: 23 SPYGAVEKI-LIFEKNTGV--QALVQFDSVESAENAKKALNGR 62
>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 = 26.6 bits (59), Expect = 1.6
Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
E +F K+G ++ + + N G Y+++ E A +AV ++ + +
Sbjct: 20 EKLF----KKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEKTISV 75
Query: 80 ELS 82
+S
Sbjct: 76 AIS 78
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 26.5 bits (59), Expect = 1.6
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 25 ECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
+KYGE+ ++ + D G +++F + DAE A++ ++ + GR
Sbjct: 17 RVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGR 68
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 26.5 bits (59), Expect = 1.7
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 17/76 (22%)
Query: 2 IISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 61
+ VT+E+++ N FE +YGEI+ +++ G Y+ +DA
Sbjct: 10 LSKKVTEEDLK----NLFE--------EYGEIQSIDMIPPRG-----CAYVCMETRQDAH 52
Query: 62 KAVNDLNNRWFGGRPV 77
+A+ L N G+ +
Sbjct: 53 RALQKLRNVKLAGKKI 68
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Although
the cellular function of RBM23 remains unclear, it
shows high sequence homology to RBM39 and contains two
RRMs. It may possibly function as a pre-mRNA splicing
factor. .
Length = 73
Score = 26.5 bits (59), Expect = 1.9
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N+T+++++ ++ F E FV+ + E G +I+F EDA+KA+
Sbjct: 9 NITEDDLRGIFEPFGEIEFVQLQRD----PETGRSKGYG-------FIQFADAEDAKKAL 57
Query: 65 NDLNNRWFGGRPV 77
LN GRP+
Sbjct: 58 EQLNGFELAGRPI 70
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 26.3 bits (58), Expect = 2.0
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 28 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG--GRPVYAE 80
KYG ++ + D G ++ E DAE A+ L+N FG R + E
Sbjct: 22 GKYGRVDRV-------DMKSGFAFVYMEDERDAEDAIRGLDNFEFGRQRRRLRVE 69
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 26.5 bits (59), Expect = 2.0
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGR 75
G +I F EDA K V LNN+ GR
Sbjct: 44 GVAFILFLDREDAHKCVKALNNKELFGR 71
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 26.3 bits (59), Expect = 2.1
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 30 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV---YA 79
+G + ++ L + G ++ F+ E A A+ L F +P+ YA
Sbjct: 27 FGPVLDIVASKTLK--MRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQYA 77
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 26.5 bits (58), Expect = 2.2
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTD 86
++ F EDA A+N LN + G P+ L+ D
Sbjct: 48 FVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKPVD 83
>gnl|CDD|220941 pfam11013, DUF2851, Protein of unknown function (DUF2851). This
bacterial family of proteins has no known function.
Length = 377
Score = 27.6 bits (62), Expect = 2.2
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 1 MIISNVTDEEMQEHYDNFFE-DVFVECEDKYGEIEEM 36
+ + + EE+ E+Y+ E ++ CE ++ E+
Sbjct: 106 LELKDYVPEELLENYEKLLENKKWIPCESEFAEVPSF 142
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 26.0 bits (58), Expect = 2.2
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 28 DKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
++GEIEE V D G ++ F+ +E AE+A D N
Sbjct: 22 SQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPN 63
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182
family proteins. This subfamily corresponds to the RRM
of the GW182 family which includes three paralogs of
TNRC6 (GW182-related) proteins comprising GW182/TNGW1,
TNRC6B (containing three isoforms) and TNRC6C in
mammal, a single Drosophila ortholog (dGW182, also
called Gawky) and two Caenorhabditis elegans orthologs
AIN-1 and AIN-2, which contain multiple miRNA-binding
sites and have important functions in miRNA-mediated
translational repression, as well as mRNA degradation
in Metazoa. The GW182 family proteins directly interact
with Argonaute (Ago) proteins, and thus function as
downstream effectors in the miRNA pathway, responsible
for inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 26.2 bits (58), Expect = 2.3
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
GN I++ +E+A KA + LNN G + AE
Sbjct: 38 GNALIRYSSKEEAAKAQSALNNCVLGNTTLLAEF 71
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 26.3 bits (58), Expect = 2.4
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGR 75
++ F EDA++A+ L N+ GR
Sbjct: 45 FVTFAMLEDAQEALAKLKNKKLHGR 69
>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 = 26.0 bits (58), Expect = 2.5
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 28 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
++GE++++ +++F AE A++ LN R F G +
Sbjct: 23 SQFGEVKDIRETPLRPSQ----KFVEFYDIRAAEAALDALNGRPFLGGRL 68
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 26.1 bits (57), Expect = 2.5
Identities = 10/44 (22%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 28 DKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 70
+++G + E+ + D H G ++K+ ++A++A+ L+N+
Sbjct: 21 EEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRALHNQ 64
>gnl|CDD|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM4 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 88
Score = 26.3 bits (58), Expect = 2.7
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 40 DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 89
DN G L G ++F+ E+DA K+ L+ + GR V+ L + R+
Sbjct: 35 DNNGQGL-GQALVQFKSEDDARKS-ERLHRKKLNGRDVFLHLVTAEEMRD 82
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM2 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 25.9 bits (57), Expect = 2.8
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+++F E D ++A+ ++ + GGRP+
Sbjct: 48 FVRFSDENDQQRALIEMQGVYCGGRPM 74
>gnl|CDD|188611 TIGR04096, dnd_rel_methyl, DNA phosphorothioation-associated
putative methyltransferase. Members of this protein
family show distant local sequence similarity to a
number of S-adenosyl-methionine-dependent
methyltransferases. The family is identified by Partial
Phylogenetic Profiling as closely tied to the DNA
phosphorothioation system (dnd), and members are found
adjacent to dnd genes in at least 13 species
(Streptomyces lividans TK24, Shewanella frigidimarina
NCIMB 400, Mycobacterium abscessus ATCC 19977, Nostoc
punctiforme PCC 73102, Vibrio fischeri MJ11, etc.). The
DNA phosphorothioation enables a novel form of
restriction enzyme activity. Most members of this family
appear in species with the DNA phosphorothioation system
[DNA metabolism, Restriction/modification].
Length = 478
Score = 27.3 bits (61), Expect = 2.8
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 12/57 (21%)
Query: 72 FGGRPVYAELSPVT---------DFREACCRQYEMVLETKNADPV---CTREKAKKK 116
FG RP +++L +++AC ++ + + + C K
Sbjct: 270 FGKRPKFSQLPETLKRDIKAFFGSYKKACALADRLLFSLGDPEIIEKACNNSPVGKL 326
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 26.0 bits (58), Expect = 3.1
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVY 78
++ F EE A +A+ +N + V+
Sbjct: 47 FVHFETEEAAVRAIEKVNGMLLNDKKVF 74
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 26.6 bits (59), Expect = 3.3
Identities = 29/126 (23%), Positives = 42/126 (33%), Gaps = 31/126 (24%)
Query: 22 VFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND-----------LNNR 70
V + +D G+ V LGD + V+ E D AV+ NN
Sbjct: 32 VIADIDDDAGQ----AVAAELGDPDISFVHCDVTVEADVRAAVDTAVARFGRLDIMFNNA 87
Query: 71 WFGGRPVYAELSPVTDFREACCRQYEMVLE---------TKNADPVCTREKAKKKMGVYE 121
G P Y E ++E VL+ TK+A V K + V
Sbjct: 88 GVLGAPCY-------SILETSLEEFERVLDVNVYGAFLGTKHAARVMIPAKKGSIVSVAS 140
Query: 122 ISGVST 127
++GV
Sbjct: 141 VAGVVG 146
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 84
Score = 25.8 bits (56), Expect = 3.3
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N ++ F GEIE V D + +G ++ + DA+KA+N LN
Sbjct: 14 NMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLN 66
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 25.6 bits (57), Expect = 3.4
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF-GGR 75
+ FED V +K G I E+ + + G ++ + +E A++AV L+N G+
Sbjct: 12 DLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGK 71
Query: 76 PVYAELS 82
+ +S
Sbjct: 72 RLGVCIS 78
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 25.5 bits (56), Expect = 3.5
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G + F +A AV +LN R G R V
Sbjct: 43 GEATVAFDTHREAMAAVRELNGRPIGTRKV 72
>gnl|CDD|220003 pfam08752, Gamma-COP, Coatomer gamma subunit appendage domain.
COPI-coated vesicles function in retrograde transport
from the Golgi to the ER, and in intra-Golgi transport.
This domain corresponds to the coatomer gamma subunit
appendage domain. It contains a protein-protein
interaction site and a second proposed binding site that
interacts with the alpha, beta,epsilon COPI subcomplex.
Length = 269
Score = 26.8 bits (60), Expect = 3.7
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 19 FEDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAE 61
E+V VE E E EE+ + D L + G+VY+ + E +
Sbjct: 65 LENVSVELEPSEEEYEELFIIPIDKLPYNQPGSVYVLLEKPEGED 109
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes.
Since the Hu proteins share high homology with the
Drosophila embryonic lethal abnormal vision (ELAV)
protein, the Hu family is sometimes referred to as the
ELAV family. Drosophila ELAV is exclusively expressed
in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress.
Moreover, HuR has an anti-apoptotic function during
early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Hu proteins
perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 79
Score = 25.7 bits (57), Expect = 3.7
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 CDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
CDN+ G +I+F + +AE+A+ LN
Sbjct: 34 CDNVTGLSRGVGFIRFDKRIEAERAIKALNG 64
>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 = 25.6 bits (57), Expect = 3.7
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 51 YIKFRREEDAEKAVNDLN 68
++ F EDAE+A+ LN
Sbjct: 45 FVTFHTREDAERAIEKLN 62
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A).
This subgroup corresponds to the RRM of Setd1A, also
termed SET domain-containing protein 1A (Set1A), or
lysine N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is
localized to euchromatic nuclear speckles and
associates with a complex containing six human homologs
of the yeast Set1/COMPASS complex, including CXXC
finger protein 1 (CFP1; homologous to yeast Spp1),
Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to
yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82
(homologous to yeast Swd2). Set1A contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
an N- SET domain, and a C-terminal catalytic SET domain
followed by a post-SET domain. In contrast to Set1B,
Set1A additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 26.1 bits (57), Expect = 3.7
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG 73
DN E + K+GE+EE+ + HL G + F A+ V L+N
Sbjct: 12 DNVREPFLADMCRKFGEVEEVEILLHPKTRKHL-GLARVLFTSTRGAKDTVKHLHNTSVM 70
Query: 74 GRPVYAEL 81
G ++A+L
Sbjct: 71 GNIIHAQL 78
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM,
but unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might
share similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 25.4 bits (56), Expect = 3.9
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAE 80
++ E+A K + L+ GR + E
Sbjct: 45 FVTMASVEEAAKCIQHLHRTELHGRVISVE 74
>gnl|CDD|240876 cd12430, RRM_LARP4_5_like, RNA recognition motif in La-related
protein 4 (LARP4), La-related protein 5 (LARP5 or
LARP4B) and similar proteins. This subfamily
corresponds to the RRM of LARP4 and LARP5. LARP4 is a
cytoplasmic factor that can bind poly(A) RNA and
interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP5 is a cytosolic protein that co-sediments
with polysomes and accumulates upon stress induction in
cellular stress granules. It can interact with the
cytosolic poly(A) binding protein 1 (PABPC1) and the
receptor for activated C Kinase (RACK1), a component of
the 40S ribosomal subunit. LARP5 may function as a
stimulatory factor of translation through bridging mRNA
factors of the 3' end with initiating ribosomes. Both,
LARP4 and LARP5, are structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 and LARP5 contain a La motif
(LAM) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 76
Score = 25.4 bits (56), Expect = 4.0
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 51 YIKFRREEDAEKAVNDLNNRW--FGGRPVYA 79
++ F EEDA++A L F G+P+ A
Sbjct: 41 FVTFETEEDAQEAYRYLREEVKTFQGKPIMA 71
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 25.7 bits (57), Expect = 4.6
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 30 YGEIEEMNVCDNLGDHLVGNVY-IKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
YG IEE + D VY IKF + A A L+ R F G ++ +P
Sbjct: 34 YGTIEEYRLLDEYPCEEFTEVYLIKFETIQSARFAKRKLDERSFFGGLLHVCYAP----- 88
Query: 89 EACCRQYEMVLETK 102
+YE V +T+
Sbjct: 89 -----EYETVQDTR 97
>gnl|CDD|163713 cd08157, catalase_fungal, Fungal catalases similar to yeast
catalases A and T. Catalase is a ubiquitous enzyme
found in both prokaryotes and eukaryotes, which is
involved in the protection of cells from the toxic
effects of peroxides. It catalyzes the conversion of
hydrogen peroxide to water and molecular oxygen.
Catalases also utilize hydrogen peroxide to oxidize
various substrates such as alcohol or phenols. This
family of fungal catalases has a relatively small
subunit size, and binds a protoheme IX (heme b) group
buried deep inside the structure. Fungal catalases also
bind NADPH as a second redox-active cofactor. They form
tetramers; in eukaryotic cells, catalases are typically
located in peroxisomes. Saccharomyces cerevisiae
catalase T is found in the cytoplasm, though.
Length = 451
Score = 26.5 bits (59), Expect = 4.7
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 43 GDHLVGNVYIKFRREEDAEK---AVNDLNNRW----FGGRPV 77
GD+ VY++ E AEK + DL W F RPV
Sbjct: 221 GDYPSWTVYVQVMTPEQAEKLRFNIFDLTKVWPHKDFPLRPV 262
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 26.5 bits (58), Expect = 4.8
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 11/59 (18%)
Query: 3 ISNVTDEEMQEHYDNFFED--------VFVECE-DKYGEIEEMNVCDNLGDHLVGNVYI 52
+ N+ ++ E Y + F+D V ++CE DK +I + + +G H+ G YI
Sbjct: 153 VGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVI--TIGKHVKGYHYI 209
>gnl|CDD|193577 cd09888, NGN_Euk, Eukaryotic N-Utilization Substance G (NusG)
N-terminal (NGN) domain, including plant KTF1 (KOW
domain-containing Transcription Factor 1). The
N-Utilization Substance G (NusG) protein and its
eukaryotic homolog, Spt5, are involved in transcription
elongation and termination. NusG contains an NGN domain
at its N-terminus and Kyrpides Ouzounis and Woese (KOW)
repeats at its C-terminus. Spt5 forms an Spt4-Spt5
complex that is an essential RNA polymerase II
elongation factor. NusG was originally discovered as an
N-dependent antitermination enhancing activity in
Escherichia coli, and has a variety of functions such
as its involvement in RNA polymerase elongation and
Rho-termination in bacteria. Orthologs of the NusG gene
exist in all bacteria, but their functions and
requirements are different. Spt5-like is homologous to
the Spt5 proteins present in all eukaryotes, which is
unique as it encodes a protein with an additional long
carboxy-terminal extension that contains WG/GW motifs.
Spt5-like, or KTF1 (KOW domain-containing Transcription
Factor 1), is a RNA-directed DNA methylation (RdDM)
pathway effector in plants.
Length = 86
Score = 25.2 bits (56), Expect = 5.0
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 44 DHLVGNVYIKFRREEDAEKAVNDLNN 69
D L G +YI+ R+E + A+ L
Sbjct: 42 DGLKGYIYIEARKEAHVKDAIEGLRG 67
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 25.2 bits (56), Expect = 5.5
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
+++F EEDA+ A+ +N G+P+
Sbjct: 44 FVEFLSEEDADYAIKIMNMIKLYGKPI 70
>gnl|CDD|234925 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
Length = 682
Score = 26.2 bits (59), Expect = 5.5
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 16 DNFFEDVFVECEDK 29
D FF++V V ED+
Sbjct: 641 DAFFDNVMVMAEDE 654
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in
RNA-binding protein MRN1 and similar proteins. This
subgroup corresponds to the RRM2 and RRM4 of MRN1, also
termed multicopy suppressor of RSC-NHP6 synthetic
lethality protein 1, or post-transcriptional regulator
of 69 kDa, and is an RNA-binding protein found in
yeast. Although its specific biological role remains
unclear, MRN1 might be involved in translational
regulation. Members in this family contain four copies
of conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 82
Score = 25.2 bits (55), Expect = 5.6
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 3 ISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEK 62
I NV+D + + +++ ECE KYGEIE + + +I F +A
Sbjct: 7 IGNVSDVGDERNLPE--KELRKECE-KYGEIESIRILRE-----KACAFINFMNIPNAIA 58
Query: 63 AVNDLNNR 70
A+ LN +
Sbjct: 59 ALQTLNGK 66
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 25.0 bits (54), Expect = 5.6
Identities = 13/50 (26%), Positives = 25/50 (50%)
Query: 28 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
+K GE+ + + + G ++F+ EE +KA+ +N GRP+
Sbjct: 22 EKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLNGRPL 71
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast
RNA-binding protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or
modifier of damage tolerance Mdt1, a novel
phosphothreonine (pThr)-containing protein that
specifically interacts with the pThr-binding site of
the Rad53 FHA1 domain. It is encoded by gene MDT1
(YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is
involved in normal G2/M cell cycle progression in the
absence of DNA damage and functions as a novel target
of checkpoint-dependent cell cycle arrest pathways. It
contains an N-terminal RRM, a nuclear localization
signal, a coiled coil, and a total of 15 SQ/TQ motifs.
cip1 (Csx1-interacting protein 1) and cip2
(Csx1-interacting protein 2) are novel cytoplasmic
RRM-containing proteins that counteract Csx1 function
during oxidative stress. They are not essential for
viability in fission yeast Schizosaccharomyces pombe.
Both cip1 and cip2 contain one RRM. Like PIN4, Cip2
also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 25.1 bits (55), Expect = 5.7
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 80
G + FR E+A+ V LN GR + E
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVE 76
>gnl|CDD|241113 cd12669, RRM1_Nop12p_like, RNA recognition motif 1 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM1 of Nop12p which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 105
Score = 25.4 bits (56), Expect = 5.8
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 49 NVYIKFRREEDAEKAVNDLNNRWFGGR 75
N YI ++ A KA LN F GR
Sbjct: 69 NAYIVYKTPALAAKAAKKLNGTVFLGR 95
>gnl|CDD|240883 cd12437, RRM_BRAP2_like, RNA recognition motif in
BRCA1-associated protein (BRAP2) and similar proteins.
This subfamily corresponds to the RRM domain of BRAP2,
also termed impedes mitogenic signal propagation (IMP),
or ring finger protein 52, or renal carcinoma antigen
NY-REN-63, a novel cytoplasmic protein interacting with
the two functional nuclear localisation signal (NLS)
motifs of BRCA1, a nuclear protein linked to breast
cancer. It also binds to the SV40 large T antigen NLS
motif and the bipartite NLS motif found in mitosin.
BRAP2 may serve as a cytoplasmic retention protein and
play a role in the regulation of nuclear protein
transport. The family also includes RING finger protein
ETP1 and its homologs found in fungi. ETP1, also termed
BRAP2 homolog, or ethanol tolerance protein 1, is the
yeast homolog of BRCA1-associated protein (BRAP2) found
in vertebrates. It may be involved in ethanol and
salt-induced transcriptional activation of the NHA1
promoter and heat shock protein genes (HSP12 and
HSP26), and participate in ethanol-induced turnover of
the low-affinity hexose transporter Hxt3p. Members in
this family contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C3HC4-type
ring finger domain and a UBP-type zinc finger. .
Length = 82
Score = 24.9 bits (55), Expect = 6.1
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 33 IEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 72
I +M + N G V IKFR +EDA+ ND N + F
Sbjct: 26 ISDMRILRNEGRGNRYMVLIKFRSQEDADSFYNDFNGKPF 65
>gnl|CDD|238755 cd01478, Sec23-like, Sec23-like: Protein and membrane traffic in
eukaryotes is mediated by at least in part by the
budding and fusion of intracellular transport vesicles
that selectively carry cargo proteins and lipids from
donor to acceptor organelles. The two main classes of
vesicular carriers within the endocytic and the
biosynthetic pathways are COP- and clathrin-coated
vesicles. Formation of COPII vesicles requires the
ordered assembly of the coat built from several
cytosolic components GTPase Sar1, complexes of
Sec23-Sec24 and Sec13-Sec31. The process is initiated by
the conversion of GDP to GTP by the GTPase Sar1 which
then recruits the heterodimeric complex of Sec23 and
Sec24. This heterodimeric complex generates the
pre-budding complex. The final step leading to membrane
deformation and budding of COPII-coated vesicles is
carried by the heterodimeric complex Sec13-Sec31. The
members of this CD belong to the Sec23-like family. Sec
23 is very similar to Sec24. The Sec23 and Sec24
polypeptides fold into five distinct domains: a
beta-barrel, a zinc finger, a vWA or trunk, an all
helical region and a carboxy Gelsolin domain. The
members of this subgroup lack the consensus MIDAS motif
but have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 267
Score = 26.2 bits (58), Expect = 6.2
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 13 EHYDNFFE---------DVFVECEDKYGEIEEMNVCDNLGDHLV 47
+ YD+ + D+F C D+ G +E + ++ G H+V
Sbjct: 208 KFYDSLAKRLAANGHAVDIFAGCLDQVGLLEMKVLVNSTGGHVV 251
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 76
Score = 24.9 bits (54), Expect = 6.6
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G + F ++A AV DLN+R G R V
Sbjct: 44 GEAMVAFESRDEAMAAVVDLNDRPIGSRKV 73
>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 = 24.8 bits (54), Expect = 7.4
Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 14/70 (20%)
Query: 7 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVN 65
T EE++ H F C G I + + CD H G YI+F D+ +A
Sbjct: 12 TAEELEAH--------FSGC----GPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAV 58
Query: 66 DLNNRWFGGR 75
L+ F GR
Sbjct: 59 ALDESSFRGR 68
>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin),
alpha and beta subunits [Energy production and
conversion].
Length = 317
Score = 25.8 bits (57), Expect = 7.5
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 37 NVCDNLGDHLV-----GNVYIKFRREEDAEKAVNDLNN 69
++ + GD L+ + I EDA+ V +L
Sbjct: 52 DIAEKYGDGLIHITSRQGLEIPGISPEDADDVVEELRE 89
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 24.7 bits (54), Expect = 7.6
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 29 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 75
KYG + E+++ D L G ++ + E A KA +L+ F GR
Sbjct: 25 KYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQGR 72
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in
vertebrate. It has been reported to be involved in
pre-splicesome assembly and to interact with the
Ca2+-signaling protein ALG-2. It also plays an
important role in embryogenesis. RBM22 contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a zinc finger of the unusual type
C-x8-C-x5-C-x3-H, and a C-terminus that is unusually
rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 24.5 bits (54), Expect = 7.9
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 17/66 (25%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
VT+++++ D+F++ +GEI + V ++ F E AEKA
Sbjct: 12 RVTEKDLR---DHFYQ---------FGEIRSITVV-----PRQQCAFVTFTTREAAEKAA 54
Query: 65 NDLNNR 70
L N+
Sbjct: 55 ERLFNK 60
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 24.9 bits (54), Expect = 8.2
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
+ +ED V ++ G+I E + G ++ + +E+A+ A+ LNN
Sbjct: 12 DMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNN 64
>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 = 24.5 bits (54), Expect = 8.4
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPV 77
++ F +DA KA+ ++N + G P+
Sbjct: 39 FVHFEERDDAVKAMEEMNGKELEGSPI 65
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 24.7 bits (54), Expect = 8.5
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
Y+ F EDA+KA+ ++ + GRP+ + S
Sbjct: 45 YVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>gnl|CDD|227365 COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of the
PI-3 kinase family [Signal transduction mechanisms / Cell
division and chromosome partitioning / Chromatin
structure and dynamics / DNA replication, recombination,
and repair / Intracellular trafficking and secretion].
Length = 2105
Score = 25.9 bits (57), Expect = 9.3
Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 1/57 (1%)
Query: 15 YDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW 71
D E + C + E +NV + L KF + K+V L +
Sbjct: 2033 RDPLIEWRRLPCFREIQNNEIVNVLERFRLKLSEKDAEKF-VDLLINKSVESLITQA 2088
>gnl|CDD|148918 pfam07566, DUF1543, Domain of Unknown Function (DUF1543). This
domain is found as 1-2 copies in a small family of
proteins of unknown function.
Length = 52
Score = 24.1 bits (53), Expect = 9.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 58 EDAEKAVNDLNNRWFGGR 75
+ E+A L RWFG +
Sbjct: 14 DSIEEAKPRLRRRWFGDK 31
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 24.6 bits (54), Expect = 9.7
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 51 YIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
++ ++ EE+A+KA+ NN + + E+
Sbjct: 45 FVGYKTEEEAQKALKHFNNSFIDTSKITVEI 75
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
0.317 0.135 0.402
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,699,247
Number of extensions: 594986
Number of successful extensions: 847
Number of sequences better than 10.0: 1
Number of HSP's gapped: 835
Number of HSP's successfully gapped: 186
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
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 (21.6 bits)
S2: 53 (24.3 bits)