RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7051
(158 letters)
>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 = 121 bits (306), Expect = 5e-37
Identities = 65/73 (89%), Positives = 71/73 (97%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
LKVDNLTYRTTPDDLRRVFE+ GEVGD+YIPRDR+TRESRGFAFVRF+DKRDAEDA+DAM
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 76 DGRMLDGRELRVQ 88
DG+ LDGRELRVQ
Sbjct: 61 DGKELDGRELRVQ 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 92.3 bits (230), Expect = 2e-25
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL TT ++LR +F + G+V + + RD+ T +S+GFAFV F + DAE AL+A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 75 MDGRMLDGRELRV 87
++G+ LDGR L+V
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 86.5 bits (215), Expect = 3e-23
Identities = 36/71 (50%), Positives = 47/71 (66%), Gaps = 1/71 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL TT +DL+ +F + G + I I RD T S+GFAFV F D+ DAE AL+A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 76 DGRMLDGRELR 86
+G+ L GRELR
Sbjct: 60 NGKELGGRELR 70
>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 = 84.3 bits (209), Expect = 2e-22
Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 1/73 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL TT +DLR +F + GE+ + I RD+ +S+GFAFV F DAE AL+A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 76 DGRMLDGRELRVQ 88
+G+ LDGR+L+V
Sbjct: 60 NGKELDGRKLKVS 72
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 77.6 bits (192), Expect = 1e-19
Identities = 29/76 (38%), Positives = 47/76 (61%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L+ RTT +L +F + G V ++ + +D T ESRGF FV F DA+ A+ +
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 76 DGRMLDGRELRVQMAR 91
+G+ L+GR ++V+ A+
Sbjct: 64 NGKELEGRVIKVEKAK 79
>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 = 77.8 bits (192), Expect = 1e-19
Identities = 41/80 (51%), Positives = 53/80 (66%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V N+ T PDDLRR+F + G + D+YIP D +TR RGFA+V+F D RDAEDAL
Sbjct: 2 SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61
Query: 75 MDGRMLDGRELRVQMARYGR 94
+D GRE+ +Q A+ R
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81
>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 = 73.8 bits (182), Expect = 3e-18
Identities = 30/76 (39%), Positives = 40/76 (52%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL Y T +DL+ +F + GEV + DR T SRGF FV +A A++ +
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61
Query: 76 DGRMLDGRELRVQMAR 91
+G GR L V AR
Sbjct: 62 NGTDFGGRTLTVNEAR 77
>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 = 72.2 bits (178), Expect = 1e-17
Identities = 29/73 (39%), Positives = 40/73 (54%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V LT D L+ +F G V D+ +P DR RG+A+V F DAE A+ M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 76 DGRMLDGRELRVQ 88
DG +DG+E+ V+
Sbjct: 61 DGGQIDGQEVTVE 73
>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 = 71.8 bits (177), Expect = 2e-17
Identities = 29/77 (37%), Positives = 47/77 (61%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+++V NL+ DDLR +F G + +Y+ +D+ T +SRGFAFV F + DAE A++
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 75 MDGRMLDGRELRVQMAR 91
++G D L V+ A+
Sbjct: 61 LNGFGYDNLILSVEWAK 77
>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 = 71.2 bits (175), Expect = 3e-17
Identities = 30/72 (41%), Positives = 44/72 (61%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL + TT ++LR +FE GE+ ++++P D+ T+ S+GFAFV F A A +
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 76 DGRMLDGRELRV 87
DG + GR L V
Sbjct: 62 DGSIFQGRLLHV 73
>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 = 71.2 bits (175), Expect = 4e-17
Identities = 27/76 (35%), Positives = 48/76 (63%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
++ V NL + T +DL ++F + G+V + I +D+ TR+S+G AF+ F D+ DA + A
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62
Query: 75 MDGRMLDGRELRVQMA 90
++ + L GR L+ +A
Sbjct: 63 LNNKELFGRTLKCSIA 78
>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 = 70.0 bits (172), Expect = 8e-17
Identities = 30/72 (41%), Positives = 45/72 (62%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL + T DDLR +FE GE+ + + RD T S+G+ F++F D DA+ AL+ +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 76 DGRMLDGRELRV 87
+G L GR ++V
Sbjct: 61 NGFELAGRPIKV 72
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are highly conserved
proteins that bind to the poly(A) tail present at the
3' ends of most eukaryotic mRNAs. They have been
implicated in the regulation of poly(A) tail length
during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 69.6 bits (171), Expect = 1e-16
Identities = 28/73 (38%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y TTP++L+ F+ CG + I I D+FT + +GFA++ F DK E+AL
Sbjct: 1 SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-L 59
Query: 75 MDGRMLDGRELRV 87
++ GR+++V
Sbjct: 60 LNESEFRGRQIKV 72
>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 = 68.4 bits (168), Expect = 4e-16
Identities = 31/75 (41%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESR---GFAFVRFFDKRDAEDALDA 74
V NL ++ DDLR +F + GEV I IP+ + ++ R GFAFV F D AE+AL
Sbjct: 5 VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-Q 63
Query: 75 MDGRMLDGRELRVQM 89
++G L GR++ V +
Sbjct: 64 LNGTELGGRKISVSL 78
>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 = 67.4 bits (165), Expect = 1e-15
Identities = 26/72 (36%), Positives = 44/72 (61%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL Y DDL ++F + GE+ ++++ D+ + +S+GFA+V F D DA A +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 76 DGRMLDGRELRV 87
DG++ GR + +
Sbjct: 65 DGKVFQGRLIHI 76
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 65.6 bits (161), Expect = 4e-15
Identities = 28/70 (40%), Positives = 45/70 (64%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL++ TT + + +F RCG++ I + DRFT+ GF FV ++ + DAE+A+ ++G
Sbjct: 3 VGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNG 62
Query: 78 RMLDGRELRV 87
LD R +RV
Sbjct: 63 TKLDDRIIRV 72
>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 = 64.2 bits (157), Expect = 2e-14
Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L Y TT D LR+ F + GE+ + + DR T +SRG+ FV F DK AE A +
Sbjct: 5 VGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPN- 63
Query: 78 RMLDGRELRVQMA 90
++DGR+ V +A
Sbjct: 64 PIIDGRKANVNLA 76
>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 = 64.2 bits (156), Expect = 2e-14
Identities = 38/80 (47%), Positives = 53/80 (66%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V N+ T +DLRR F R G + D+Y+P D +TR RGFA+V+F D RDAEDAL
Sbjct: 2 SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61
Query: 75 MDGRMLDGRELRVQMARYGR 94
+D + + GR++ +Q A+ R
Sbjct: 62 LDRKWICGRQIEIQFAQGDR 81
>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 = 63.9 bits (155), Expect = 3e-14
Identities = 37/80 (46%), Positives = 54/80 (67%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V N+ T P+DLRR F R G + D+Y+P D +TR RGFA+++F D RDAEDAL
Sbjct: 2 SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61
Query: 75 MDGRMLDGRELRVQMARYGR 94
++ + + GR++ +Q A+ R
Sbjct: 62 LNRKWVCGRQIEIQFAQGDR 81
>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 = 63.4 bits (155), Expect = 3e-14
Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL ++ T DL+++F G V ++ IPR + +GFAFV+F K DAE A+ +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGK-KKGFAFVQFTSKADAEKAIKGV 60
Query: 76 DGRMLDGRELRVQMA 90
+G+ + GR + V A
Sbjct: 61 NGKKIKGRPVAVDWA 75
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 63.0 bits (154), Expect = 4e-14
Identities = 31/71 (43%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +DLR F G+V + + R+ RGFAFV F DAE AL +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58
Query: 76 DGRMLDGRELR 86
+G +LDGR LR
Sbjct: 59 NGLVLDGRTLR 69
>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 = 63.3 bits (154), Expect = 5e-14
Identities = 30/75 (40%), Positives = 50/75 (66%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + L++ T L +VF + G++ ++ + +DR T+ SRGF FV F + DA+DA+ AM
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 76 DGRMLDGRELRVQMA 90
+G+ +DGR++RV A
Sbjct: 63 NGKSVDGRQIRVDQA 77
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33
(Cyp33) and similar proteins. This subfamily
corresponds to the RRM of Cyp33, also termed
peptidyl-prolyl cis-trans isomerase E (PPIase E), or
cyclophilin E, or rotamase E. Cyp33 is a nuclear
RNA-binding cyclophilin with an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal PPIase domain. Cyp33 possesses RNA-binding
activity and preferentially binds to polyribonucleotide
polyA and polyU, but hardly to polyG and polyC. It
binds specifically to mRNA, which can stimulate its
PPIase activity. Moreover, Cyp33 interacts with the
third plant homeodomain (PHD3) zinc finger cassette of
the mixed lineage leukemia (MLL) proto-oncoprotein and
a poly-A RNA sequence through its RRM domain. It
further mediates downregulation of the expression of
MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a
proline isomerase-dependent manner. Cyp33 also
possesses a PPIase activity that catalyzes cis-trans
isomerization of the peptide bond preceding a proline,
which has been implicated in the stimulation of folding
and conformational changes in folded and unfolded
proteins. The PPIase activity can be inhibited by the
immunosuppressive drug cyclosporin A. .
Length = 73
Score = 61.9 bits (151), Expect = 1e-13
Identities = 29/72 (40%), Positives = 37/72 (51%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L L F G++ DI IP D T++ RGFAFV F + DA A+D M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 76 DGRMLDGRELRV 87
+ L GR +RV
Sbjct: 61 NESELFGRTIRV 72
>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 = 61.6 bits (150), Expect = 2e-13
Identities = 30/75 (40%), Positives = 43/75 (57%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL++ + L+ FE+ G V + DR T SRGF +V F DA+ A++AM
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61
Query: 76 DGRMLDGRELRVQMA 90
DG+ LDGR + V +
Sbjct: 62 DGKELDGRPINVDFS 76
>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 = 61.3 bits (149), Expect = 3e-13
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + NL Y T +DL ++F + G + ++++P D+ T++ +GFAFV + A A +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 76 DGRMLDGRELRV 87
DG + GR L +
Sbjct: 65 DGTVFQGRLLHL 76
>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 = 60.7 bits (148), Expect = 3e-13
Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L+V NL Y T +DL +F R GEV + I DR + S G A V F + DAE A+
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61
Query: 76 DGRMLDGRELRVQM 89
+G +LDG+ ++V++
Sbjct: 62 NGVLLDGQPMQVEL 75
>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 = 60.3 bits (147), Expect = 4e-13
Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 5/74 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL R T +L FE+ G + +++ R GFAFV F D RDAEDA+ A+DG
Sbjct: 4 VGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRALDG 58
Query: 78 RMLDGRELRVQMAR 91
R + G +RV+++R
Sbjct: 59 RRICGNRVRVELSR 72
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 60.7 bits (148), Expect = 4e-13
Identities = 29/77 (37%), Positives = 45/77 (58%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
+ + L Y T D+ VF + GE+ DI + RD+ T +S+GFAF+ + D+R A+D +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 76 DGRMLDGRELRVQMARY 92
+G L GR +RV R
Sbjct: 72 NGIKLLGRTIRVDHVRN 88
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 60.4 bits (147), Expect = 5e-13
Identities = 31/74 (41%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL++ DDL F+ CGEV D+ I +D R S+GF V F + A+ AL G
Sbjct: 4 VGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR-SKGFGHVEFATEEGAQKAL-EKSG 61
Query: 78 RMLDGRELRVQMAR 91
L GRE+RV +A
Sbjct: 62 EELLGREIRVDLAT 75
>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 = 60.1 bits (146), Expect = 6e-13
Identities = 26/75 (34%), Positives = 43/75 (57%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+ L T ++LR +FE G + I RDR T +S G+ FV + D+ DA+ A++ +
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62
Query: 76 DGRMLDGRELRVQMA 90
+G + + L+V A
Sbjct: 63 NGFEIRNKRLKVSYA 77
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 77
Score = 60.1 bits (146), Expect = 7e-13
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L ++TT DL+ F GE+ + + +D T +S+GF FVRF D ED + +
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKVL 58
Query: 76 DGR-MLDGRELRVQMAR 91
R M+DGR V++
Sbjct: 59 SQRHMIDGRWCDVKIPN 75
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 59.3 bits (144), Expect = 1e-12
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ + LR F GE+ D + +D T +S+G+ FV F K DAE+A+ +M+G
Sbjct: 4 VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63
Query: 78 RMLDGRELR 86
+ L GR +R
Sbjct: 64 QWLGGRAIR 72
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2),
TRA2-alpha, TRA2-beta (also termed SFRS10), and similar
proteins found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent
GnRH pre-mRNA splicing. TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. Both, TRA2-alpha and TRA2-beta, contains a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), flanked by the N- and C-terminal
arginine/serine (RS)-rich regions. .
Length = 78
Score = 59.6 bits (145), Expect = 1e-12
Identities = 30/72 (41%), Positives = 42/72 (58%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L+ TT DLR VF R G + + + D+ T SRGF FV F DA++A + +
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61
Query: 76 DGRMLDGRELRV 87
+G +DGR +RV
Sbjct: 62 NGMEIDGRRIRV 73
>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 = 58.4 bits (142), Expect = 2e-12
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL TT + LR +F GEV + +D +AFV F ++ DA A++ M
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 76 DGRMLDGRELRVQMAR 91
+G+ L+G + V +A+
Sbjct: 56 NGKELEGSPIEVSLAK 71
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 58.8 bits (143), Expect = 2e-12
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T + L +F + G V +++IP+DR T+ +G+ FV F + DA+ A+ M+
Sbjct: 3 VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62
Query: 78 RMLDGRELRV 87
L G+ +RV
Sbjct: 63 IKLYGKPIRV 72
>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 = 58.7 bits (143), Expect = 3e-12
Identities = 27/73 (36%), Positives = 40/73 (54%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V +L T L +F G V I + RD TR S G+A+V F + DAE ALD
Sbjct: 1 SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60
Query: 75 MDGRMLDGRELRV 87
++ ++ G+ +R+
Sbjct: 61 LNFDVIKGKPIRI 73
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 58.8 bits (143), Expect = 3e-12
Identities = 31/76 (40%), Positives = 43/76 (56%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L Y TT LRR FE G + I + RD+ T + RG+AF+ F +RD + A
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 76 DGRMLDGRELRVQMAR 91
DG+ +DGR + V + R
Sbjct: 64 DGKKIDGRRVLVDVER 79
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins.
This subfamily includes the RRM1 and RRM2 of
RNA-binding protein 5 (RBM5 or LUCA15 or H37) and
RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). These RBMs share high sequence homology and may
play an important role in regulating apoptosis. RBM5 is
a known modulator of apoptosis. It may also act as a
tumor suppressor or an RNA splicing factor. RBM6 has
been predicted to be a nuclear factor based on its
nuclear localization signal. Both, RBM6 and RBM5,
specifically bind poly(G) RNA. RBM10 is a paralog of
RBM5. It may play an important role in mRNA generation,
processing and degradation in several cell types. The
rat homolog of human RBM10 is protein S1-1, a
hypothetical RNA binding protein with poly(G) and
poly(U) binding capabilities. All family members
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a
G-patch/D111 domain. .
Length = 84
Score = 57.9 bits (141), Expect = 4e-12
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 20 NLTYRTTPDDLRRVFERCGEVG--DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
L TT +D+ + V D+ + RD+ T SRGFAFV F DA +DA
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 75 MDGRMLDGRELRV 87
+D ++DGR +RV
Sbjct: 69 LDPFVIDGRVVRV 81
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 57.6 bits (140), Expect = 5e-12
Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + ++LR+ FE CG+V + I RDR T +GF +V F K AL ++G
Sbjct: 4 VGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNG 62
Query: 78 RMLDGRELRVQ 88
L GR++RV+
Sbjct: 63 IKLKGRKIRVK 73
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 61.5 bits (148), Expect = 6e-12
Identities = 41/135 (30%), Positives = 67/135 (49%), Gaps = 1/135 (0%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL Y T +DLR +F++ G V + + RDR T +SRGFAFV F + AE A++
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176
Query: 75 MDGRMLDGRELRVQMARYGRPP-SSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRS 133
++G+ L+GR LRVQ A+ P S + ++ R ++ + + +
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLK 236
Query: 134 GSKSPRKARSKSIDR 148
++ KS
Sbjct: 237 TAEEELADLFKSRGD 251
>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 = 57.2 bits (139), Expect = 8e-12
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N+ Y T + L +F G V + DR T + +G+ F F D A A+ ++G
Sbjct: 3 VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62
Query: 78 RMLDGRELRVQMA 90
+GR LRV A
Sbjct: 63 YEFNGRALRVDFA 75
>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 = 56.0 bits (136), Expect = 2e-11
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
L ++F G V I + ++ GFAFV F + AE A+ ++G + GR LRV
Sbjct: 1 LYKLFSPFGNVEKI-----KLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Query: 90 A 90
+
Sbjct: 56 S 56
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 56.1 bits (136), Expect = 2e-11
Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA----MD 76
L++ TT + LR F + GEV D I +D T SRGF FV F D + L A +D
Sbjct: 6 LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLD 65
Query: 77 GRMLD 81
GR +D
Sbjct: 66 GREID 70
>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 = 56.2 bits (135), Expect = 2e-11
Identities = 26/73 (35%), Positives = 45/73 (61%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T +D++ F G++ D + +D T +S+G+ FV F++K DAE+A+ M G
Sbjct: 6 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 65
Query: 78 RMLDGRELRVQMA 90
+ L GR++R A
Sbjct: 66 QWLGGRQIRTNWA 78
>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 = 55.6 bits (135), Expect = 3e-11
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
+L ++NL + D+L+R +F + G V DI T + RG AFV F D A +
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATN 57
Query: 71 ALDAMDGRMLDGRELRVQMAR 91
AL A+ G + +R+Q A+
Sbjct: 58 ALRALQGFPFYDKPMRIQYAK 78
>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 = 55.7 bits (135), Expect = 3e-11
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T ++L+R F G + ++ + +D+ G+AFVRF A A+ A++G
Sbjct: 5 VGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAVNG 58
Query: 78 RMLDGRELRV 87
++G+ ++
Sbjct: 59 TSINGQTVKC 68
>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 = 55.5 bits (133), Expect = 4e-11
Identities = 28/73 (38%), Positives = 44/73 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T DD++ F G + D + +D T +S+G+ FV FF+K DAE+A+ M G
Sbjct: 6 VGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 65
Query: 78 RMLDGRELRVQMA 90
+ L GR++R A
Sbjct: 66 QWLGGRQIRTNWA 78
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 54.9 bits (133), Expect = 6e-11
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-----FTRESRGFAFVRFFDKRDAE 69
+L V NL ++TT + L++ FE+CG V + I + + S G+ FV F K A+
Sbjct: 2 TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 70 DALDAMDGRMLDGRELRVQM 89
AL + G +LDG L +++
Sbjct: 62 KALKRLQGTVLDGHALELKL 81
>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 = 54.9 bits (133), Expect = 7e-11
Identities = 20/52 (38%), Positives = 36/52 (69%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
T +D+R +FE G + ++ I RD+ T +S+G AFV+F + +A+ A++A+ G
Sbjct: 12 TEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 56.6 bits (136), Expect = 7e-11
Identities = 36/89 (40%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + L++ T LR F G+V D + DR T SRGF FV F D+ A A+ M
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96
Query: 76 DGRMLDGRELRVQMARYGRPPSSSRSRGG 104
DG+ L+GR +RV A PS+ R+ GG
Sbjct: 97 DGKELNGRHIRVNPAN--DRPSAPRAYGG 123
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 53.8 bits (130), Expect = 1e-10
Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N+ + T +LR +F G+V + +P+ +F RGFAFV F K++A++A++A+
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Query: 76 DGRMLDGRELRVQMA 90
L GR L ++ A
Sbjct: 62 KSTHLYGRHLVLEYA 76
>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 = 53.9 bits (130), Expect = 2e-10
Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 2/68 (2%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML--DG 82
T DDLR F GE+ DI++ +D+ T+ES+G A+V+F A A++ M+G+ L D
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
Query: 83 RELRVQMA 90
+ L+V +A
Sbjct: 74 KPLKVLIA 81
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 23/74 (31%), Positives = 40/74 (54%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL Y TT + L F G + ++ +D+ +++ RGF +V F + DA+ AL+
Sbjct: 4 VRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKK 63
Query: 78 RMLDGRELRVQMAR 91
GR++ V+ A+
Sbjct: 64 TKFGGRKIHVEFAK 77
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 54.1 bits (131), Expect = 2e-10
Identities = 21/87 (24%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAE 69
+EG + + V + +D+ F GE+ ++++ DR T +G+A + + K++A+
Sbjct: 4 VEGWI-IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQ 62
Query: 70 DALDAMDGRMLDGRELRVQMARYGRPP 96
A++ ++G+ L G+ + V A + + P
Sbjct: 63 AAIEGLNGKELLGQTISVDWA-FVKGP 88
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 53.5 bits (129), Expect = 2e-10
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V+ L T + L+ VF + G V + +PR + T + +GFAF+ F +A+ A +
Sbjct: 4 VECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
+ NL + T ++L+ +F + GEV I +D+ T S+G AFV+F K A+ L+A
Sbjct: 5 IRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADN 64
Query: 75 --MDGRMLDGRELRVQMA 90
G LDGR L V +A
Sbjct: 65 AEDSGLSLDGRRLIVTLA 82
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 53.7 bits (129), Expect = 2e-10
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y T ++L F CG V + I D+F+ +GFA++ F DK AL A
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-A 59
Query: 75 MDGRMLDGRELRVQMAR 91
+D + GR+++V R
Sbjct: 60 LDESLFRGRQIKVMPKR 76
>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 = 53.3 bits (129), Expect = 3e-10
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + L+ +F + G++ + +D +S+GF FV F + A+ A++ ++G
Sbjct: 6 VKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64
Query: 78 RMLDGRELRV 87
+ ++G++L V
Sbjct: 65 KEVNGKKLYV 74
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This
subgroup corresponds to the RRM3 of the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
proteins, a family of structurally related RNA-binding
proteins involved in the regulation of pre-mRNA
splicing in the nucleus and in the control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or
NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or
ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed
BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also
termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts. .
Length = 73
Score = 53.0 bits (128), Expect = 3e-10
Identities = 20/60 (33%), Positives = 34/60 (56%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
DL ++F G V + D+ T +S+ F FV + + A+ A+ AM+G + G+ L+VQ
Sbjct: 14 DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 52.7 bits (127), Expect = 4e-10
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 6/72 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T ++ + +F + GEV ++++ +++ GF F+R + +AE A +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKAEL 57
Query: 76 DGRMLDGRELRV 87
DG M GR+LRV
Sbjct: 58 DGIMRKGRQLRV 69
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise
role of PPIase remains unclear. PPIase contains a
conserved N-terminal peptidyl-prolyl cistrans isomerase
(PPIase) motif, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 52.7 bits (127), Expect = 4e-10
Identities = 23/63 (36%), Positives = 36/63 (57%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
TT +DL +F R G++ + RD+ T +S +AF+ F K D E+A MD ++D R
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRR 74
Query: 85 LRV 87
+ V
Sbjct: 75 IHV 77
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 52.7 bits (127), Expect = 5e-10
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL R T + L +F + G + + IP+D + + FAFV F + A+
Sbjct: 3 TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSVPYAIQL 61
Query: 75 MDGRMLDGRELRVQ 88
++G L GRELR++
Sbjct: 62 LNGIRLFGRELRIK 75
>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 = 52.4 bits (126), Expect = 6e-10
Identities = 24/72 (33%), Positives = 38/72 (52%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL++ D + F GE+ + +P D + +GF +V F + A+ ALDA+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 76 DGRMLDGRELRV 87
G L GR +R+
Sbjct: 61 GGTDLLGRPVRL 72
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 52.1 bits (125), Expect = 7e-10
Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T D+R +F G++ + +P+ +F + +RGFAFV F ++A +A++A+
Sbjct: 5 VKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMNALKD 63
Query: 78 RMLDGRELRVQMA 90
L GR L +Q A
Sbjct: 64 THLLGRRLVLQYA 76
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 51.9 bits (125), Expect = 7e-10
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N+ ++LR +FE+ G++ +Y + RGF V ++D R A A A+
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRAL 58
Query: 76 DGRMLDGRELRVQ 88
G L GR+L +
Sbjct: 59 QGTELGGRKLDIH 71
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 51.9 bits (125), Expect = 8e-10
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V NLT+ TT +DL G +V I + +S+GFA+V F + A +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 74 AMDGRMLDGRELRVQ 88
++GR +G++ V
Sbjct: 61 KLEGREFNGKKCVVT 75
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM1 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 51.8 bits (124), Expect = 1e-09
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL R T D L+++F+ G V ++ I D+ + + FV + DAE AL +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 76 DGRMLDGRELRVQMA 90
+GR ++ E+RV A
Sbjct: 60 NGRQIENNEIRVNWA 74
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 51.5 bits (124), Expect = 1e-09
Identities = 22/66 (33%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL Y D+LR++F +CGE+ D+ + ++ + S+G+A+V F ++ ++AL +D
Sbjct: 4 VSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK-SKGYAYVEFENEESVQEAL-KLDR 61
Query: 78 RMLDGR 83
++ GR
Sbjct: 62 ELIKGR 67
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 52.0 bits (124), Expect = 1e-09
Identities = 33/75 (44%), Positives = 46/75 (61%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L+ TT DLR VF + G + D+ I D+ +R SRGFAFV F + DA++A +
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71
Query: 76 DGRMLDGRELRVQMA 90
+G LDGR +RV +
Sbjct: 72 NGMELDGRRIRVDFS 86
>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 = 51.3 bits (122), Expect = 2e-09
Identities = 25/77 (32%), Positives = 45/77 (58%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T ++L+ +F GE+ + RD+ T +S G+ FV + D +DAE A++
Sbjct: 6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65
Query: 75 MDGRMLDGRELRVQMAR 91
++G L + ++V AR
Sbjct: 66 LNGLRLQTKTIKVSYAR 82
>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 = 54.6 bits (131), Expect = 2e-09
Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
E +L V+ L T +++R +F GE+ + RD+ T +S G+ FV + DAE
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Query: 71 ALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
A+++++G L + ++V AR PSS +G
Sbjct: 61 AVNSLNGLRLQNKTIKVSYAR----PSSDSIKG 89
Score = 38.0 bits (88), Expect = 0.001
Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 5/105 (4%)
Query: 1 MSYGRPPP-RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
+SY RP I+G +L V L T +L +F G++ I D T S+G F
Sbjct: 77 VSYARPSSDSIKG-ANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGF 135
Query: 60 VRFFDKRD-AEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRG 103
+R FDKRD A+ A+ ++G G + + ++ PSSS S+G
Sbjct: 136 IR-FDKRDEADRAIKTLNGTTPSGCTEPITV-KFANNPSSSNSKG 178
Score = 36.1 bits (83), Expect = 0.004
Identities = 22/70 (31%), Positives = 37/70 (52%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL+ T L ++F G V ++ I RD T + +G+ FV + +A A+ +++G
Sbjct: 274 VYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNG 333
Query: 78 RMLDGRELRV 87
L R L+V
Sbjct: 334 YTLGNRVLQV 343
>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 = 50.9 bits (122), Expect = 2e-09
Identities = 25/75 (33%), Positives = 42/75 (56%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+ L T D++R +F GE+ + RD+ T +S G+ FV + D DAE A++ +
Sbjct: 4 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63
Query: 76 DGRMLDGRELRVQMA 90
+G L + ++V A
Sbjct: 64 NGLRLQNKTIKVSYA 78
>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 = 51.3 bits (122), Expect = 2e-09
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T ++ R +F GE+ + RD+ T +S G+ FV + D +DAE A++
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75 MDGRMLDGRELRVQMARYGRPPS 97
++G L + ++V Y RP S
Sbjct: 64 LNGLRLQTKTIKVS---YARPSS 83
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 50.4 bits (121), Expect = 3e-09
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL Y TT +DL F+ G + + D+ T +S+G AFV F AL +
Sbjct: 5 VGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-LHH 63
Query: 78 RMLDGRELRVQ 88
+L GR++ V+
Sbjct: 64 TLLKGRKINVE 74
>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 = 49.9 bits (120), Expect = 3e-09
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 8/71 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL TT ++LR +FE+ G V + + ++ + FV ++ DAEDA+ A++G
Sbjct: 4 VGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKALNG 55
Query: 78 RMLDGRELRVQ 88
G+ + V+
Sbjct: 56 YEFMGKRINVE 66
>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 = 54.0 bits (130), Expect = 4e-09
Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V+L V NL T + LR +F CGE+ + D SRGF FV F + +A A+
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344
Query: 74 AMDGRMLDGRELRVQMA 90
M GRML G+ L V +A
Sbjct: 345 EMHGRMLGGKPLYVALA 361
Score = 45.2 bits (107), Expect = 4e-06
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V +L T L +F+ G V + + RD TR S G+ +V F + DAE AL+
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSRS 101
M+ + L G+ +R+ ++ R PS RS
Sbjct: 62 MNFKRLGGKPIRIMWSQ--RDPSLRRS 86
Score = 44.4 bits (105), Expect = 7e-06
Identities = 33/114 (28%), Positives = 53/114 (46%), Gaps = 14/114 (12%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL D LR +F + GE+ + +D + SRGFAFV F DA A++ M
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239
Query: 76 DGRMLD----GRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
+G+ + G++L V A + R R+ + RR + R +++
Sbjct: 240 NGKKIGLAKEGKKLYVGRA---------QKRAEREAELRRKFEELQQERKMKAQ 284
Score = 33.2 bits (76), Expect = 0.046
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDK 65
P R G+ ++ V NL L F + G + + D + SRG+ FV F +
Sbjct: 81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKE 139
Query: 66 RDAEDALDAMDGRMLDGRELRV 87
A+ A+ ++G +L+ +E+ V
Sbjct: 140 ESAKAAIQKVNGMLLNDKEVYV 161
>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 = 50.2 bits (120), Expect = 4e-09
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V N+ Y +T ++L F CG + + I D+F+ +G+A++ F RD+ +A A
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIE-FATRDSVEAAVA 59
Query: 75 MDGRMLDGRELRV 87
+D GR ++V
Sbjct: 60 LDESSFRGRVIKV 72
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of
RBM23 remains unclear, it shows high sequence homology
to RBM39 and contains two RRMs. It may possibly
function as a pre-mRNA splicing factor. .
Length = 73
Score = 49.9 bits (120), Expect = 4e-09
Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L+ + DL F + G+V D+ I RDR +R S+G A+V F+D+ AL + G
Sbjct: 4 VMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTG 62
Query: 78 RMLDGRELRVQ 88
+ L G+ + VQ
Sbjct: 63 QRLLGQPIMVQ 73
>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 = 53.7 bits (129), Expect = 4e-09
Identities = 32/96 (33%), Positives = 54/96 (56%)
Query: 7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKR 66
P I + L V NL + T +LR++FE G++ D+ + RD T S+GF F++F D
Sbjct: 180 PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE 239
Query: 67 DAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSR 102
+A++AL+ M+G L GR ++V A+ + +
Sbjct: 240 EAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANT 275
Score = 39.1 bits (91), Expect = 4e-04
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L + DL F + G+V D+ +DR +R S+G A+V F+D AL A+ G
Sbjct: 94 VLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTG 152
Query: 78 RMLDGRELRVQ 88
+ML GR + VQ
Sbjct: 153 QMLLGRPIIVQ 163
Score = 39.1 bits (91), Expect = 4e-04
Identities = 24/61 (39%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 95 PPSSSRSRGGRDRDRRRDRS-RSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHE 153
S R R R RDRS R RDR Y R R SRSRS ++ R +S RD++
Sbjct: 15 RRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRS 74
Query: 154 R 154
Sbjct: 75 G 75
Score = 35.6 bits (82), Expect = 0.007
Identities = 21/51 (41%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 97 SSSRSRG-GRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSK-SPRKARSKS 145
R RG R+ RR D+ R R RR +RSR S R R R+ RS+S
Sbjct: 2 YRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRS 52
Score = 33.7 bits (77), Expect = 0.031
Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 105 RDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHERNGRS 158
R RDR R R R+ RR + R RSR S+S ++R + DRD R GRS
Sbjct: 1 RYRDRERGRLRNDTRRSDKGR---ERSRRRSRSRDRSR-RRRDRDYYRGRRGRS 50
Score = 26.4 bits (58), Expect = 8.9
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 12/72 (16%)
Query: 94 RPPSSSRSRGGRDRDR-------RRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSI 146
R S SR R R RDR R RSRS +R Y R + + +
Sbjct: 25 RRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRG--DRSYRRDDRRSGR---NTK 79
Query: 147 DRDNKHERNGRS 158
+ + ER+ R+
Sbjct: 80 EPLTEAERDDRT 91
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein
orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which
is a putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 50.3 bits (121), Expect = 5e-09
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYI--PRDRFTR-ESRGFAFVRFFDKRDAEDAL 72
L V NL + T + L + F R G + + I PR R +R FV F ++ DAE AL
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 73 DAMDGRMLDGRELRV 87
D +DG+ + G EL++
Sbjct: 64 DELDGKDVMGYELKL 78
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 71
Score = 49.6 bits (119), Expect = 6e-09
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V LT T +DLR+ F + GEV D+YIP+ R FAFV F D A+ +
Sbjct: 5 VGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG--ED 57
Query: 78 RMLDGRELRVQMAR 91
++ G + V A
Sbjct: 58 HIIKGVSVHVSNAE 71
>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 = 49.9 bits (120), Expect = 6e-09
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 9 RIEGMVS---LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR---DRFTRESRGFAFVRF 62
+ MV+ L+ D Y +D++ + G+V + IPR + G FV F
Sbjct: 5 CLLNMVTPEELEDDE-EYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEF 63
Query: 63 FDKRDAEDALDAMDGRMLDGRELRVQ 88
D DA+ A A+ GR DGR +
Sbjct: 64 ADVEDAQKAQLALAGRKFDGRTVVAS 89
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily
corresponds to the RRM2 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 49.7 bits (119), Expect = 6e-09
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
L F CGE+ + IP DR T S+GFA++ F E AL+ +DG L G L V
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 49.9 bits (120), Expect = 6e-09
Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 3/54 (5%)
Query: 30 LRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
LR++F + G ++ IY+P D T +++G+AFV F +A++A+ A++G LD
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 49.5 bits (119), Expect = 6e-09
Identities = 18/62 (29%), Positives = 33/62 (53%)
Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
+LR+ F + G V + + R + T +S+G+AFV F A+ + M+ +L R L+
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72
Query: 87 VQ 88
+
Sbjct: 73 CK 74
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 49.6 bits (119), Expect = 7e-09
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV--GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V NL + T DL+ +F CG V D+ D S+GF V F DA+ A++
Sbjct: 3 VRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR---SKGFGTVLFESPEDAQRAIEMF 59
Query: 76 DGRMLDGRELRV 87
+G L+GREL V
Sbjct: 60 NGYDLEGRELEV 71
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1)
is a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation,
and tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator
of the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 75
Score = 49.4 bits (118), Expect = 7e-09
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA----MD 76
L+++TT + LR F + GE+ + + RD T+ SRGF FV F D + L +D
Sbjct: 6 LSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELD 65
Query: 77 GRMLD 81
G+ +D
Sbjct: 66 GKKID 70
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 49.3 bits (118), Expect = 7e-09
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
D++R+FE CG V + + +R + AF+ F + A+ A++ ++G +DG ++VQ
Sbjct: 15 DVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 49.4 bits (118), Expect = 8e-09
Identities = 28/68 (41%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA--- 74
V L++ TT + LRR F + GEV D I +D+ T SRGF FV+F D L
Sbjct: 4 VGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPH 63
Query: 75 -MDGRMLD 81
+DGR +D
Sbjct: 64 TLDGRTID 71
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 49.2 bits (118), Expect = 8e-09
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T D L +F + G + + R+ + +AFV ++D R A AL M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57
Query: 76 DGRMLDGRELRVQMA 90
+GR++ G+E++V A
Sbjct: 58 NGRLILGQEIKVNWA 72
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 48.8 bits (117), Expect = 1e-08
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
+ ++L RVFE+ G V D+ +P + + FV + DA A DA++G+ L+
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGK------PYCFVSYSSIEDAAAAYDALNGKELE 65
>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 = 48.7 bits (116), Expect = 2e-08
Identities = 27/76 (35%), Positives = 39/76 (51%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL + T +DL F + + D T ESRG+ FV F DA++AL
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 75 MDGRMLDGRELRVQMA 90
+ + L GR LR+ +A
Sbjct: 61 LKNKKLHGRILRLDIA 76
>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 = 48.4 bits (115), Expect = 2e-08
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 5/74 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+NL+Y + D L+ VFE+ I IP++ +G+AFV F DA++AL++
Sbjct: 4 LVVNNLSYSASEDSLQEVFEK---ATSIRIPQNN--GRPKGYAFVEFESAEDAKEALNSC 58
Query: 76 DGRMLDGRELRVQM 89
+ ++GR +R++
Sbjct: 59 NNTEIEGRSIRLEF 72
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 48.8 bits (117), Expect = 2e-08
Identities = 27/73 (36%), Positives = 42/73 (57%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L+ +TT + LR VF R G++ + + RD T S+G+AFV + +RDA A
Sbjct: 5 TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64
Query: 75 MDGRMLDGRELRV 87
++DG E+ V
Sbjct: 65 AHKLVIDGSEIFV 77
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 47.9 bits (114), Expect = 2e-08
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL + + LR +F+ G+V ++ R T R FV FFD RDA AL A
Sbjct: 3 TLVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALRA 57
Query: 75 MDGRMLDGRELRVQ 88
M+G+ + G+ + ++
Sbjct: 58 MNGKEISGKPVVIE 71
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 48.0 bits (115), Expect = 2e-08
Identities = 20/70 (28%), Positives = 35/70 (50%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + +L + F CGEV + I R++ T +S G+ FV F AE AL +
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
Query: 75 MDGRMLDGRE 84
++G+ + +
Sbjct: 61 LNGKPIPNTQ 70
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 47.4 bits (113), Expect = 4e-08
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 24 RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR 83
T +D+ ++FE G + I + FAFV F D DA AL+A+ G +DG
Sbjct: 11 TTREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRIDGS 62
Query: 84 ELRVQMAR 91
L V+ +
Sbjct: 63 VLTVEFVK 70
>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 = 47.6 bits (114), Expect = 4e-08
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L V NL T +L+ F + GE+ D+ + R + SR AF+ + + +A+ A D
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTEEEAQKAKDY 61
Query: 75 MDGRMLDGRELRVQMA 90
+ ++ ++ V+ A
Sbjct: 62 FNNTYINTSKISVEFA 77
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM1 in hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 78
Score = 47.0 bits (112), Expect = 6e-08
Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L+Y TT D L+ F + GE+ D + +D T+ SRGF FV F + + A++A + +
Sbjct: 7 LSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHK-V 65
Query: 81 DGRELRVQMA 90
DGRE+ + A
Sbjct: 66 DGREVEPKRA 75
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate
nucleolin. This subfamily corresponds to the RRM2 of
ubiquitously expressed protein nucleolin, also termed
protein C23, a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines.RRM2,
together with RRM1, binds specifically to RNA
stem-loops containing the sequence (U/G)CCCG(A/G) in
the loop. .
Length = 77
Score = 47.1 bits (112), Expect = 6e-08
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL Y T D+L+ VFE + DI +P + S+G A++ F + +AE AL+
Sbjct: 5 TLFVKNLPYNITVDELKEVFE---DAVDIRLPSGK-DGSSKGIAYIEFKTEAEAEKALEE 60
Query: 75 MDGRMLDGRELRV 87
G +DGR + V
Sbjct: 61 KQGAEVDGRSIVV 73
>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 = 46.8 bits (112), Expect = 7e-08
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V+L V NL + LR F G + + D R S+GF FV F +A A+
Sbjct: 2 VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGR-SKGFGFVCFSSPEEATKAVT 60
Query: 74 AMDGRMLDGRELRVQMA 90
M+GR++ G+ L V +A
Sbjct: 61 EMNGRIIGGKPLYVALA 77
>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 = 47.0 bits (111), Expect = 7e-08
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T ++ + +F GE+ + RD+ T +S G+ FV + D DA+ A++
Sbjct: 5 NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64
Query: 75 MDGRMLDGRELRVQMARYGRPPS 97
++G L + ++V Y RP S
Sbjct: 65 LNGLKLQTKTIKVS---YARPSS 84
>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 = 47.0 bits (111), Expect = 7e-08
Identities = 26/77 (33%), Positives = 43/77 (55%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T D+LR +F GEV + RD+ S G+ FV + + +DAE A++
Sbjct: 3 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62
Query: 75 MDGRMLDGRELRVQMAR 91
++G L + ++V AR
Sbjct: 63 LNGLRLQSKTIKVSYAR 79
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 46.8 bits (111), Expect = 7e-08
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA--LDAM 75
V NL + + L RVF +CG + + I RD T +GFA+V+F D+ E A L+
Sbjct: 4 VGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEK 63
Query: 76 DGRMLDGRELRVQMAR 91
+ RELRV +
Sbjct: 64 KFPPMLPRELRVSRCK 79
>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 = 46.7 bits (111), Expect = 8e-08
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V + V N+ T+ ++LR +FE G V + R FAFV + A+ A++
Sbjct: 1 VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIE 52
Query: 74 AMDGRMLDGRELRVQMA 90
++GR L GR+L V+ +
Sbjct: 53 ELNGRELHGRKLVVEHS 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 = 46.7 bits (111), Expect = 8e-08
Identities = 22/70 (31%), Positives = 35/70 (50%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L+ T L F D + D + SRG+ FV F ++DAE+A++ M+G
Sbjct: 4 VGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNG 63
Query: 78 RMLDGRELRV 87
+ L R +R
Sbjct: 64 KWLGSRPIRC 73
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2
and forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3
or NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2
protein. Its message is detected exclusively in
post-mitotic regions of embryonic brain. Like RBFOX1,
both RBFOX2 and RBFOX3 bind to the hexanucleotide
UGCAUG elements and modulate brain and muscle-specific
splicing of exon EIIIB of fibronectin, exon N1 of
c-src, and calcitonin/CGRP. Members in this family also
harbor one RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 76
Score = 46.6 bits (111), Expect = 8e-08
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N+ +R DLR++F + G + D+ I + R S+GF FV F + DA+ A + +
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNE--RGSKGFGFVTFANSADADRAREKL 60
Query: 76 DGRMLDGRELRVQMA 90
G +++GR++ V A
Sbjct: 61 HGTVVEGRKIEVNNA 75
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2
protein homolog alpha (TRA-2 alpha) and similar
proteins. This subgroup corresponds to the RRM of
TRA2-alpha or TRA-2-alpha, also termed transformer-2
protein homolog A, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein (SRp40) that
specifically binds to gonadotropin-releasing hormone
(GnRH) exonic splicing enhancer on exon 4 (ESE4) and is
necessary for enhanced GnRH pre-mRNA splicing. It
strongly stimulates GnRH intron A excision in a
dose-dependent manner. In addition, TRA2-alpha can
interact with either 9G8 or SRp30c, which may also be
crucial for ESE-dependent GnRH pre-mRNA splicing.
TRA2-alpha contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 79
Score = 46.9 bits (111), Expect = 9e-08
Identities = 31/72 (43%), Positives = 43/72 (59%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L+ TT DLR VF R G + + + D+ T SRGFAFV F D+++A++
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHA 61
Query: 76 DGRMLDGRELRV 87
+G LDGR +RV
Sbjct: 62 NGMELDGRRIRV 73
>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 = 46.4 bits (111), Expect = 1e-07
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
D+L +FE+ G + ++ + D F+ +RG+AFV + +K A+ A+ + L E+R
Sbjct: 15 EDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAV-----KQLHNYEIR 68
Query: 87 VQM 89
Sbjct: 69 PGK 71
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 46.5 bits (111), Expect = 1e-07
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR------ESRGFAFVRFFDKRDAE 69
L + NL R T L ++F + G++ F + + RG+ FV F K +AE
Sbjct: 2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDF---LFHKSGPLKGQPRGYCFVTFETKEEAE 58
Query: 70 DALDAMDGRMLDGRELRVQMAR 91
AL +++G+ G++L V+ A
Sbjct: 59 KALKSLNGKTALGKKLVVRWAH 80
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 46.2 bits (110), Expect = 1e-07
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ NL + T DD+R F+ C E+ + + D+ T E +GF V F D+ + AL +DG
Sbjct: 4 IGNLAWDITEDDVREFFKGC-EITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLDG 61
Query: 78 RMLDGRELRV 87
+L GR +R+
Sbjct: 62 TVLCGRPIRI 71
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 46.1 bits (110), Expect = 1e-07
Identities = 23/73 (31%), Positives = 36/73 (49%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T + R + G V ++ T ES+G+ FV + K A A + +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 76 DGRMLDGRELRVQ 88
DG+ + GR+L+V
Sbjct: 62 DGKQIGGRKLQVD 74
>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 = 45.8 bits (109), Expect = 2e-07
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L T D+LR +F GE+ + IP +G FV+F + AE A+ + G
Sbjct: 6 VGGLDPAVTEDELRSLFGPFGEIVYVKIP------PGKGCGFVQFVHRAAAEAAIQQLQG 59
Query: 78 RMLDGRELRVQ 88
++ G +R+
Sbjct: 60 TIIGGSRIRLS 70
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 45.8 bits (109), Expect = 2e-07
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L YR D+ R F+ G + +I + GF FV F D RDA+DA+ ++G
Sbjct: 4 IGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYELNG 55
Query: 78 RMLDGRELRVQMAR 91
+ L G + V+ AR
Sbjct: 56 KELCGERVIVEHAR 69
>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 = 46.0 bits (109), Expect = 2e-07
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL + T D+LR++FE G + + RD+ T RG AFVR+ + +A+ A+ +
Sbjct: 2 NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61
Query: 75 MDGRMLDGRELRVQM 89
++G + G + + +
Sbjct: 62 LNGTIPPGSTMPLSV 76
>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 = 45.9 bits (109), Expect = 2e-07
Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L + T ++L ++F++ G V + + +R + + +G A+V + ++ A A+ M
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63
Query: 76 DGRMLDGRELRVQMARYGRPP 96
DG + + + V ++ PP
Sbjct: 64 DGTEIKEKTISVAIS---NPP 81
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM2 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and is highly conserved between
plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 45.6 bits (108), Expect = 2e-07
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL + DDL ++F GE+ +I R T R F+ F+D R AE AL A
Sbjct: 3 TLVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALKA 57
Query: 75 MDGRMLDGRELRVQ 88
++ + G+ ++++
Sbjct: 58 LNRSEIAGKRIKLE 71
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to
the RRM1 of hnRNP A0 which is a low abundance hnRNP
protein that has been implicated in mRNA stability in
mammalian cells. It has been identified as the
substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 79
Score = 45.6 bits (108), Expect = 2e-07
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L V L +T+ LRR F R G++ + + D T+ SRGF F+ F +A++A++A
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63
Query: 75 MDGRMLDGRELRVQMA 90
+DG ++ ++ A
Sbjct: 64 Q-PHSIDGNQIELKRA 78
>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 = 45.6 bits (108), Expect = 2e-07
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
P L+++F R G+V + IPR R + GFAFV +++AE AL+ +G +DGR +
Sbjct: 15 PVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVA 73
Query: 87 VQMA 90
V A
Sbjct: 74 VDWA 77
>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 = 45.6 bits (109), Expect = 2e-07
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ NL Y T D L +VF G V I I F + + A V+F AE+A A++G
Sbjct: 6 ISNLLYPVTVDVLHQVFSPYGAVEKILI----FEKNTGVQALVQFDSVESAENAKKALNG 61
Query: 78 RML--DGRELRVQMAR 91
R + L +Q +R
Sbjct: 62 RNIYDGCCTLDIQFSR 77
>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 = 48.5 bits (115), Expect = 3e-07
Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M + V ++++ D +RR F+ G + I + D T + +GFAFV + A+ AL
Sbjct: 107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLAL 166
Query: 73 DAMDGRMLDGRELRVQMARYGRP 95
+ M+G+ML GR ++V GRP
Sbjct: 167 EQMNGQMLGGRNIKV-----GRP 184
Score = 41.2 bits (96), Expect = 8e-05
Identities = 17/60 (28%), Positives = 32/60 (53%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
D++ VFE GE+ + R R +G+ F+ + + + +A+ +M+ L G+ LRV
Sbjct: 219 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p
encoded by YNL175c from Saccharomyces cerevisiae. It
shares high sequence similarity with nucleolar protein
12 (Nop12p). Both Nop12p and Nop13p are not essential
for growth. However, unlike Nop12p that is localized to
the nucleolus, Nop13p localizes primarily to the
nucleolus but is also present in the nucleoplasm to a
lesser extent. Nop13p contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 73
Score = 45.1 bits (107), Expect = 3e-07
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL++ TT D+LR F R G + + + + + +GFAFV F + E A +A+ G
Sbjct: 3 VGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNALKG 59
Query: 78 RMLDGRELRVQMA 90
+ L+GR LRV+
Sbjct: 60 KHLNGRALRVEYG 72
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 45.2 bits (107), Expect = 3e-07
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFT--RESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRE 84
DLR +FE+ G V I + RDR +S+G FV F+ ++ A +A +A+ + L G
Sbjct: 16 KDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKTLPGMH 75
Query: 85 LRVQM 89
+QM
Sbjct: 76 HPIQM 80
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 45.2 bits (107), Expect = 4e-07
Identities = 24/73 (32%), Positives = 39/73 (53%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N+ Y T + L+ +F G V + DR T + +G+ F + D+ A A+ ++G
Sbjct: 3 VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62
Query: 78 RMLDGRELRVQMA 90
L+GR+LRV A
Sbjct: 63 YELNGRQLRVDNA 75
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 44.9 bits (106), Expect = 4e-07
Identities = 29/68 (42%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
V L++ TT DL+ F + GEV D I D T SRGF FV F D E LD
Sbjct: 3 VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEH 62
Query: 74 AMDGRMLD 81
+DGR++D
Sbjct: 63 KLDGRVID 70
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 44.9 bits (107), Expect = 4e-07
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL ++ + ++L +F + G + I R T+E+RG AFV + D DA++A D +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQI---RIGNTKETRGTAFVVYEDIYDAKNACDHL 61
Query: 76 DGRMLDGRELRVQM 89
G + R L V
Sbjct: 62 SGFNVANRYLVVLY 75
>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 = 44.7 bits (106), Expect = 4e-07
Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL D+ +F + G + I + + R FAFV F D RDAEDA+ DG
Sbjct: 4 VGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 78 RMLDGRELRVQM 89
DG LRV+
Sbjct: 61 YDFDGYRLRVEF 72
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 44.6 bits (106), Expect = 5e-07
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ +L+ + T +DL+ +FE GE+ I IP RG A+V ++DA AL +
Sbjct: 7 IGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-------PRGCAYVCMETRQDAHRALQKLR 59
Query: 77 GRMLDGRELRVQMAR 91
L G++++V A
Sbjct: 60 NVKLAGKKIKVAWAP 74
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway; it binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 75
Score = 44.7 bits (106), Expect = 5e-07
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T ++ + F + G+V D + +D T SRGF FV FD A + + + L G++
Sbjct: 11 VTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVT-FDSESAVERVFSAGMLELGGKQ 69
Query: 85 LRVQMA 90
+ V+ A
Sbjct: 70 VEVKRA 75
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 44.5 bits (106), Expect = 5e-07
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 9/76 (11%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
++KV NL TT + +R+ F+ CGE+ ++ I E A + F ++AL A
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVES----EGGLVAVIEF---ETEDEALAA 54
Query: 75 M--DGRMLDGRELRVQ 88
+ D + L G E+ V
Sbjct: 55 LTKDHKRLGGNEISVS 70
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for
growth. Srp1p is closely related to the SR protein
family found in metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. Some family members also contain another RRM
domain.
Length = 78
Score = 44.4 bits (105), Expect = 6e-07
Identities = 29/65 (44%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE--LR 86
DL FER G + IP R T +SR FAFV + RDAEDA + M GR L
Sbjct: 15 DLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDTLH 73
Query: 87 VQMAR 91
VQ A+
Sbjct: 74 VQWAK 78
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 77
Score = 44.2 bits (105), Expect = 7e-07
Identities = 19/62 (30%), Positives = 38/62 (61%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+ DD++ VFE G++ + D T + +G+ F+ + + + A+DA+ +M+ L G++L
Sbjct: 13 SEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72
Query: 86 RV 87
RV
Sbjct: 73 RV 74
>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 = 44.1 bits (104), Expect = 7e-07
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N++ T D+LR +FE G V + +D +AFV + +A A++A++G
Sbjct: 5 VGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEALNG 56
Query: 78 RMLDGRELRVQM 89
+ + GR + V++
Sbjct: 57 KEVKGRRINVEL 68
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 44.5 bits (105), Expect = 8e-07
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L + T ++ VF G V DIY+ RD ++SRG AFV++ K A+ A+ A+
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAIKAL 60
Query: 76 DG 77
+G
Sbjct: 61 NG 62
>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 = 44.1 bits (105), Expect = 1e-06
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 35 ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
+ G V I + G +V+F A+ + A++GR DGR++
Sbjct: 33 SKFGPVEHIKV----DKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITA 81
>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 = 43.7 bits (104), Expect = 1e-06
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+++ L + T +D+R F I+I D R + G A+V F DA AL
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRAL-R 59
Query: 75 MDGRMLDGRELRV 87
+ GR + V
Sbjct: 60 KHNNKMGGRYIEV 72
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 43.5 bits (103), Expect = 1e-06
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + Y +T D++R F CGE+ ++ + T RG AF+ F + A+ AL A+DG
Sbjct: 3 VGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-ALDG 61
Query: 78 RMLDGRELRVQ 88
+ GR L+V+
Sbjct: 62 EDMGGRFLKVE 72
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear
molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 43.8 bits (104), Expect = 1e-06
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL L ++F G V ++ + RD T + +G+ FV + +A A+ +++G
Sbjct: 6 VYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNG 65
Query: 78 RMLDGRELRV 87
L GR L+V
Sbjct: 66 YRLGGRVLQV 75
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 43.6 bits (103), Expect = 1e-06
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
+L++ F + G V ++ + R + T S+ + F++F + A A +M+ +L G+ L+V
Sbjct: 15 ELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVH 74
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 43.5 bits (103), Expect = 1e-06
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
S+ V L+ T ++L F R G++ ++ I R + FAF++F ++ A A++
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKR---ANHTNAFAFIKFEREQAAARAVE 61
Query: 74 AMDGRMLDGRELRVQ 88
+ + ML + + VQ
Sbjct: 62 SENHSMLKNKTMHVQ 76
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia
(DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE.
This subfamily corresponds to the RRM domain of two
Deleted in AZoospermia (DAZ) autosomal homologs, DAZL
(DAZ-like) and BOULE. BOULE is the founder member of
the family and DAZL arose from BOULE in an ancestor of
vertebrates. The DAZ gene subsequently originated from
a duplication transposition of the DAZL gene.
Invertebrates contain a single DAZ homolog, BOULE,
while vertebrates, other than catarrhine primates,
possess both BOULE and DAZL genes. The catarrhine
primates possess BOULE, DAZL, and DAZ genes. The family
members encode closely related RNA-binding proteins
that are required for fertility in numerous organisms.
These proteins contain an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a varying number of
copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 43.4 bits (103), Expect = 2e-06
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + TT ++LR F R G V D+ I DR S+G+ FV F + DAE L AM
Sbjct: 7 VGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKIL-AMGN 64
Query: 78 RMLDGRELRVQMA 90
G++L + A
Sbjct: 65 LNFRGKKLNIGPA 77
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 43.2 bits (101), Expect = 2e-06
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL+ T + ++F + G + + + + + FV F++ RDA AL A
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 58
Query: 75 MDGRMLDGRELRVQMARYGRPPSSSR 100
M+GR + G+E++V A PSS +
Sbjct: 59 MNGRKILGKEVKVNWA---TTPSSQK 81
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 83
Score = 43.4 bits (103), Expect = 2e-06
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 45 IPRDRFTRESRGFAFVRF--FDKRDAEDALDAMDGRMLDGRELRVQMAR 91
I RD T S+GFAF+ + F+ DA A++AM+G+ L R + V A
Sbjct: 34 IMRDPDTGNSKGFAFISYDSFEASDA--AIEAMNGQYLCNRPITVSYAF 80
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic
translation initiation factor 4H (eIF-4H) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4H, also termed Williams-Beuren syndrome
chromosomal region 1 protein, which, together with
elf-4B/eIF-4G, serves as the accessory protein of RNA
helicase eIF-4A. eIF-4H contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It
stimulates protein synthesis by enhancing the helicase
activity of eIF-4A in the initiation step of mRNA
translation. .
Length = 76
Score = 43.1 bits (102), Expect = 2e-06
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T DL +F+ V + + RD+ T + +GF +V F D ++AL+ DG
Sbjct: 6 VGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YDG 63
Query: 78 RMLDGRELRVQMA 90
+ D R LRV +A
Sbjct: 64 ALFDDRSLRVDIA 76
>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 = 43.0 bits (102), Expect = 2e-06
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 28 DDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
+LR +F + GEV DI P + FV F+D R AE ALDA++GR G L+
Sbjct: 16 QELRSLFSQFGEVKDIRETPLRPSQK------FVEFYDIRAAEAALDALNGRPFLGGRLK 69
Query: 87 VQ 88
V+
Sbjct: 70 VK 71
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 42.8 bits (101), Expect = 3e-06
Identities = 14/48 (29%), Positives = 29/48 (60%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
DLR +FE+ G++ ++ + +D++T +G AF+ + + A A A+
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 2 (Musashi-2 ) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 76
Score = 42.4 bits (99), Expect = 4e-06
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+ L+++T+PD LR F + GE+ + + RD T+ SRGF FV F D + L
Sbjct: 4 IGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>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 = 42.3 bits (100), Expect = 4e-06
Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD-AEDALDA 74
L V L T +L +F G + I D T SRG F+R FDKR AE A+ A
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIR-FDKRIEAERAIKA 61
Query: 75 MDGRMLDG 82
++G + G
Sbjct: 62 LNGTIPPG 69
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 42.4 bits (100), Expect = 4e-06
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES-RGFAFVRFFDKRDAEDALDAM- 75
V N+ + T +LR +F GE+ + +P+ S RGF FV F K+DA+ A A+
Sbjct: 5 VRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALC 64
Query: 76 DGRMLDGRELRVQMA 90
L GR L ++ A
Sbjct: 65 HSTHLYGRRLVLEWA 79
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 41.9 bits (98), Expect = 6e-06
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L+++TT + LR F + GEV + + RD T+ SRGF FV F D+ + L A
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSR 63
Query: 78 RMLDGRELRVQMA 90
LD + + ++A
Sbjct: 64 HELDSKTIDPKVA 76
>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 = 41.8 bits (99), Expect = 6e-06
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 53 ESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
S+G+ FV F + A A++ ++G +L+ +++ V
Sbjct: 41 GSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM1 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single-
and double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. It forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manneras well as with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 41.4 bits (97), Expect = 6e-06
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +++R++FE+ G+ G+I+I +D +GF F+R + AE A +
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAEL 57
Query: 76 DGRMLDGRELRVQ 88
D L G++LRV+
Sbjct: 58 DNMPLRGKQLRVR 70
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and
U3 small nucleolar RNAs (snoRNAs). MRD1 is essential
for the initial processing at the A0-A2 cleavage sites
in the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which may play an important structural role in
organizing specific rRNA processing events. .
Length = 84
Score = 41.8 bits (98), Expect = 7e-06
Identities = 28/83 (33%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYI-----PRDRFTRESRGFAFVRFFDKRDA 68
+L V NL + TT L F+ + P+ S GF FV F K A
Sbjct: 1 ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60
Query: 69 EDALDAMDGRMLDGRELRVQMAR 91
+ AL AMDG +LDG L V+ +
Sbjct: 61 QAALKAMDGFVLDGHTLVVKFSH 83
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 41.6 bits (98), Expect = 7e-06
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V ++++ D +R+ F G + I + D T + +GFAFV + A+ AL+ M+G
Sbjct: 5 VGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG 64
Query: 78 RMLDGRELRV 87
ML GR ++V
Sbjct: 65 VMLGGRNIKV 74
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 41.5 bits (97), Expect = 8e-06
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL +L R F G + ++I R+ GFAFV F D RDAEDA+ +DG
Sbjct: 4 VGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG 58
Query: 78 RMLDGRELRVQMA 90
+++ G +RV+++
Sbjct: 59 KVICGSRVRVELS 71
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition, steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway. It binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 76
Score = 41.4 bits (97), Expect = 8e-06
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA---MDG 77
L + TT D LR F + GEV D + RD T SRGF F+ F + + + +DG
Sbjct: 6 LNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDG 65
Query: 78 RMLD 81
+++D
Sbjct: 66 KIID 69
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 41.1 bits (96), Expect = 1e-05
Identities = 27/68 (39%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L++ T+ DL+ F + GEV D I D T SRGF F+ F D E L+ +
Sbjct: 4 VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEH 63
Query: 78 RMLDGREL 85
R LDGR +
Sbjct: 64 R-LDGRLI 70
>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 = 41.5 bits (97), Expect = 1e-05
Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L T +L ++F + G + I RD+ T SRG F+RF + +AE+A+
Sbjct: 2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61
Query: 75 MDGRMLDG 82
++G+ +G
Sbjct: 62 LNGQKPEG 69
>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 = 43.9 bits (103), Expect = 1e-05
Identities = 28/82 (34%), Positives = 44/82 (53%)
Query: 1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
+SY RP +L V NL T D L +F + G++ I RD+ T RG AFV
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFV 240
Query: 61 RFFDKRDAEDALDAMDGRMLDG 82
RF + +A++A+ A++ + +G
Sbjct: 241 RFNKREEAQEAISALNNVIPEG 262
Score = 35.0 bits (80), Expect = 0.009
Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V+ L T +L +F G + I RD T S G+AFV F + D++ A+
Sbjct: 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN 168
Query: 75 MDGRMLDGRELRVQMARYG 93
++G + + L+V AR G
Sbjct: 169 LNGITVRNKRLKVSYARPG 187
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 40.8 bits (96), Expect = 1e-05
Identities = 23/68 (33%), Positives = 36/68 (52%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
T ++ R +F G V + I RD+ T S GF FV + DA+ A+ ++G L + +
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72
Query: 86 RVQMARYG 93
+V AR G
Sbjct: 73 KVAYARPG 80
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 40.9 bits (96), Expect = 1e-05
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N+ TT DL +F+ G + + DR GFAFV+ A A+ + G
Sbjct: 5 VGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIVQLQG 58
Query: 78 RMLDGRELR 86
+ GR LR
Sbjct: 59 FPVHGRPLR 67
>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 = 40.7 bits (96), Expect = 1e-05
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL T D LR FE GEV D+ + R R +SR F FV F + DA+ A+ +
Sbjct: 5 VKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYFNK 63
Query: 78 RMLDGRELRVQMA 90
+D ++ V++A
Sbjct: 64 TFIDTSKISVELA 76
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 40.8 bits (96), Expect = 1e-05
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVF-ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L + NL+ DLR++F E V + + + G+AFV D+ A+ A++
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDCPDQSWADKAIEK 53
Query: 75 MDGRMLDGRELRV 87
++G++L G+ + V
Sbjct: 54 LNGKILQGKVIEV 66
>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 = 40.3 bits (95), Expect = 2e-05
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T DD+ +F G + G A V + K DA A+D
Sbjct: 3 LVVSNLHPSVTEDDIVELFSAIGALKRA-------RLVRPGVAEVVYVRKDDALTAIDKY 55
Query: 76 DGRMLDGRELRVQM 89
+ R LDG+ ++ ++
Sbjct: 56 NNRELDGQPMKCKL 69
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 40.4 bits (95), Expect = 2e-05
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V L+ TT + +R F + G + +I +P D+ T + RGF F+ F D+E+ +
Sbjct: 4 VGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPVK 55
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DDLR E+ G+V + + F R G A V+F + +A+ ++A++GR GR+L
Sbjct: 27 DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82
Query: 88 Q 88
+
Sbjct: 83 E 83
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 40.4 bits (94), Expect = 2e-05
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL+ T + ++F + G + D T + + FV FF+ R A +L A
Sbjct: 1 TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58
Query: 75 MDGRMLDGRELRVQMA 90
M+GR + G+E++V A
Sbjct: 59 MNGRKIMGKEVKVNWA 74
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit
4 (THOC4) and similar proteins. This subgroup
corresponds to the RRM of THOC4, also termed
transcriptional coactivator Aly/REF, or ally of AML-1
and LEF-1, or bZIP-enhancing factor BEF, an mRNA
transporter protein with a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It is
involved in RNA transportation from the nucleus. THOC4
was initially identified as a transcription coactivator
of LEF-1 and AML-1 for the TCRalpha enhancer function.
In addition, THOC4 specifically binds to rhesus (RH)
promoter in erythroid. It might be a novel
transcription cofactor for erythroid-specific genes. .
Length = 75
Score = 40.3 bits (95), Expect = 2e-05
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL + + DD++ +F G + + DR R S G A V F + DA A+
Sbjct: 3 LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGR-SLGTADVVFERRADALKAMKQY 61
Query: 76 DGRMLDGRELRVQM 89
+G LDGR +++Q+
Sbjct: 62 NGVPLDGRPMKIQL 75
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 40.4 bits (94), Expect = 2e-05
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL +L R F G + +++ R+ GFAFV F D RDA DA+ +DG
Sbjct: 9 VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 63
Query: 78 RMLDGRELRVQMA 90
R L G +RV+++
Sbjct: 64 RTLCGCRVRVELS 76
>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 = 43.0 bits (101), Expect = 2e-05
Identities = 31/97 (31%), Positives = 39/97 (40%), Gaps = 4/97 (4%)
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDR-SRSRDRRYTRS 124
RD E + R D + R R S R R R R+R SR RDRR S
Sbjct: 1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60
Query: 125 RSFSSRSRSG---SKSPRKARSKSIDRDNKHERNGRS 158
RS S S S+ + RS+S+ +H R R
Sbjct: 61 RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRD 97
Score = 34.1 bits (78), Expect = 0.021
Identities = 20/82 (24%), Positives = 39/82 (47%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
+ + NL D ++ + E G++ + +D T S+G+AF + D + A+ A+
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357
Query: 76 DGRMLDGRELRVQMARYGRPPS 97
+G+ +L VQ A G +
Sbjct: 358 NGKDTGDNKLHVQRACVGANQA 379
Score = 31.8 bits (72), Expect = 0.15
Identities = 17/54 (31%), Positives = 18/54 (33%)
Query: 95 PPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDR 148
P S S R RDR R RSRS R RS S + D
Sbjct: 63 PRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116
Score = 31.4 bits (71), Expect = 0.17
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR---DRFTRESRGFAFVRFFDKRDAEDALDA 74
+D+ Y +D++ F + G + +I IPR DR + G F+ + D R AE A++
Sbjct: 424 MDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEG 483
Query: 75 MDGRMLDGR 83
M+GR + R
Sbjct: 484 MNGRKFNDR 492
Score = 29.1 bits (65), Expect = 0.90
Identities = 20/61 (32%), Positives = 20/61 (32%)
Query: 91 RYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDN 150
RY S R R R R RSR R R RS S RK K D
Sbjct: 57 RYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116
Query: 151 K 151
K
Sbjct: 117 K 117
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 40.4 bits (95), Expect = 2e-05
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL Y+ L+ VF+ G+V I D+ +SRG V+F +A A+ +G
Sbjct: 3 VANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAISMFNG 61
Query: 78 RMLDGRELRVQM 89
+ML R +RV+M
Sbjct: 62 QMLFDRPMRVKM 73
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast
pre-mRNA-splicing factor Cwc2 and similar proteins.
This subfamily corresponds to the RRM of yeast protein
Cwc2, also termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and an intervening loop,
also termed RNA-binding loop or RB loop, between ZnF
and RRM, all of which are necessary and sufficient for
RNA binding. The ZnF is also responsible for mediating
protein-protein interaction. The C-terminal flexible
region of Cwc2 interacts with the WD40 domain of Prp19.
Length = 78
Score = 40.3 bits (95), Expect = 2e-05
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 8/61 (13%)
Query: 26 TPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
+ LRR F G++ DI +P S+G AFVR+ + AE A +AM + LDG E
Sbjct: 18 IEEILRRHFGEWGDIEDIRVLP-------SKGIAFVRYKYRASAEFAKEAMADQSLDGGE 70
Query: 85 L 85
+
Sbjct: 71 V 71
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 40.4 bits (94), Expect = 2e-05
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 10/78 (12%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR--DRFTRESRGFAFVRFFDKRDAEDALD 73
L V NL TT + ++ F + + P +R ++ R +AFV FF++ DA A+
Sbjct: 4 LYVRNLMISTTEETIKAEFNK-------FKPGVVER-VKKLRDYAFVHFFNREDAVAAMS 55
Query: 74 AMDGRMLDGRELRVQMAR 91
M+G+ +DG + V +A+
Sbjct: 56 VMNGKCIDGASIEVTLAK 73
>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 = 40.2 bits (94), Expect = 2e-05
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
S+ V +L+ DL +F+ R I D T SRG+ FVRF D+ D + AL
Sbjct: 3 SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62
Query: 74 AMDGRMLDGRELRVQMA 90
M G GR +R+ A
Sbjct: 63 EMQGVYCGGRPMRISTA 79
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup
corresponds to the RRM1 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Its
cellular function remains unknown currently, however,
PSPC1 forms a novel heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 39.9 bits (93), Expect = 2e-05
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T +D +++FE+ GE +++I RDR GF F+R + AE A +
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 57
Query: 76 DGRMLDGRELRVQ 88
DG +L R LR++
Sbjct: 58 DGTILKNRPLRIR 70
>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 = 40.2 bits (95), Expect = 3e-05
Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
D+R +FE+ GE+ I P RF + +R F +V+F A A+ ++G++ +G +L V+
Sbjct: 16 DIRDLFEQYGEILSIRFPSLRFNK-TRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVK 74
Query: 89 M 89
+
Sbjct: 75 I 75
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 40.4 bits (95), Expect = 3e-05
Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 15/81 (18%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEV------GDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
V NL TT D L F + GEV GD + TR +AFV F ++ +A
Sbjct: 9 VGNLDPTTTADQLLEFFSQAGEVKYVRMAGD----ETQPTR----YAFVEFAEQTSVINA 60
Query: 72 LDAMDGRMLDGRELRVQMARY 92
L ++G M GR L+V +
Sbjct: 61 L-KLNGAMFGGRPLKVNHSNN 80
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has
been identified as a regulator of the hematopoietic
stem cell (HSC) compartment and of leukemic stem cells
after transplantation of cells with loss and gain of
function of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 39.7 bits (93), Expect = 3e-05
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V L+ TT DD+++ F + G+V D + D+ T RGF FV F ++ED +D
Sbjct: 4 VGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF----ESEDVVD 55
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 39.6 bits (93), Expect = 3e-05
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + +L+ F + G+V +P D+ T S+G+ FV F RD +
Sbjct: 4 VGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVS-FSSRDGLENALQKQK 62
Query: 78 RMLDGRELRVQ 88
+L+G +L+VQ
Sbjct: 63 HILEGNKLQVQ 73
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 39.9 bits (94), Expect = 4e-05
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF------TRESRGFAFVRFFDKRDAE 69
L V NL+ R T +DL +F R V ++ F +G AFV F + A
Sbjct: 4 LYVKNLSKRVTEEDLVYIFGR--FVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61
Query: 70 DALDAMDGRMLDGRELRVQMA 90
AL+ ++G +L G+ + +Q
Sbjct: 62 KALNLVNGYVLKGKPMVIQFG 82
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 39.7 bits (93), Expect = 4e-05
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL TT DLR FER GE+ DI I + + +AF+++ D A+
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK---QGGNPAYAFIQYADIASVVKAMRK 60
Query: 75 MDGRMLDGRELRV 87
MDG L +++
Sbjct: 61 MDGEYLGNNRVKL 73
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 39.1 bits (92), Expect = 4e-05
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
V NL T + + +DL +F + G++ I + +G+ FV+F ++ DA A+ +
Sbjct: 5 VGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGEN 56
Query: 77 GRMLDGREL 85
GR + G++L
Sbjct: 57 GREIAGQKL 65
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 39.2 bits (92), Expect = 5e-05
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGR 78
L TT +DL ++ + G++ D+ T + +G+ FV F A A++ ++GR
Sbjct: 8 LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM1 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 39.1 bits (91), Expect = 5e-05
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V L V NL T ++R +FE+ G+V + I ++ + FV DK A++A+
Sbjct: 1 VKLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIR 52
Query: 74 AMDGRMLDGRELRVQ 88
+ L G + V+
Sbjct: 53 NLHHYKLHGVAINVE 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 = 39.1 bits (92), Expect = 5e-05
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V NL + TT ++LR +FE+ G +G + +P SR A V F + DA A ++
Sbjct: 5 VKNLPFGTTEEELRELFEKFGSLGRLLLP------PSRTIALVEFLEPSDARKAFKSL 56
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate
RNA-binding protein 7 (RBM7). This subfamily
corresponds to the RRM of RBM7, a ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. RBM7 interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20. It may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM7 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
.
Length = 75
Score = 39.1 bits (91), Expect = 6e-05
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL + T + + +F + G V + IP+D+ + + FAFV F + A++
Sbjct: 3 TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNL 61
Query: 75 MDGRMLDGRELRVQ 88
++G L GR L +Q
Sbjct: 62 LNGIKLYGRPLNIQ 75
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 77
Score = 39.1 bits (92), Expect = 6e-05
Identities = 18/73 (24%), Positives = 36/73 (49%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L + D ++ + E G++ + +D T S+G+AF + D + A+ ++G
Sbjct: 5 IGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNG 64
Query: 78 RMLDGRELRVQMA 90
L ++L VQ A
Sbjct: 65 MQLGDKKLTVQRA 77
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and
similar proteins. This subfamily corresponds to the
RRM of Nab3p, an acidic nuclear polyadenylated
RNA-binding protein encoded by Saccharomyces cerevisiae
NAB3 gene that is essential for cell viability. Nab3p
is predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA
processing. Nab3p contains an N-terminal
aspartic/glutamic acid-rich region, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal region rich in glutamine and proline
residues. .
Length = 71
Score = 39.0 bits (91), Expect = 7e-05
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 22 TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
T R + +DL R+F GE+ I + + FV+F +A++ G+M+
Sbjct: 9 TKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAINCEQGKMIR 60
Query: 82 GRELRVQMAR 91
GR+L +++++
Sbjct: 61 GRKLHLEVSK 70
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 38.8 bits (90), Expect = 7e-05
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
+ L++ TT DL+ F + GEV D + D T SRGF FV F + + +D
Sbjct: 3 IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH 62
Query: 74 AMDGRMLDGRE 84
++G+++D +
Sbjct: 63 KLNGKVIDPKR 73
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells, and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1) and has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
It represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 38.8 bits (90), Expect = 7e-05
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
V L+ TT +D+++ FE+ G+V D + D+ T RGF FV F ++ED ++
Sbjct: 4 VGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF----ESEDIVE 55
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 38.6 bits (90), Expect = 8e-05
Identities = 30/74 (40%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL D+ +F + G + DI D R FAFV F D RDAEDA+ DG
Sbjct: 4 VGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59
Query: 78 RMLDGRELRVQMAR 91
DG LRV+ R
Sbjct: 60 YDYDGYRLRVEFPR 73
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM3 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 86
Score = 39.1 bits (92), Expect = 8e-05
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDI---YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
N+ + T + L ++ + G+ G Y+P D + + G+AF+ F + AE A +
Sbjct: 5 NIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKAFN 64
Query: 77 GRMLDGRELR 86
G+ + +
Sbjct: 65 GKKWKNFKSK 74
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 39.2 bits (92), Expect = 8e-05
Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 16 LKVDNL--TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L VD L T+R LR++F + G+ + + RGFAFV + DAE+A
Sbjct: 5 LFVDRLPKTFRDV-SILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQ 62
Query: 74 AMDGRMLDGRELRVQMARYGRP 95
A++G L G +RV GRP
Sbjct: 63 ALNGHSLQGSPIRVSFGNPGRP 84
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 38.4 bits (90), Expect = 9e-05
Identities = 18/40 (45%), Positives = 23/40 (57%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFD 64
T +DLR F + G V + I D+ T + RGFAFV F D
Sbjct: 11 VTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD 50
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 80
Score = 38.9 bits (91), Expect = 9e-05
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
T DLR+ F + G V ++ + D + RGF F+ F ++ED++D
Sbjct: 15 TETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF----ESEDSVDQ 59
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 38.4 bits (90), Expect = 9e-05
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 16 LKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
L V NL TPD L F G GD+ R + + A ++ D + A+ AL
Sbjct: 2 LLVSNLNEEMVTPDAL---FTLFGVYGDVV--RVKILFNKKDTALIQMADPQQAQTALTH 56
Query: 75 MDGRMLDGRELRVQMARY 92
++G L G++LRV ++++
Sbjct: 57 LNGIRLHGKKLRVTLSKH 74
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 38.4 bits (89), Expect = 1e-04
Identities = 15/36 (41%), Positives = 26/36 (72%)
Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMA 90
+GFAFV++ ++R+A A+ DGRM+ G+ L + +A
Sbjct: 36 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 71
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 38.4 bits (90), Expect = 1e-04
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 27 PDD-LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
PD L VF R G + D+Y+ + + + ++ D+ AE A+ + G+ ++G +L
Sbjct: 12 PDYILEDVFCRFGGLIDVYLVPGK------NYGYAKYADRESAERAITTLHGKEVNGVKL 65
Query: 86 RV 87
+V
Sbjct: 66 KV 67
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 38.5 bits (89), Expect = 1e-04
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
V L+ TT + ++ F GE+ +I +P D T E RGF FV + D+ + L++
Sbjct: 4 VGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVF-ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
S+ V +L T L+ F R V + D T S+G+ FVRF D+ + + AL
Sbjct: 3 SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62
Query: 74 AMDGRMLDGRELRVQMA 90
M+G R +RV A
Sbjct: 63 EMNGVYCSSRPMRVSPA 79
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 38.4 bits (89), Expect = 1e-04
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD---- 73
+ L++ T+ DL R GEV D I D T SRGF FV F D + L+
Sbjct: 4 IGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEH 63
Query: 74 AMDGRMLDGRELR 86
+DG+++D + +
Sbjct: 64 KLDGKLIDPKRAK 76
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to
the RRM domain in the G3BP family of RNA-binding and
SH3 domain-binding proteins. G3BP acts at the level of
RNA metabolism in response to cell signaling, possibly
as RNA transcript stabilizing factors or an RNase.
Members include G3BP1, G3BP2 and similar proteins.
These proteins associate directly with the SH3 domain
of GTPase-activating protein (GAP), which functions as
an inhibitor of Ras. They all contain an N-terminal
nuclear transfer factor 2 (NTF2)-like domain, an acidic
domain, a domain containing PXXP motif(s), an RNA
recognition motif (RRM), and an Arg-Gly-rich region
(RGG-rich region, or arginine methylation motif).
Length = 81
Score = 38.1 bits (89), Expect = 1e-04
Identities = 18/71 (25%), Positives = 26/71 (36%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T D+L+ F+ G V ++ I F FV F D + L
Sbjct: 8 VGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPI 67
Query: 78 RMLDGRELRVQ 88
L V+
Sbjct: 68 YFRGDHRLNVE 78
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the
formation of D-loops in superhelical duplex DNA, and is
involved in cell proliferation. PSF can also interact
with multiple factors. It is an RNA-binding component
of spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions,
such as DNA recombination and RNA synthesis,
processing, and transport. PSF contains two conserved
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for interactions with RNA and for
the localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 71
Score = 38.0 bits (88), Expect = 1e-04
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T D+ +++F + GE G+++I + +GF F++ + AE A +
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAEL 57
Query: 76 DGRMLDGRELRVQ 88
D + GR+LRV+
Sbjct: 58 DDTPMRGRQLRVR 70
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 38.2 bits (89), Expect = 1e-04
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL T ++LRR FER G V D+ I R + + +AFV+F + A A A
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGN-AYAFVKFLNLDMAHRAKVA 62
Query: 75 MDGRML 80
M G+ +
Sbjct: 63 MSGQYI 68
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, and is an abundant eukaryotic nuclear
RNA-binding protein that may modulate splice site
selection in pre-mRNA splicing. hnRNP A1 has been
characterized as a splicing silencer, often acting in
opposition to an activating hnRNP H. It silences exons
when bound to exonic elements in the alternatively
spliced transcripts of c-src, HIV, GRIN1, and
beta-tropomyosin. hnRNP A1 can shuttle between the
nucleus and the cytoplasm. Thus, it may be involved in
transport of cellular RNAs, including the packaging of
pre-mRNA into hnRNP particles and transport of poly A+
mRNA from the nucleus to the cytoplasm. The cytoplasmic
hnRNP A1 has high affinity with AU-rich elements,
whereas the nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 81
Score = 38.1 bits (88), Expect = 2e-04
Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
L + L++ TT + LR FE+ G + D + RD T+ SRGF FV + + + A++A
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64
Query: 75 ---MDGRMLD 81
+DGR+++
Sbjct: 65 PHKVDGRVVE 74
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 37.7 bits (88), Expect = 2e-04
Identities = 27/70 (38%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V + + DDL+ F CGEV + + DR + S FAFV F D A AL + G
Sbjct: 5 VGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDR--QHSARFAFVEFADAESALSAL-NLSG 61
Query: 78 RMLDGRELRV 87
+L G LRV
Sbjct: 62 TLLGGHPLRV 71
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p
encoded by YNL175c from Saccharomyces cerevisiae. It
shares high sequence similarity with nucleolar protein
12 (Nop12p). Both, Nop12p and Nop13p, are not essential
for growth. However, unlike Nop12p that is localized to
the nucleolus, Nop13p localizes primarily to the
nucleolus but is also present in the nucleoplasm to a
lesser extent. Nop13p contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 85
Score = 37.9 bits (88), Expect = 2e-04
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 12/79 (15%)
Query: 18 VDNLTYRTTPDDLRRVFER-------CGEVGDIYIPRDRFTR----ESRGFAFVRFFDKR 66
+ NL++ TT + LR+ F ++ +++P + R +++GFA+V F +
Sbjct: 3 IGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYV-DFTSQ 61
Query: 67 DAEDALDAMDGRMLDGREL 85
+A A A+ ++L+GR+L
Sbjct: 62 EATKAAIALSEKILNGRKL 80
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 37.8 bits (88), Expect = 2e-04
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
T +DLR F+ G++ + I +D+ T ES+GF +V+F A AL+ D
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCD 63
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 37.2 bits (87), Expect = 2e-04
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
T + L++ F G + +I + +++ FV F A+ A+ ++G + G +L
Sbjct: 15 TEEILKKAFSPFGNIINISMEKEK------NCGFVTFEKMESADRAIAELNGTTVQGVQL 68
Query: 86 RVQMAR 91
+V +AR
Sbjct: 69 KVSLAR 74
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 37.4 bits (87), Expect = 2e-04
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
G++ IYI + RG ++ F DA A+ ++GR DGR ++
Sbjct: 20 GKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 37.4 bits (86), Expect = 3e-04
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
L + L++ TT D LR FE+ G + D + RD T+ SRGF FV + + + A+ A
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64
Query: 75 ---MDGRMLD 81
+DGR+++
Sbjct: 65 PHKVDGRVVE 74
>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 = 37.3 bits (87), Expect = 3e-04
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRFFDKRDAEDALD 73
L V NL D LR++FE G + D+ + ++T++ R F FV + + +A+ AL
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQL---KYTKDGKFRKFGFVGYKTEEEAQKALK 59
Query: 74 AMDGRMLDGRELRVQ 88
+ +D ++ V+
Sbjct: 60 HFNNSFIDTSKITVE 74
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins.
This subgroup corresponds to the RRM1 of SF2, also
termed SR1 protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal domain rich in proline, serine
and lysine residues (PSK domain), a composition
reminiscent of histones. This PSK domain harbors a
putative phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 37.1 bits (86), Expect = 3e-04
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 56 GFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
G+AF+ F D RDAEDA+ DG DG+ LRV++
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDFDGQRLRVEL 72
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 37.2 bits (87), Expect = 3e-04
Identities = 20/71 (28%), Positives = 36/71 (50%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V +L T + L R F + + RD+ T +S+G+ FV F D D A+ M+G
Sbjct: 11 VGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNG 70
Query: 78 RMLDGRELRVQ 88
+ + R ++++
Sbjct: 71 KYVGNRPIKLR 81
>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 = 37.3 bits (86), Expect = 4e-04
Identities = 15/40 (37%), Positives = 30/40 (75%)
Query: 52 RESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
++ R +AFV F ++ DA DA++A++G+++DG + V +A+
Sbjct: 41 KKIRDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80
>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 = 39.2 bits (91), Expect = 4e-04
Identities = 29/95 (30%), Positives = 46/95 (48%), Gaps = 12/95 (12%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL TT + + + F E + R ++ R +AFV F D+ DA A+D +
Sbjct: 236 LYVRNLMTTTTEEIIEKSF---SEFKPGKVER---VKKIRDYAFVHFEDREDAVKAMDEL 289
Query: 76 DGRMLDGRELRVQMAR------YGRPPSSSRSRGG 104
+G+ L+G E+ V +A+ Y R + RG
Sbjct: 290 NGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGK 324
Score = 35.0 bits (80), Expect = 0.010
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 11/89 (12%)
Query: 3 YGRPPPRIEGM-----VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGF 57
YG PPP G+ + V + D+L +FE+ G + ++ + D F+ ++RG+
Sbjct: 43 YGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGY 101
Query: 58 AFVRFFDKRDAEDALDAMDGRMLDGRELR 86
AFV F K +A++A+ ++L+ E+R
Sbjct: 102 AFVTFCGKEEAKEAV-----KLLNNYEIR 125
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 36.9 bits (85), Expect = 4e-04
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
D+L +FE+ G + D+ + D + ++RG+AF+ F K A++A+ ++ D E+R
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV-----KLCDNYEIR 69
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contains three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
strongly expressed in kidney, brain, and testis, is
also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in an muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element,
MSE2. CELF-6 also promotes skipping of exon 11 of
insulin receptor, a known target of CELF activity that
is expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous
potential phosphorylation sites, a potential nuclear
localization signal (NLS) at the C terminus, and an
alanine-rich region within the divergent linker region.
.
Length = 79
Score = 36.8 bits (85), Expect = 4e-04
Identities = 20/60 (33%), Positives = 33/60 (55%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
+L ++F G V + DR T +S+ F FV F + A+ A+ AM+G + + L+VQ
Sbjct: 20 ELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ 79
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM1 of hnRNP A2/B1 which is an RNA trafficking
response element-binding protein that interacts with
the hnRNP A2 response element (A2RE). Many mRNAs, such
as myelin basic protein (MBP), myelin-associated
oligodendrocytic basic protein (MOBP), carboxyanhydrase
II (CAII), microtubule-associated protein tau, and
amyloid precursor protein (APP) are trafficked by hnRNP
A2/B1. hnRNP A2/B1 also functions as a splicing factor
that regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Moreover, the overexpression of hnRNP A2/B1 has been
described in many cancers. It functions as a nuclear
matrix protein involving in RNA synthesis and the
regulation of cellular migration through alternatively
splicing pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 81
Score = 37.0 bits (85), Expect = 5e-04
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 4/70 (5%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA- 74
L + L++ TT + LR +E+ G++ D + RD ++ SRGF FV F + + A+ A
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64
Query: 75 ---MDGRMLD 81
+DGR+++
Sbjct: 65 PHTIDGRVVE 74
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 36.5 bits (84), Expect = 6e-04
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T+ D +++ F G+ + R ++ R +AFV F + DA A++ +
Sbjct: 4 LYVRNLMIETSEDTIKKTF---GQFNPGCVER---VKKIRDYAFVHFTSREDAVHAMNNL 57
Query: 76 DGRMLDGRELRVQMAR 91
+G L+G + V +A+
Sbjct: 58 NGTELEGSCIEVTLAK 73
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM2 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 96
Score = 37.0 bits (86), Expect = 6e-04
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V+N+TY T D L ++F + G V I FT+ ++ A ++F D A+ A ++DG
Sbjct: 8 VENMTYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALIQFADAVSAQAAKLSLDG 63
Query: 78 R 78
+
Sbjct: 64 Q 64
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 36.5 bits (85), Expect = 6e-04
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 53 ESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRELRVQMA 90
SRG+ FVRF D+ + + AL M G L G+ +RV +A
Sbjct: 41 NSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLA 79
>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 = 36.6 bits (85), Expect = 7e-04
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD--RFTRESR----GFAFVRFFDKRDA 68
+ + NL+Y ++ +DL + V + IP R R R G A+ F A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 69 EDALDAMDGRMLDGRELRVQM 89
E + ++G++ R+L V++
Sbjct: 60 EKVVKDLNGKVFKNRKLFVKL 80
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 2 (Musashi-2) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 79
Score = 36.2 bits (83), Expect = 8e-04
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
V L+ T +D+++ FE+ G+V D + D+ T RGF FV F
Sbjct: 8 VGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
>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 = 36.0 bits (83), Expect = 8e-04
Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 6/59 (10%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
D+L +FER G++ + + + F+ E+RG+AFV + K +A+ A+ R+L+ E+R
Sbjct: 16 DELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAI-----RILNNYEIR 68
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 77
Score = 36.1 bits (84), Expect = 8e-04
Identities = 29/71 (40%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD-AEDALDAMD 76
+D L T L R F R G V + I R RG A V FFDK + A+ A++ M
Sbjct: 12 LDGLDESVTEQYLTRHFSRYGPVVHVVIDR------QRGQALV-FFDKVEAAQAAVNEMK 64
Query: 77 GRMLDGRELRV 87
GR L GR+L+V
Sbjct: 65 GRKLGGRKLQV 75
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 36.8 bits (85), Expect = 8e-04
Identities = 18/58 (31%), Positives = 25/58 (43%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+L V NL Y T + L F + G V D+ T ++G FV F D+ L
Sbjct: 3 TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing
Sarcoma Protein (EWS). This subgroup corresponds to
the RRM of EWS, also termed Ewing sarcoma breakpoint
region 1 protein, a member of the FET (previously TET)
(FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding
proteins whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the
FET family, EWS contains an N-terminal Ser, Gly, Gln
and Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U
RNA. It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor
gene. .
Length = 84
Score = 36.0 bits (83), Expect = 9e-04
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRFFDKR 66
++ V L T ++L F+ CG V + I D+ T + +G A V + D
Sbjct: 2 TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61
Query: 67 DAEDALDAMDGRMLDGRELRVQM 89
A+ A++ DG+ G +L+V +
Sbjct: 62 SAKAAVEWFDGKDFQGSKLKVSL 84
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 35.9 bits (83), Expect = 0.001
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVG-----------DIYIPRDRFTRESRGFAFVRFFDKR 66
V NL TT DL F G +G I++ +D+ T E +G A V + D
Sbjct: 3 VSNLPPNTTEQDLAEHF---GSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPH 59
Query: 67 DAEDALDAMDGRMLDGRELRVQMA 90
A A++ + + G ++V +A
Sbjct: 60 AASAAIEWFNNKDFMGNTIKVSLA 83
>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 = 35.8 bits (83), Expect = 0.001
Identities = 19/74 (25%), Positives = 34/74 (45%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L+ T DL+++F + G+V I + + +R F FV +A +
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60
Query: 75 MDGRMLDGRELRVQ 88
+ L GR + V+
Sbjct: 61 LHRTELHGRVISVE 74
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM1 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 91
Score = 36.1 bits (84), Expect = 0.001
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 18/87 (20%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYI---------PRDRFTRESRGF--------AFV 60
V NL T DL+++F++ G + + + + F A+V
Sbjct: 5 VGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYV 64
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRV 87
F ++ AE AL ++G +G +RV
Sbjct: 65 VFKEEESAEKAL-KLNGTEFEGHHIRV 90
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 35.8 bits (83), Expect = 0.001
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 30 LRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG----RE 84
++R F GE V + I R++ T G+ FV F D+ AE L ++G+ + G +
Sbjct: 16 IKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPGSNPPKR 75
Query: 85 LRVQMARYG 93
++ A YG
Sbjct: 76 FKLNRATYG 84
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 35.8 bits (82), Expect = 0.001
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T L+ F +CG V ++ +S+G VRF AE A M+G
Sbjct: 4 VRNLPFDLTWQKLKEKFSQCGHV--MFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61
Query: 78 RMLDGRELRVQMAR 91
++GRE+ V++ R
Sbjct: 62 IKINGREIDVRLDR 75
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 35.4 bits (81), Expect = 0.001
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T + L + F G++ + ++ + +AFV F ++ A A+D M
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEERDAAVRAMDEM 55
Query: 76 DGRMLDGRELRVQMAR 91
+G+ ++G E+ + +A+
Sbjct: 56 NGKEIEGEEIEIVLAK 71
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate
nucleolin. This subfamily corresponds to the RRM4 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 78
Score = 35.3 bits (81), Expect = 0.002
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L+ TT + L+ F+ G + I DR T S+GF FV F + DA+ A +A
Sbjct: 2 TLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58
Query: 75 MDGRMLDGRELRVQMAR 91
M+ +DG ++ + A+
Sbjct: 59 MEDGEIDGNKVTLDFAK 75
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 35.3 bits (82), Expect = 0.002
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYI-PRDRFTRE--SRGFAFVRFFDKRDAEDAL 72
++V N++ + T + +R +F G++ ++ + P D S+ FV++ D D AL
Sbjct: 2 VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSK-VCFVKYEDPEDVGVAL 60
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM3 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B) and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and is a
novel component of the NXF1 pathway. It binds to NXF1
and serves as receptor for the RNA export element RTE.
It also possess mRNA export activity and can facilitate
the access of DEAD-box protein DBP5 to mRNA at the
nuclear pore complex (NPC). RNA-binding protein 15B
(RBM15B), also termed one twenty-two 3 (OTT3), is a
paralog of RBM15 and therefore has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF.
Members in this family belong to the Spen (split end)
protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 72
Score = 34.9 bits (81), Expect = 0.002
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L T+ +L R F+R G + I R +A++ + A+ A +A+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEYESIEAAQAAKEAL 54
Query: 76 DGRML--DGRELRVQMAR 91
G L GR LRV A
Sbjct: 55 RGFPLGGPGRRLRVDFAD 72
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large
number of non-snRNP proteins, including polypyrimidine
tract binding protein (PTB), polypyrimidine-tract
binding protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. U1A contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and may be free to bind other proteins. U1A
also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 89
Score = 35.4 bits (81), Expect = 0.002
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 7/81 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + D+L++ +F R G++ DI + R + + RG AFV F + A +
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 61
Query: 71 ALDAMDGRMLDGRELRVQMAR 91
AL +M G + +R+Q A+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAK 82
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 35.1 bits (81), Expect = 0.002
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 32 RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
F + G + + + RD R+ R +AFV+F + DA++AL G +LDGR +R + A+
Sbjct: 25 EHFSKYGTLVFVKVLRD--WRQ-RPYAFVQFTNDDDAKNALAKGQGTILDGRHIRCERAK 81
Query: 92 YGR 94
R
Sbjct: 82 VNR 84
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although
their biological roles remain unclear, these proteins
show high sequence similarity to the fission yeast
Vip1. Like Vip1 protein, members in this family contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 69
Score = 34.7 bits (80), Expect = 0.002
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
++V NL+ + T D+ F G++ + I R +S+ A+V F D + E AL
Sbjct: 1 VEVTNLSPKATERDIYDFFSFSGDIEYVEIQRSGE--QSQ-TAYVTFKDPQAQETALLLS 57
Query: 76 DGRMLDGR 83
++D
Sbjct: 58 GATIVDQS 65
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 35.0 bits (80), Expect = 0.002
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
D+L +FE+ G + D+ + D T +RG+AFV F K A++A+ ++ + E+R
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV-----KLYNNHEIR 69
>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 = 34.6 bits (80), Expect = 0.002
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 15 SLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
+ V NL R++ L+ F++ G+V + + T R +A V F DAE
Sbjct: 1 GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKV---HGTGSER-YAIVFFRKPEDAEK 56
Query: 71 ALDAMDGRMLDGRELRVQ 88
AL+ G++ G E+ V
Sbjct: 57 ALEVSKGKLFFGAEIEVT 74
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells. And it also regulates the neurite elongation and
morphological differentiation. HuD specifically bound
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 35.1 bits (80), Expect = 0.003
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 21 LTYRTTPDD----LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
Y +PD L ++F G V ++ + RD T + +GF FV + +A A+ +++
Sbjct: 7 FVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66
Query: 77 GRMLDGRELRV 87
G L R L+V
Sbjct: 67 GYRLGDRVLQV 77
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase,
or COMPASS component SET1, or lysine
N-methyltransferase 2, or Set1 complex component, is
encoded by SET1 from the fission yeast S. pombe. It is
essential for the H3 lysine-4 methylation. in vivo, and
plays an important role in telomere maintenance and DNA
repair in an ATM kinase Rad3-dependent pathway. spSet1p
is the homology counterpart of Saccharomyces cerevisiae
Set1p (scSet1p). However, it is more closely related to
Set1 found in mammalian. Moreover, unlike scSet1p,
spSet1p is not required for heterochromatin assembly in
fission yeast. spSet1p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a conserved SET domain that may play a role in DNA
repair and telomere function. .
Length = 86
Score = 34.6 bits (80), Expect = 0.003
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRD--------AE 69
+ L+ TTP +R F GE+ + + D T +S G V F A+
Sbjct: 3 ITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEAAK 62
Query: 70 DALDAMDGRMLDGRELRVQMARYG 93
A+D ++GR + G+ +RV++ R G
Sbjct: 63 AAVDGLNGRRIGGKRVRVELDRDG 86
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 98
Score = 34.9 bits (80), Expect = 0.003
Identities = 14/45 (31%), Positives = 21/45 (46%)
Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
GFA V + AE+ AMDG + G +++ G P S+
Sbjct: 44 GGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPGAPGRST 88
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 34.6 bits (79), Expect = 0.003
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
LR FE+ G++ I + DR + + RGFAFV FD D D + ++G V+
Sbjct: 16 HLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVT-FDDHDTVDKIVVQKYHTINGHNCEVK 74
Query: 89 MA 90
A
Sbjct: 75 KA 76
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 34.1 bits (78), Expect = 0.003
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L+Y D++R F G++ +I + G+ FV F D RDA+DA+ ++G
Sbjct: 4 IGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYELNG 55
Query: 78 RMLDGRELRVQMAR 91
+ L G + V+ AR
Sbjct: 56 KDLCGERVIVEHAR 69
>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 = 34.6 bits (80), Expect = 0.003
Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 28 DDLRRVF-----ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
D++ F ++ GEV ++ I T + G A V F + A+ ++ ++ + G
Sbjct: 12 DNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMG 71
Query: 83 RELRVQMARYGRPPS 97
+ ++V + G
Sbjct: 72 KIIKVFLDPKGEIRK 86
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 34.2 bits (78), Expect = 0.003
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V N++ T +LR FE G V + I +D +AFV DA +A+ +
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 54
Query: 76 DGRMLDGRELRVQ 88
D G+ + VQ
Sbjct: 55 DNTEFQGKRMHVQ 67
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus
(HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and
enhancing HCV internal ribosome entry site
(IRES)-mediated translation initiation via the 3'-UTR.
IGF2BP1 contains four hnRNP K-homology (KH) domains,
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. It also
contains two putative nuclear export signals (NESs) and
a putative nuclear localization signal (NLS). .
Length = 77
Score = 34.2 bits (78), Expect = 0.004
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-RDRFTRESRGFAFVRFFDKRDAEDA 71
M L + NL TP DL +VFE D I +F +S G+AFV D++ A A
Sbjct: 1 MNKLYIGNLNESVTPADLEKVFE------DHKISYSGQFLVKS-GYAFVDCPDEQWAMKA 53
Query: 72 LDAMDGRM-LDGRELRVQ 88
++ G++ L G+ L ++
Sbjct: 54 IETFSGKVELHGKRLEIE 71
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 34.6 bits (79), Expect = 0.004
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L R P DL F G+V D+ + DR +R S+G A+V F D A+ R+L
Sbjct: 9 LAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVL 68
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM2 of RBM5, also termed protein
G15, or putative tumor suppressor LUCA15, or renal
carcinoma antigen NY-REN-9, a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor. RBM5 shows high sequence
similarity to RNA-binding protein 6 (RBM6 or NY-LU-12
or g16 or DEF-3). Both, RBM5 and RBM6, specifically
bind poly(G) RNA. They contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), two C2H2-type zinc
fingers, a nuclear localization signal, and a
G-patch/D111 domain. .
Length = 86
Score = 34.5 bits (79), Expect = 0.004
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 40 VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM----LDGRELRVQMAR 91
V +I + +D+ T+++RGFAFV+ +A L + +DG+ + V A+
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFAK 86
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers.
Moreover, hnRNP M is able to interact with early
spliceosomes, further influencing splicing patterns of
specific pre-mRNAs. hnRNP M functions as the receptor
of carcinoembryonic antigen (CEA) that contains the
penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 34.2 bits (78), Expect = 0.004
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL + T L+ F CG V +Y +S+G VRF AE A M+G
Sbjct: 4 VRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61
Query: 78 RMLDGRELRVQMAR 91
L+GRE+ V++ R
Sbjct: 62 YKLNGREIDVRIDR 75
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells and also regulates the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 34.3 bits (78), Expect = 0.004
Identities = 21/68 (30%), Positives = 36/68 (52%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L T +L ++F + G + I D+ T SRG F+RF + +AE+A+
Sbjct: 4 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63
Query: 75 MDGRMLDG 82
++G+ G
Sbjct: 64 LNGQKPSG 71
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of
Oskar (Osk) expression. It mediates repression by
binding to regulatory Bruno response elements (BREs) in
the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 79
Score = 34.2 bits (78), Expect = 0.005
Identities = 20/63 (31%), Positives = 32/63 (50%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
T DL + F G V + D+ T S+ F FV + + A+ A+ AM+G + + L
Sbjct: 17 TDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRL 76
Query: 86 RVQ 88
+VQ
Sbjct: 77 KVQ 79
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), in the middle and
an RGG box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 33.8 bits (77), Expect = 0.005
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V L+ T + +R F GEV I +P D T + RGF F+ F ++ + ++
Sbjct: 4 VGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
>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 = 33.9 bits (78), Expect = 0.005
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 30 LRRVFERCGEVGDIYIPR--DRFTRESRGF-AFVRFFDKRDAEDALDAMDGRML-DGREL 85
L F + G +Y + + GF AFV+F+ R A A A +G+ L G L
Sbjct: 21 LCSAFSQ---FGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRAQKACNGKWLFQGSPL 77
Query: 86 RVQ 88
+V+
Sbjct: 78 KVR 80
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 33.8 bits (77), Expect = 0.006
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + L T D+ +F R G + + + D+ T SRG AF+RF + +AE+A+ +
Sbjct: 2 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Query: 75 MDG 77
+G
Sbjct: 62 FNG 64
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 33.9 bits (78), Expect = 0.006
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V L+ + T DD+RR+FE G + + I R S+G AFV+F +A+ A++A+
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAINAL 62
Query: 76 DGRM 79
G
Sbjct: 63 HGSQ 66
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 77
Score = 33.3 bits (76), Expect = 0.007
Identities = 18/73 (24%), Positives = 29/73 (39%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T ++ + G + ++ T S+G+ FV + K A A +
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61
Query: 76 DGRMLDGRELRVQ 88
G+ L L Q
Sbjct: 62 LGKQLGESTLFAQ 74
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM3 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR),
both of which belong to the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) family of
RNA-binding proteins that have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contain
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are important for localization in
the cytoplasm. The splicing activation or repression
activity of CELF-2 on some specific substrates is
mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2,
can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 33.9 bits (77), Expect = 0.007
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
DL ++F G V + D+ T S+ F FV + + A+ A+ AM+G + + L+VQ
Sbjct: 23 DLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQ 82
Query: 89 MAR 91
+ R
Sbjct: 83 LKR 85
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 85
Score = 33.5 bits (76), Expect = 0.008
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL+ L ++F G V ++ + RD T + +GF FV + +A A+ +++G
Sbjct: 6 VYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNG 65
Query: 78 RMLDGRELRV 87
L R L+V
Sbjct: 66 YRLGDRVLQV 75
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important
role in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 80
Score = 33.4 bits (76), Expect = 0.008
Identities = 16/45 (35%), Positives = 22/45 (48%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
V L T + +R F GE+ I +P D T + RGF F+ F
Sbjct: 9 VGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITF 53
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of
specific mRNAs during gametogenesis. .
Length = 81
Score = 33.2 bits (76), Expect = 0.008
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
V + ++T +DLR+ F + G V ++ I DR S+G+ FV F + DA+ L
Sbjct: 7 VGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKIL 60
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 33.5 bits (77), Expect = 0.008
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 1/67 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L + NL DL + + G+V I RD +SRG F R + ED +
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG-QSRGVGFARMESREKCEDIISKF 61
Query: 76 DGRMLDG 82
+G+ L G
Sbjct: 62 NGKYLKG 68
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 33.6 bits (76), Expect = 0.008
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L T +L ++F + G + I D+ T SRG F+RF + +AE+A+
Sbjct: 7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66
Query: 75 MDGR 78
++G+
Sbjct: 67 LNGQ 70
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 33.4 bits (76), Expect = 0.009
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
T LR FE+ G++ I I DR + + RGFAFV FD D+ D + ++G
Sbjct: 12 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT-FDDHDSVDKIVIQKYHTVNGHN 70
Query: 85 LRVQMA 90
V+ A
Sbjct: 71 CEVRKA 76
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 33.0 bits (75), Expect = 0.010
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
M L + NL+ T +DLR++F GD +P G+AFV + D+ A A+
Sbjct: 1 MNKLYIGNLSPAVTAEDLRQLF------GDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAI 54
Query: 73 DAMDGRM-LDGRELRV 87
+ + G++ L G+ + V
Sbjct: 55 ETLSGKVELHGKVMEV 70
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 35.2 bits (81), Expect = 0.010
Identities = 33/131 (25%), Positives = 50/131 (38%), Gaps = 23/131 (17%)
Query: 5 RPPPRIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
P G V L V L + D R+F G++ R +F + + A +
Sbjct: 268 GPAGGGPGSV-LMVSGLHQEKVNCD---RLFNLFCVYGNVE--RVKFMKNKKETALIEMA 321
Query: 64 DKRDAEDALDAMDGRMLDGRELR--------VQMARYGRPPSSSRSRGGRDRDRRRDRSR 115
D A+ AL ++G L G+ LR VQ R G+ S +D S
Sbjct: 322 DPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTS--------YKDYSS 373
Query: 116 SRDRRYTRSRS 126
SR+ R+ + S
Sbjct: 374 SRNHRFKKPGS 384
Score = 31.7 bits (72), Expect = 0.15
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V+N Y T D L ++F G+V I FT+ + A V F A+ A A++G
Sbjct: 101 VENPMYPITLDVLYQIFNPYGKVLRIVT----FTKNNVFQALVEFESVNSAQHAKAALNG 156
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 33.1 bits (75), Expect = 0.010
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 8/67 (11%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
D+ +F + G V + +G+AFV++ ++R A A+ +GR+L G+ L +
Sbjct: 18 DVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAVIGENGRVLAGQTLDIN 69
Query: 89 MARYGRP 95
MA +P
Sbjct: 70 MAGEPKP 76
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM2 of U1A/U2B"/SNF protein family,
containing Drosophila sex determination protein SNF and
its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs) connected by a variable, flexible linker.
SNF is an RNA-binding protein found in the U1 and U2
snRNPs of Drosophila where it is essential in sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). U1A is an RNA-binding protein associated with
the U1 snRNP, a small RNA-protein complex involved in
pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent on U2 snRNA binding. .
Length = 72
Score = 32.9 bits (76), Expect = 0.010
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 12/65 (18%)
Query: 16 LKVDNLTYRTTPDDLRRVFER---CGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
L + NL TT + L +F + EV +PR RG AFV F + A AL
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVR--LVPR-------RGIAFVEFETEEQATVAL 55
Query: 73 DAMDG 77
A+ G
Sbjct: 56 QALQG 60
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 86
Score = 33.1 bits (75), Expect = 0.010
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 21 LTYRTTPDD----LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
Y PD L ++F G V ++ + RD T + +GF FV + +A A+ +++
Sbjct: 7 FVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66
Query: 77 GRMLDGRELRV 87
G L R L+V
Sbjct: 67 GYRLGDRVLQV 77
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 33.0 bits (75), Expect = 0.010
Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + ++L++ +F + G++ DI + T + RG AFV F D A +
Sbjct: 1 TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK---TLKMRGQAFVVFKDISSATN 57
Query: 71 ALDAMDGRMLDGRELRVQMAR 91
AL +M G + +R+ ++
Sbjct: 58 ALRSMQGFPFYDKPMRIAYSK 78
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 33.0 bits (75), Expect = 0.011
Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V NL T + L + F + G++ + ++ + +AF+ F ++ A A++ M
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 55
Query: 76 DGRMLDGRELRVQMAR 91
+G+ L+G + + A+
Sbjct: 56 NGKELEGENIEIVFAK 71
>gnl|CDD|241227 cd12783, RRM2_PTBP2, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM2 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 101
Score = 33.5 bits (76), Expect = 0.011
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+DN+ Y T D L ++F + G V I FT+ ++ A +++ D +A+ A A+DG
Sbjct: 8 IDNMYYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYGDPVNAQQAKLALDG 63
Query: 78 R 78
+
Sbjct: 64 Q 64
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM1 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 protein 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 = 32.9 bits (75), Expect = 0.011
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
SL V N+ T LRR+FE G+V + R S G V F+D RDA+ A+
Sbjct: 3 SLFVINVPRDVTESTLRRLFEVYGDVRGVQT-----ERISEGIVTVHFYDIRDAKRAVRE 57
Query: 75 MDGRMLDGREL 85
+ GR + + L
Sbjct: 58 LCGRHMQQQAL 68
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily
corresponds to the RRM2 of La and LARP7. La is a highly
abundant nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. LARP7 is an oligopyrimidine-binding
protein that binds to the highly conserved 3'-terminal
U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable
component of the 7SK small nuclear ribonucleoprotein
(7SK snRNP), intimately associates with all the nuclear
7SK and is required for 7SK stability. LARP7 also acts
as a negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. LARP7 plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. Both La and LARP7 contain an N-terminal
La motif (LAM), followed by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 33.0 bits (76), Expect = 0.011
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
LK+ ++ T +D++ VF + GEV Y+ FT + ++RF A+ A +A
Sbjct: 4 LKITSIGPGVTREDIKAVFAQFGEV--KYV---DFTEGAD-TGYIRFKTPEAAQKAREAF 57
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate
probable RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 33.1 bits (75), Expect = 0.012
Identities = 21/60 (35%), Positives = 30/60 (50%)
Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
L R P DL F G+V D+ I DR +R S+G A+V F + + A+ R+L
Sbjct: 9 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLL 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 = 33.0 bits (75), Expect = 0.012
Identities = 15/50 (30%), Positives = 30/50 (60%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
T ++R +FE G V ++ I +D+ T +G FV++ + +A+ A+ A+
Sbjct: 12 TEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61
>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 = 32.6 bits (75), Expect = 0.013
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 12/82 (14%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYI-PRDRFTRESRGFAFVRFFDKRDAEDALD 73
+L V L R T DLR F + GE+ I + PR + AFV F + AE A +
Sbjct: 3 TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-------QQCAFVTFTTREAAEKAAE 55
Query: 74 AMDGR-MLDGRELRVQMARYGR 94
+ + +++GR L++ ++GR
Sbjct: 56 RLFNKLIINGRRLKL---KWGR 74
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 32.6 bits (74), Expect = 0.013
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
D+ R F+ G + DI + RGF FV F D RDA+DA+ +DG+ L + ++
Sbjct: 15 DVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAVYELDGKELCNERVTIE 66
Query: 89 MAR 91
AR
Sbjct: 67 HAR 69
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 32.7 bits (75), Expect = 0.014
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 13/79 (16%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE------SRGFAFVRFFDKRDAEDA 71
+ NL Y T +D++ F + + R RE RGF + F D+ A
Sbjct: 6 LGNLPYDVTEEDIKEFFR------GLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59
Query: 72 LDAMDGRMLDGRELRVQMA 90
L +++ L R +RV +A
Sbjct: 60 L-SLNDESLKNRRIRVDIA 77
>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM4 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 = 72
Score = 32.3 bits (74), Expect = 0.015
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
V NL T +LR +F + G +G + +P T A V F + +A+ A
Sbjct: 5 VKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT------AIVEFLEPSEAKLA 52
>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 = 32.4 bits (74), Expect = 0.016
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V T+ +R +F G V ++ + FAFV F A A D++
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDSV 53
Query: 76 DGRMLDGRELRV 87
G++L+ L V
Sbjct: 54 HGKVLNNNPLYV 65
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 32.6 bits (74), Expect = 0.017
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL + + +LRR F++ G + ++ I R + +AF++F + A A A
Sbjct: 10 NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPA-RGQGGAYAFLKFQNLDMAHRAKVA 68
Query: 75 MDGRMLDGRELRV 87
M GR++ +++
Sbjct: 69 MSGRVIGRNPIKI 81
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 32.6 bits (74), Expect = 0.018
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
DL F + G V + D+ T + RGF FV +F D+ D + ++G + V+
Sbjct: 15 DLTEHFSQFGPVEKAEVIADKQTGKKRGFGFV-YFQNHDSADKAAVVKFHPINGHRVEVK 73
Query: 89 MA 90
A
Sbjct: 74 KA 75
>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 = 32.7 bits (75), Expect = 0.019
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 33 VFE---RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
+FE + GEV + + D G +V+F D+ A AL A+ GR DGR + V+
Sbjct: 43 IFEELSKFGEVEALNVC-DNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVE 100
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 32.3 bits (74), Expect = 0.020
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRFFDKRDAE 69
+ L T D L +F G + I I D+ T E +G A V + D A+
Sbjct: 3 ISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSAAQ 61
Query: 70 DALDAMDGRMLDGRELRVQM 89
A++ +G G +++V +
Sbjct: 62 AAIEWFNGYEFRGNKIKVSL 81
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 31.9 bits (73), Expect = 0.020
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + + LRR E+ G V + + + G V F+D R AEDAL
Sbjct: 3 ALLLSGVPPHIPETQLRRDLEQWGAVRAV-----QMDAMAEGIVTVHFYDLRHAEDALRD 57
Query: 75 MDGR 78
+ +
Sbjct: 58 IRAQ 61
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 32.4 bits (73), Expect = 0.020
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 1/75 (1%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V + T LR FE G++ I I DR + + RGF FV FD D D +
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVT-FDDHDPVDKIVLQ 61
Query: 76 DGRMLDGRELRVQMA 90
++G V+ A
Sbjct: 62 KYHTINGHNAEVRKA 76
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 32.1 bits (73), Expect = 0.021
Identities = 27/71 (38%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL DL +F + G + DI + + R FAFVRF D RDAEDA+ +G
Sbjct: 4 VGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60
Query: 78 RMLDGRELRVQ 88
LRV+
Sbjct: 61 YDFGQCRLRVE 71
>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM1 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 32.3 bits (73), Expect = 0.021
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-RDRFTRESRGFAFVRFFDKRDAEDA 71
M L + NL+ +P DL +F+ D IP F +S G+AFV D+ A A
Sbjct: 1 MNKLYIGNLSENASPLDLESIFK------DSKIPFSGPFLVKS-GYAFVDCPDESWAMKA 53
Query: 72 LDAMDGRM-LDGRELRVQ 88
+D + G++ L G+ + V+
Sbjct: 54 IDTLSGKVELHGKVIEVE 71
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 32.3 bits (73), Expect = 0.022
Identities = 18/64 (28%), Positives = 35/64 (54%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V L + ++ ++F + G + I D+ T SRG F+RF + +AE+A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62
Query: 75 MDGR 78
++G+
Sbjct: 63 LNGQ 66
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and is essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 32.0 bits (73), Expect = 0.023
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEV--GDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
L V+NL+ R + DL+ + GEV D + ++ V F D + A++
Sbjct: 3 LIVENLSSRVSWQDLKDFMRKAGEVTYADAH-------KQRPNEGVVEFATYSDMKRAIE 55
Query: 74 AMDGRMLDGRELRV 87
+DG L+GR++++
Sbjct: 56 KLDGTELNGRKIKL 69
>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 = 32.0 bits (73), Expect = 0.025
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
RG AF F +A+ ++A++G + GR LRV+ R
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 32.1 bits (73), Expect = 0.025
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 8/64 (12%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
GM+S K + +D+R +F G + + + RD+ +SRG AFV F ++ A +A
Sbjct: 7 GMLSKKCNE-------NDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNA 58
Query: 72 LDAM 75
+ AM
Sbjct: 59 IKAM 62
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog
of DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 32.1 bits (73), Expect = 0.026
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
V + R ++R F + G V ++ I DR T S+G+ FV F+D D + +++
Sbjct: 10 VGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVES 65
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 86
Score = 32.1 bits (73), Expect = 0.028
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 40 VGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM----LDGRELRVQMAR 91
V +I + +D+ T+++RGFAFV+ +A L + +DG+ + V A+
Sbjct: 31 VSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVDFAK 86
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 31.8 bits (73), Expect = 0.030
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD----AMDGRMLD 81
T DL F R G V D+ I + + RGFA++ R +E L ++G
Sbjct: 12 TESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL---RTSEAQLKKCKSTLNGTKWK 68
Query: 82 GRELRVQMAR 91
G L+++ A+
Sbjct: 69 GSVLKIEEAK 78
>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 = 31.7 bits (72), Expect = 0.033
Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 10/74 (13%)
Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM 79
N Y ++ R+F + G V DR +S GFAFV D+RDAEDA+ +D
Sbjct: 7 NFEYDARQSEIERLFGKYGRV-------DRVDMKS-GFAFVYMEDERDAEDAIRGLDNFE 58
Query: 80 L--DGRELRVQMAR 91
R LRV+ A+
Sbjct: 59 FGRQRRRLRVEWAK 72
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 31.4 bits (72), Expect = 0.035
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRG-FAFVRFFDKRDAEDALDA 74
L V NL TT ++LR++F R G R + + G FV F D A AL++
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQ--PG---FRRLKMHNKGGGPVCFVEFEDVSFATQALNS 59
Query: 75 MDGRML---DGRELRVQMAR 91
+ G +L D +R++ A+
Sbjct: 60 LQGAVLSSSDRGGIRIEYAK 79
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 31.6 bits (71), Expect = 0.036
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
L ++F G V ++ + RD T + +GF FV + +A A+ +++G L + L+V
Sbjct: 18 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQV 75
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 31.6 bits (72), Expect = 0.038
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ L T +D+R G E D+ + R + T SRGFAFV F +A ++
Sbjct: 7 LRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMELNQ 66
Query: 77 GRMLDGR 83
G++
Sbjct: 67 GKLQLQD 73
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 31.8 bits (72), Expect = 0.038
Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 17/106 (16%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
++N+ Y T D L VF G V I I F + A +++ D A +A +A++G
Sbjct: 8 IENMQYAVTVDVLHTVFSAFGFVQKIAI----FEKNGGFQALIQYPDVPTAVNAKEALEG 63
Query: 78 RML-DGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYT 122
+ DG ++ + S SR D + + + RSRD YT
Sbjct: 64 HCIYDGGYCKLHL-------SYSRH---TDLNVKVNNDRSRD--YT 97
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.5 bits (71), Expect = 0.040
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL ++ L+ VF G V I D+ +SRG V F +A A+ +G
Sbjct: 5 VANLDFKVGWKKLKEVFSIAGTVKRADIKEDK-DGKSRGMGTVTFEQPIEAVQAISMFNG 63
Query: 78 RMLDGRELRVQM 89
+ L R + V+M
Sbjct: 64 QFLFDRPMHVKM 75
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4
is a splicing regulatory serine/arginine (SR) protein
that plays an important role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
For instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, it activates splicing of the cardiac troponin
T (cTNT) alternative exon by direct interactions with
the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between
the nucleus and cytoplasm. It contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 31.1 bits (70), Expect = 0.045
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
+ L+Y+ D+ R F+ G++ ++ + G+ FV F D RDA+DA+ ++G
Sbjct: 4 IGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYELNG 55
Query: 78 RMLDGRELRVQMARYGR 94
+ L G + V+ AR R
Sbjct: 56 KDLCGERVIVEHARGPR 72
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 92
Score = 31.4 bits (71), Expect = 0.050
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSS 99
+GFA + + AE DG L G +RV G PP S
Sbjct: 44 KGFAVLEYESAEMAEMVQQQADGLSLAGSHIRVSFCAPG-PPGRS 87
>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 = 31.1 bits (70), Expect = 0.050
Identities = 19/61 (31%), Positives = 39/61 (63%), Gaps = 2/61 (3%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRELR 86
D+L + E+ G++ ++ + D F +RG+AFV F +K++A++A+ ++ + +GR L
Sbjct: 16 DELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLG 74
Query: 87 V 87
V
Sbjct: 75 V 75
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 31.2 bits (71), Expect = 0.054
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V ++ + T + L +F CG+V D + D FAF+ F D+ A AL ++ G
Sbjct: 7 VSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAAL-SLSG 63
Query: 78 RMLDGRELRVQMAR 91
ML +RV ++
Sbjct: 64 TMLGFYPVRVLPSK 77
>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 = 31.1 bits (70), Expect = 0.068
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 23 YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
Y +D++ ++ G V + IP++ +G FV + + D++ A + GR+ DG
Sbjct: 23 YEDIIEDIKEECQKYGPVVSLLIPKEN---PGKGQVFVEYANAGDSKAAQKLLTGRIFDG 79
Query: 83 R 83
+
Sbjct: 80 K 80
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 30.3 bits (69), Expect = 0.083
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 15 SLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALD 73
++ + N++ + ++ FE +V I + F + G A V F DA A
Sbjct: 2 TIGLFNVSDTVNEEQIKAFFEKIGPDVRKIEL----FP-DHEG-ALVEFESPSDAGKASL 55
Query: 74 AMDGRMLDGRELRV 87
+++G G+ +++
Sbjct: 56 SLNGSQFGGKTIKI 69
>gnl|CDD|240972 cd12528, RRM2_MEI2_fungi, RNA recognition motif 2 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM2 of fungal Mei2-like proteins.The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 81
Score = 30.5 bits (69), Expect = 0.085
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 60 VRFFDKRDAEDALDAMDGRMLD 81
FFD RDA++A+D ++GR++D
Sbjct: 53 CEFFDTRDADNAVDELNGRVVD 74
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 30.3 bits (69), Expect = 0.093
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 57 FAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
FAFV F + + + AL+ +DG GR L ++A+
Sbjct: 44 FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAK 78
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers. hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 30.4 bits (68), Expect = 0.10
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V NL Y+ L+ VF G V I D+ +SRG V F +A A+ +G
Sbjct: 5 VANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAISMFNG 63
Query: 78 RMLDGRELRVQM 89
++L R + V+M
Sbjct: 64 QLLFDRPMHVKM 75
>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 = 30.1 bits (68), Expect = 0.11
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 13/79 (16%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDI------YIPRDRFTRESRGFAFVRFFDKRDAEDA 71
V NL T +R F ++G I Y + S G A + F DA A
Sbjct: 4 VSNLPKDVTEAQIREYFVS--QIGPIKRVLLSYNEGGK----STGIANITFKRAGDATKA 57
Query: 72 LDAMDGRMLDG-RELRVQM 89
D +GR+ DG R+++V++
Sbjct: 58 YDKFNGRIDDGNRKMKVEV 76
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 72
Score = 30.0 bits (68), Expect = 0.11
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
V N Y TT ++LR +FE G++ + +P + A V F + + A A A+
Sbjct: 5 VKNFPYGTTAEELRDLFEPHGKLTRVLMP------PAGTIAIVEFANPQQARLAFKAL 56
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate
RNA-binding protein 11 (RBM11). This subfamily
corresponds to the RRM or RBM11, a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. RBM11 is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. RBM11 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a region
lacking known homology at the C-terminus. The RRM of
RBM11 is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 29.9 bits (67), Expect = 0.12
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L V NL R + L +F + G + + I +D+ + + F FV F A+
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESVPYAIAL 61
Query: 75 MDGRMLDGRELRVQ 88
++G L GR ++V
Sbjct: 62 LNGIRLYGRPIKVH 75
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B") a unique protein that comprises the U2
snRNP. It was initially identified as binding to
stem-loop IV (SLIV) at the 3' end of U2 snRNA.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B"
does not require an auxiliary protein for binding to
RNA. In addition, the nuclear transport of U2B" is
independent of U2 snRNA binding. U2B" contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It also contains a nuclear localization signal (NLS) in
the central domain. However, nuclear import of U2B''
does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 91
Score = 30.4 bits (68), Expect = 0.12
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 15 SLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAED 70
++ ++NL + ++L+R +F + G V DI + T + RG AFV F + A +
Sbjct: 3 TIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSATN 59
Query: 71 ALDAMDGRMLDGRELRVQMAR 91
AL + G G+ +R+Q A+
Sbjct: 60 ALRQLQGFPFYGKPMRIQYAK 80
>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage
factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar
proteins. This subgroup corresponds to the RRM of
CFIm68. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm68,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF6), or cleavage and
polyadenylation specificity factor 68 kDa subunit
(CPSF68), or protein HPBRII-4/7. CFIm68 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. The N-terminal RRM of CFIm68 mediates the
interaction with CFIm25. It also serves to enhance RNA
binding and facilitate RNA looping. .
Length = 77
Score = 30.1 bits (68), Expect = 0.12
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDAL 72
+L V NLT+ TT DL + G ++ +I +R +S+GFA + + + +
Sbjct: 1 ALYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSSRKLM 60
Query: 73 DAMDGRMLDGR 83
D + + L G+
Sbjct: 61 DKLPKKELHGQ 71
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as
cyclin D1, where it represses transcription by
disrupting complex formation. TAF15 (TAFII68), also
termed TATA-binding protein-associated factor 2N
(TAF2N), or RNA-binding protein 56 (RBP56), originally
identified as a TAF in the general transcription
initiation TFIID complex, is a novel RNA/ssDNA-binding
protein with homology to the proto-oncoproteins FUS and
EWS (also termed EWSR1), belonging to the FET family as
well. TAF15 likely functions in RNA polymerase II (RNAP
II) transcription by interacting with TFIID and
subunits of RNAP II itself. TAF15 is also associated
with U1 snRNA, chromatin and RNA, in a complex distinct
from the Sm-containing U1 snRNP that functions in
splicing. Like other members in the FET family, both
FUS and TAF15 contain an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. .
Length = 86
Score = 30.3 bits (68), Expect = 0.13
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 48 DRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
DR T + +G A V F D A+ A+D DG+ G ++V
Sbjct: 45 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 84
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 31.8 bits (73), Expect = 0.13
Identities = 20/92 (21%), Positives = 28/92 (30%)
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
+ D D + R R + GR R R++ RR+ RD R R
Sbjct: 170 DERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGR 229
Query: 126 SFSSRSRSGSKSPRKARSKSIDRDNKHERNGR 157
R + D D+ R GR
Sbjct: 230 RRRRDRRDARGDDNREDRGDRDGDDGEGRGGR 261
Score = 30.6 bits (70), Expect = 0.32
Identities = 12/64 (18%), Positives = 21/64 (32%)
Query: 94 RPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHE 153
+ R R R R+ ++ R R R + R R + R+ +
Sbjct: 161 AERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR 220
Query: 154 RNGR 157
R+G
Sbjct: 221 RDGG 224
Score = 29.1 bits (66), Expect = 1.0
Identities = 19/57 (33%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRR 120
D+R D D R D RE R R RG R RDR R R D
Sbjct: 225 DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR-RGRRFRDRDRRGRRGGDGG 280
Score = 28.7 bits (65), Expect = 1.4
Identities = 25/92 (27%), Positives = 29/92 (31%), Gaps = 5/92 (5%)
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
R E D D D RE + GR R R RDRR R
Sbjct: 192 RREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRD 251
Query: 126 SFSSRSRSGSKSPRKARSKSIDRDNKHERNGR 157
R G + R+ R DRD + R G
Sbjct: 252 GDDGEGRGGRRG-RRFR----DRDRRGRRGGD 278
Score = 28.3 bits (64), Expect = 1.7
Identities = 11/67 (16%), Positives = 23/67 (34%)
Query: 91 RYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDN 150
+P + +R+ + R R ++ + R G + R DR +
Sbjct: 148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207
Query: 151 KHERNGR 157
+ E+ R
Sbjct: 208 RREQGDR 214
Score = 27.9 bits (63), Expect = 2.9
Identities = 21/95 (22%), Positives = 31/95 (32%), Gaps = 4/95 (4%)
Query: 64 DKRDAEDALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTR 123
D + + + + R RE R A G D RRDR DRR R
Sbjct: 159 DAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREER 218
Query: 124 SRSFSSRSRSGSKSPRKARSKSIDRDNKHERNGRS 158
R R + R+ R + R + + +
Sbjct: 219 GR----RDGGDRRGRRRRRDRRDARGDDNREDRGD 249
>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 = 29.9 bits (68), Expect = 0.13
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 51 TRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
R+ G V F + D E AL +DG GR +RV
Sbjct: 33 DRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 69
>gnl|CDD|241226 cd12782, RRM2_PTBP1, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM2 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there
is an unusual and conserved interdomain interaction
between RRM3 and RRM4. It is widely held that only RRMs
3 and 4 are involved in RNA binding and RRM2 mediates
PTB homodimer formation. However, new evidence shows
that the RRMs 1 and 2 also contribute substantially to
RNA binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 100
Score = 30.5 bits (68), Expect = 0.14
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V+NL Y T D L ++F + G V I FT+ ++ A +++ D A+ A ++DG
Sbjct: 9 VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSAQHAKLSLDG 64
Query: 78 R 78
+
Sbjct: 65 Q 65
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 29.5 bits (67), Expect = 0.19
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+ D+LR++F + G+V D+ + + +G A V F K+ AE A++ G L L
Sbjct: 17 SEDELRKIFSKYGDVSDVVVSSKK-----KGSAIVEFASKKAAEAAVENECG--LPSNPL 69
Query: 86 RVQ 88
V
Sbjct: 70 LVS 72
>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 = 29.5 bits (66), Expect = 0.19
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
+LR+ E+ GE+ I R RE + AF+ F + +A AL ++G+ +
Sbjct: 20 PEKELRKECEKYGEIESI-----RILRE-KACAFINFMNIPNAIAALQTLNGKKPYDTIV 73
Query: 86 RV 87
R+
Sbjct: 74 RI 75
>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 = 29.5 bits (67), Expect = 0.20
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 11/68 (16%)
Query: 28 DDLRRVFERCGEVGDIYI------PRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLD 81
D++ E+ G+V ++ + D R FV F D +A A+ A++GR
Sbjct: 21 DEIEEECEKYGKVLNVIVHEVASSEADDAVR-----IFVEFSDADEAIKAVRALNGRFFG 75
Query: 82 GRELRVQM 89
GR++ +
Sbjct: 76 GRKVTARF 83
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 29.3 bits (65), Expect = 0.22
Identities = 13/53 (24%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
+R+ F G++ ++ + D+ G++FVRF A A+ +++G ++G
Sbjct: 17 MRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVSVNGTTIEG 63
>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 = 29.5 bits (67), Expect = 0.24
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
D+ R GE+ D+ + D G +V+F + DAE AL A++GR GR L
Sbjct: 41 DVFLELSRFGEIEDLVVC-DNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPL 96
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 30.8 bits (70), Expect = 0.24
Identities = 19/57 (33%), Positives = 21/57 (36%)
Query: 93 GRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRD 149
SS S R RR R R RSR S R S S R+A +RD
Sbjct: 4 LALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERD 60
Score = 30.5 bits (69), Expect = 0.33
Identities = 15/51 (29%), Positives = 20/51 (39%)
Query: 82 GRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSR 132
+L ++ + S +R R R R RSR R RS SS R
Sbjct: 1 MDDLALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRR 51
Score = 27.8 bits (62), Expect = 2.7
Identities = 15/58 (25%), Positives = 17/58 (29%)
Query: 70 DALDAMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSF 127
AL + R + R GR S RSR R R S R R
Sbjct: 4 LALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61
>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 = 29.5 bits (67), Expect = 0.26
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRFFDKRDAEDALDAMDGRMLDGREL 85
DD+ FE+ GEV + + E RG +V++ + +A A +GR G++L
Sbjct: 43 DDVLPEFEKFGEVVQFKVCCNY---EPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQL 99
Query: 86 RVQM 89
+
Sbjct: 100 TCEF 103
>gnl|CDD|217277 pfam02901, PFL, Pyruvate formate lyase.
Length = 646
Score = 30.7 bits (70), Expect = 0.30
Identities = 21/71 (29%), Positives = 26/71 (36%), Gaps = 7/71 (9%)
Query: 22 TYRTTPDDLRRV--FERCGEVGDIYIPRD-----RFTRESRGFAFVRFFDKRDAEDALDA 74
T P D+RR ++ E YI D T R A R ED LD
Sbjct: 36 TEGELPVDIRRAKALKKILEHKPGYIRDDELIVGLQTDAPRKRAIFPEGGVRWVEDELDT 95
Query: 75 MDGRMLDGREL 85
+ R DG E+
Sbjct: 96 LATRPQDGFEI 106
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.9 bits (70), Expect = 0.30
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 2/71 (2%)
Query: 88 QMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSID 147
G PS S S R S + R +R+ S + S +G + R+AR+
Sbjct: 339 AAVSPGPSPSRSPSPS-RPPPPADPSSPRKRPRPSRAPSSPAAS-AGRPTRRRARAAVAG 396
Query: 148 RDNKHERNGRS 158
R + + GR
Sbjct: 397 RARRRDATGRF 407
>gnl|CDD|217084 pfam02522, Antibiotic_NAT, Aminoglycoside 3-N-acetyltransferase.
This family consists of bacterial aminoglycoside
3-N-acetyltransferases EC:2.3.1.81, these catalyze the
reaction: Acetyl-Co + a 2-deoxystreptamine antibiotic
<=> CoA + N3'-acetyl-2-deoxystreptamine antibiotic. The
enzyme can use a range of antibiotics with
2-deoxystreptamine rings as acceptor for its
acetyltransferase activity, this inactivates and confers
resistance to gentamicin, kanamycin, tobramycin,
neomycin and apramycin amongst others.
Length = 229
Score = 30.3 bits (69), Expect = 0.32
Identities = 17/68 (25%), Positives = 23/68 (33%)
Query: 4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFF 63
G P R + + VD T +D + +G + R G A R F
Sbjct: 154 GVPYKRRKRYEGILVDGERVWVTYEDYDSDSDDFERIGRAFEARGIGREGKVGGATSRLF 213
Query: 64 DKRDAEDA 71
D RD D
Sbjct: 214 DARDLVDF 221
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 30.4 bits (69), Expect = 0.33
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 17/55 (30%)
Query: 61 RFFDKRDAEDALDAMDGRMLDGRELRVQMA-----------------RYGRPPSS 98
RF+D + LD +D R LD ELR +MA RYGRP ++
Sbjct: 388 RFYDPQSGRILLDGVDLRQLDPAELRARMALVPQDPVLFAASVMENIRYGRPDAT 442
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in
Saccharomyces cerevisiae protein Nrd1,
Schizosaccharomyces pombe Rpb7-binding protein seb1 and
similar proteins. This subfamily corresponds to the
RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous
nuclear ribonucleoprotein (hnRNP)-like RNA-binding
protein encoded by gene NRD1 (for nuclear pre-mRNA
down-regulation) from yeast S. cerevisiae. It is
implicated in 3' end formation of small nucleolar and
small nuclear RNAs transcribed by polymerase II, and
plays a critical role in pre-mRNA metabolism. Nrd1
contains an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a short arginine-, serine-, and glutamate-rich
segment similar to the regions rich in RE and RS
dipeptides (RE/RS domains) in many metazoan splicing
factors, and a proline- and glutamine-rich C-terminal
domain (P+Q domain) similar to domains found in several
yeast hnRNPs. Disruption of NRD1 gene is lethal to
yeast cells. Its N-terminal domain is sufficient for
viability, which may facilitate interactions with RNA
polymerase II where Nrd1 may function as an auxiliary
factor. By contrast, the RRM, RE/RS domains, and P+Q
domain are dispensable. Seb1 is an RNA-binding protein
encoded by gene seb1 (for seven binding) from fission
yeast S. pombe. It is essential for cell viability and
bound directly to Rpb7 subunit of RNA polymerase II.
Seb1 is involved in processing of polymerase II
transcripts. It also contains one RRM motif and a
region rich in arginine-serine dipeptides (RS domain).
Length = 79
Score = 28.7 bits (64), Expect = 0.35
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
DLR F R GEV + D+ AFV+ +++RDAE+A +AM+
Sbjct: 19 DLRSGFGRFGEVQSCILNNDK------RHAFVKMYNRRDAENAREAME 60
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 28.5 bits (64), Expect = 0.37
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 18 VDNLTYRTTPDDLRRVF-ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+ N+ Y DL+ +F E+ GEV + + +D + SRG V F DK + AL+ M+
Sbjct: 4 ISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGK-SRGCGVVEFKDKESVQKALETMN 62
Query: 77 GRMLDGRELRVQ 88
L GR+L V+
Sbjct: 63 RYELKGRKLVVK 74
>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated
initially from a Japanese patient with hepatitis of
unknown aetiology, has since been found to infect both
healthy and diseased individuals and numerous prevalence
studies have raised questions about its role in
unexplained hepatitis. ORF1 is a large 750 residue
protein. The N-terminal half of this protein corresponds
to the capsid protein.
Length = 525
Score = 30.3 bits (69), Expect = 0.39
Identities = 16/35 (45%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 91 RYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSR 125
R R R R R R RRR R R R RR R R
Sbjct: 20 RRRRRA---RRRRRRRRVRRRRRGRRRRRRRRRRR 51
Score = 28.8 bits (65), Expect = 1.3
Identities = 15/30 (50%), Positives = 15/30 (50%)
Query: 91 RYGRPPSSSRSRGGRDRDRRRDRSRSRDRR 120
R R R R GR R RRR R R R RR
Sbjct: 27 RRRRRRRVRRRRRGRRRRRRRRRRRRRRRR 56
Score = 28.0 bits (63), Expect = 2.3
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 100 RSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKAR 142
R GR R RRR R+R R RR R R R + R+ R
Sbjct: 11 RRWRGRRRRRRRRRARRRRRRRRVRR----RRRGRRRRRRRRR 49
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.8 bits (64), Expect = 0.40
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELR 86
D+L VFE G + ++ + D F ++RG+AFV + K +A+ A+ R L+ E+R
Sbjct: 16 DELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAV-----RELNNYEIR 68
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 28.8 bits (64), Expect = 0.42
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + NL T DLRR F+R G + ++ I R + S + F++F + A A A
Sbjct: 9 TLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTST-YGFLKFENLDMAHRAKLA 67
Query: 75 MDGRMLDGRELRV 87
M G++L +++
Sbjct: 68 MSGKVLRRNPIKI 80
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins from plants. This
subgroup corresponds to the RRM2 in a family that
represents a novel group of arginine/serine (RS) or
serine/arginine (SR) splicing factors existing in
plants, such as A. thaliana RSp31, RSp35, RSp41 and
similar proteins. Like vertebrate RS splicing factors,
these proteins function as plant splicing factors and
play crucial roles in constitutive and alternative
splicing in plants. They all contain two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
at their N-terminus, and an RS domain at their
C-terminus.
Length = 70
Score = 28.3 bits (63), Expect = 0.44
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 23 YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDG 82
T DL R FE G++ ++ I R+ FAFV++ + DA AL++ + +
Sbjct: 10 INTRTRDLERHFEPYGKLVNVRIRRN--------FAFVQYETQEDATKALESTNMSKVLD 61
Query: 83 RELRVQMA 90
R + V+ A
Sbjct: 62 RVISVEYA 69
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 28.3 bits (63), Expect = 0.49
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V N++ +TT + F CG++ ++ + D ++ A + F A+ AL +D
Sbjct: 3 VSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQT----ATITFEKPSAAKTAL-LLDN 57
Query: 78 RMLDGRELRV 87
+L G+ ++V
Sbjct: 58 ALLGGKVIQV 67
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 30.0 bits (67), Expect = 0.50
Identities = 19/52 (36%), Positives = 22/52 (42%)
Query: 96 PSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSID 147
S G R RRR+RS SR R +RS S R R G P + D
Sbjct: 315 RRPPHSTSGERRGRRRNRSESRSRSRSRSGSRRYRRRRGRGVPGRRSESRQD 366
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM2 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 28.3 bits (63), Expect = 0.52
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
T + L+ F + ++ I++P+D + + + F++F + A ALD + G
Sbjct: 11 TEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHITG 62
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 28.1 bits (63), Expect = 0.53
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 26 TPDDLRRVFERCGEVGDIY--IPRDRFTRESRGFAFVRFF 63
T + L R+F+ G Y + RD +T +S+GFA+V +
Sbjct: 12 TQEQLHRLFDIIP--GLEYCDLKRDPYTGKSKGFAYVTYS 49
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 29.7 bits (67), Expect = 0.54
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 98 SSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRK--ARSKSIDRDNKHERN 155
+ GGR + R R R R+ SR R SP + +R+ + K +
Sbjct: 31 RTGKGGGRPSGKSRADGGRRPAR--DDRNSQSRDRKWEDSPWRTVSRAPGDETPEKADHG 88
Query: 156 GRS 158
G S
Sbjct: 89 GIS 91
Score = 29.7 bits (67), Expect = 0.61
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 93 GRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRS 124
GRP SR+ GGR R S+SRDR++ S
Sbjct: 37 GRPSGKSRADGGRRPARDDRNSQSRDRKWEDS 68
>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 = 28.4 bits (64), Expect = 0.55
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 35 ERCGEVGDIY-IPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
E+CG+ I I D+ +RE G +++ DA A A+ G DGR + V+ R
Sbjct: 28 EKCGDNNGIVHIQVDKASRE--GCVYIKCSSPEDAGKAFKALHGWWFDGRLVTVKYLR 83
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 72
Score = 28.1 bits (63), Expect = 0.62
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDA 68
LKV + + +L+ +FE+ G+V I++ + S+G V F D R A
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLL----SKGIVIVSFHDLRQA 52
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal Rrp7 domain. .
Length = 102
Score = 28.4 bits (64), Expect = 0.63
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 15/52 (28%)
Query: 26 TPDDLRRVFERCGEVGDIYIPRD-------------RFTRESRGF--AFVRF 62
T + L+R+F RCG+V + + + +GF A+V F
Sbjct: 13 TEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVF 64
>gnl|CDD|240698 cd12252, RRM_DbpA, RNA recognition motif in the DbpA subfamily of
prokaryotic DEAD-box rRNA helicases. This subfamily
corresponds to the C-terminal RRM homology domain of
dbpA proteins implicated in ribosome biogenesis. They
bind with high affinity and specificity to RNA
substrates containing hairpin 92 of 23S rRNA (HP92),
which is part of the ribosomal A-site. The majority of
dbpA proteins contain two N-terminal ATPase catalytic
domains and a C-terminal RNA binding domain, an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain). The catalytic domains bind to nearby regions
of RNA to stimulate ATP hydrolysis and disrupt RNA
structures. The C-terminal domain is responsible for
the high-affinity RNA binding. Several members of this
family lack specificity for 23S rRNA. These proteins
can generally be distinguished by a basic region that
extends beyond the C-terminal domain.
Length = 71
Score = 27.9 bits (63), Expect = 0.67
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 14/68 (20%)
Query: 26 TPDDLRRVFERCG-----EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRML 80
P DL R G ++GDI I D+F+ F V + AE ++A++G+ +
Sbjct: 13 DPRDLVGAICRAGGIPGRDIGDIDI-FDKFS-----FVEV---PEEVAEKVIEALNGKKI 63
Query: 81 DGRELRVQ 88
G+++RV+
Sbjct: 64 KGKKVRVE 71
>gnl|CDD|223010 PHA03215, PHA03215, nuclear protein UL24; Provisional.
Length = 262
Score = 29.5 bits (66), Expect = 0.75
Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 78 RMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKS 137
R L G ++ Y P +R GR R RR RSR R R + + +
Sbjct: 179 RTLQG------LSTYAVPLEPRTTRRGRRRGARRPRSRRRPRGGAAGPPVPAEPAAPERP 232
Query: 138 PRKARSKS 145
P S
Sbjct: 233 PADPTPTS 240
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein
44 (RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 27.9 bits (62), Expect = 0.80
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDG 77
V L+ + DLR F++ +V I + + R +A + F DA A+ M+G
Sbjct: 4 VGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYR----YASLHFDRASDALLAVKKMNG 58
Query: 78 RMLDGRELRVQMAR 91
+L G ++V+M +
Sbjct: 59 GVLSGLSIKVRMVK 72
>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 = 28.3 bits (64), Expect = 0.81
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 58 AFVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
A+V + K DA + A+DG LDGR L+ A +G
Sbjct: 56 AYVTYSRKEDALRCIQAVDGFYLDGRLLK---ASFG 88
>gnl|CDD|222623 pfam14247, DUF4344, Domain of unknown function (DUF4344). This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 247 and
291 amino acids in length. There is a conserved EED
sequence motif.
Length = 220
Score = 29.1 bits (66), Expect = 0.81
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 27 PDDLRRVFERCGEVGDIYIPRDR-------FTRESRG-FAFVRFFDKRDAEDALDAM 75
P DL VF CGE Y P + F ES FA D+ + A+DA+
Sbjct: 36 PYDLTIVFAECGEDNAFYDPENHTITICYEFVDESLKRFAKANDPDEEYGKAAIDAL 92
>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen. The core
antigen of hepatitis viruses possesses a carboxyl
terminus rich in arginine. On this basis it was
predicted that the core antigen would bind DNA. There is
some experimental evidence to support this.
Length = 182
Score = 28.6 bits (64), Expect = 0.93
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 99 SRSRGGRDRDRRRDRSRSRDRRYTRSRS 126
RS R RR RS+S RR ++S S
Sbjct: 152 GRSPRRRTPSPRRRRSQSPRRRRSQSPS 179
Score = 26.7 bits (59), Expect = 5.3
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 100 RSRGGRDRDRRRDRSRSRDRRYTRSRSFSSR 130
R R R R R RS+ R RS+S SS+
Sbjct: 151 RGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 27.9 bits (61), Expect = 1.1
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + L TT DL ++ + G++ D+ T + +G+ FV F A+ A+ A
Sbjct: 9 NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68
Query: 75 MDGRMLDGRELRVQMAR 91
L ++ QMA+
Sbjct: 69 -----LKASGVQAQMAK 80
>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 = 27.8 bits (62), Expect = 1.1
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 59 FVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
FV F +AE A+ A++GR GR+++ ++
Sbjct: 56 FVEFSLPSEAEKAIQALNGRWFGGRKVKAEL 86
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 27.3 bits (60), Expect = 1.2
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 55 RGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
+G+AFV++ +R A A+ + R++ G+ L +
Sbjct: 36 KGYAFVQYISERHARAAVAGENARIIAGQPLDI 68
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator
of basal transcription 1 (ABT1) and similar proteins.
This subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and
ESF2 contain an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 98
Score = 27.6 bits (62), Expect = 1.2
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 12/55 (21%)
Query: 26 TPDDLRRVFERCGEVGDIYI-PRDRFTRESRGF-----------AFVRFFDKRDA 68
P LR++ + GEVG IY+ P D R+ R +V F DK+ A
Sbjct: 13 NPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEFEDKKVA 67
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 27.6 bits (61), Expect = 1.2
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
++ V N ++ TT L +V G +V ++ +R +S+G+A V +
Sbjct: 2 AAVYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKL 61
Query: 72 LDAMDGRMLDGRELRVQMA 90
L+ + G++L+G ++ V+ A
Sbjct: 62 LELLPGKVLNGEKVDVRPA 80
>gnl|CDD|241107 cd12663, RRM1_RAVER1, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM1 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 71
Score = 27.2 bits (60), Expect = 1.2
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
F + +G AFV + AE A+ +L RE+ VQ+
Sbjct: 30 FVDKYKGTAFVTLLNGEQAESAIKEFHQSVLRDREISVQL 69
>gnl|CDD|99980 cd03808, GT1_cap1E_like, This family is most closely related to the
GT1 family of glycosyltransferases. cap1E in
Streptococcus pneumoniae is required for the synthesis
of type 1 capsular polysaccharides.
Length = 359
Score = 28.7 bits (65), Expect = 1.3
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 66 RDAEDALDAMDGRMLDGRELRVQMARYGR 94
DAE DA++ R+++ ELR +M + R
Sbjct: 314 GDAEALADAIE-RLIEDPELRARMGQAAR 341
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a CCCH class of
zinc finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 27.0 bits (60), Expect = 1.3
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 24 RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRF 62
R T +D+ F + G V D+ IP ++ R F FV F
Sbjct: 10 RFTEEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTF 44
>gnl|CDD|222011 pfam13257, DUF4048, Domain of unknown function (DUF4048). This
presumed domain is functionally uncharacterized. This
domain family is found in eukaryotes, and is typically
between 228 and 257 amino acids in length.
Length = 242
Score = 28.6 bits (64), Expect = 1.4
Identities = 17/54 (31%), Positives = 24/54 (44%)
Query: 94 RPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSID 147
R RSR R R R R + + SRS S + G+ S + ++S ID
Sbjct: 120 RTVPPPRSRRSGSRSTSRSRLRLQGGSLSSSRSSRSSTSKGATSGKDSKSADID 173
Score = 26.3 bits (58), Expect = 7.8
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 99 SRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSID 147
SR+ R RS SR R + S S SRS S K + D
Sbjct: 119 SRTVPPPRSRRSGSRSTSRSRLRLQGGS-LSSSRSSRSSTSKGATSGKD 166
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 87
Score = 27.3 bits (60), Expect = 1.5
Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 42 DIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRM----LDGRELRVQMAR 91
++ + +D+ T+ +RGFAF++ +A L + +DG+ + V+ A+
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTINVEFAK 86
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in
the system using SV40 DNA. MSSP-2 is identical with
Scr3, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 75
Score = 27.0 bits (59), Expect = 1.6
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
+L + L TT DL ++ + G++ D+ T + +G+ FV F A+ A+ A
Sbjct: 3 NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62
Query: 75 MDGRMLDGRELRVQMAR 91
L ++ QMA+
Sbjct: 63 -----LKASGVQAQMAK 74
>gnl|CDD|173864 cd08499, PBP2_Ylib_like, The substrate-binding component of an
uncharacterized ABC-type peptide import system Ylib
contains the type 2 periplasmic binding fold. This
family represents the periplasmic substrate-binding
component of an uncharacterized ATP-binding cassette
(ABC)-type peptide transport system YliB. Although the
ligand specificity of Ylib protein is not known, it
shares significant sequence similarity to the ABC-type
dipeptide and oligopeptide binding proteins. Most of
other periplasmic binding proteins are comprised of only
two globular subdomains corresponding to domains I and
III of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 474
Score = 28.3 bits (64), Expect = 1.7
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 17 KVDNLTYRTTPDDLRRVFE-RCGEVGDIY-IP 46
KVD +T++ P+D RV GE Y +P
Sbjct: 185 KVDTVTFKVVPEDGTRVAMLETGEADIAYPVP 216
>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM2 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5), is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 75
Score = 27.0 bits (59), Expect = 1.7
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+NL+ R + DL+ + GEV R + V F D ++A++ +
Sbjct: 6 LIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKLNE-----GVVEFASYSDLKNAIEKL 60
Query: 76 DGRMLDGRELRV 87
G+ ++GR++++
Sbjct: 61 SGKEINGRKIKL 72
>gnl|CDD|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936).
This family consists of several hypothetical proteins
from Arabidopsis thaliana and Oryza sativa. The function
of this family is unknown.
Length = 564
Score = 28.3 bits (63), Expect = 1.9
Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 3/67 (4%)
Query: 91 RYGRPPSSSRSRGGRDR---DRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSID 147
R G SSS+S R RS S R+ + SRS +P + S
Sbjct: 142 RRGSWDSSSKSASIDSSPTVIGPRPRSFSELNLTDRTPAKVRSSRSELGAPSPSGGTSCP 201
Query: 148 RDNKHER 154
+ R
Sbjct: 202 SSSGGRR 208
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically bind mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone and play a key role in
cell growth and differentiation. DND1 is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 26.9 bits (60), Expect = 1.9
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRD-RFTRESRGFAFVRFFDKRDAEDALD 73
L V + T +++ F + E V D+ + R ++RGFAFV + R A A
Sbjct: 4 LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARR 63
Query: 74 A-MDGRML 80
+ GR+L
Sbjct: 64 KLVPGRIL 71
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 26.6 bits (59), Expect = 2.0
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDA 68
+ NL + ++LR E+ G + I I ++ + AFV F +A
Sbjct: 8 IGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANA 52
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4), a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFRS4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, SRSF4 activates splicing of the cardiac
troponin T (cTNT) alternative exon by direct
interactions with the cTNT exon 5 enhancer RNA. SRSF4
can shuttle between the nucleus and cytoplasm. It
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 26.6 bits (58), Expect = 2.2
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+NL+ R + DL+ + GEV + R + + F D + AL+ +
Sbjct: 3 LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGR-----KNEGVIEFRSYSDMKRALEKL 57
Query: 76 DGRMLDGRELRV 87
DG ++GR++R+
Sbjct: 58 DGTEVNGRKIRL 69
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 27.5 bits (61), Expect = 2.9
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 12/82 (14%)
Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMD 76
+V NL+ + T D+ F CG + + I R + E A+V F D E A+
Sbjct: 9 EVTNLSPKATEKDVYDFFSHCGAIEHVEIIR---SGEYACTAYVTFKDAYALETAV---- 61
Query: 77 GRMLDGREL---RVQMARYGRP 95
+L G + RV + R+G+
Sbjct: 62 --LLSGATIVDQRVCITRWGQY 81
>gnl|CDD|213339 cd05137, RasGAP_CLA2_BUD2, Ras-GTPase Activating Domain of
CLA2/BUD2. CLA2/BUD2 functions as a GTPase-activating
protein (GAP) for BUD1/RSR1 and is necessary for proper
bud-site selection in yeast. BUD2 has sequence
similarity to the catalytic domain of RasGAPs, and
stimulates the hydrolysis of BUD1-GTP to BUD1-GDP.
Elimination of Bud2p activity by mutation causes a
random budding pattern with no growth defect.
Overproduction of Bud2p also alters the budding pattern.
Length = 356
Score = 27.5 bits (62), Expect = 3.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 27 PDDLRRVFE--RCGEVGDIYIPRDRFTRES--RGFAFVRFF 63
P +LR++ + R V D Y R + GF F+RFF
Sbjct: 181 PPELRKILKHIRAK-VEDRYGDFLRTVTLNSVSGFLFLRFF 220
>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 = 26.1 bits (57), Expect = 3.2
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQ 88
DL R E+ GEV + + +D +SRG V F D+ + AL+ M+ L+GR L ++
Sbjct: 18 DLMR--EKVGEVTYVELFKDA-EGKSRGCGVVEFKDEEFVKKALEVMNKYDLNGRPLNIK 74
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the
RRM of Star-PAP, also termed RNA-binding motif protein
21 (RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs
to the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both,
the poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione
S-transferase (GST)-PIPKIalpha. Star-PAP preferentially
uses ATP as a nucleotide substrate and possesses PAP
activity that is stimulated by PtdIns4,5P2. It contains
an N-terminal C2H2-type zinc finger motif followed by
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
split PAP domain linked by a proline-rich region, a PAP
catalytic and core domain, a PAP-associated domain, an
RS repeat, and a nuclear localization signal (NLS). .
Length = 74
Score = 25.8 bits (57), Expect = 3.4
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
S+ V T+ + L F G V ++ + +D+ +A V F K + L +
Sbjct: 4 SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDK-----GVYAIVEFDSKEGVDKVL-S 57
Query: 75 MDGRMLDGRELRV 87
L+G LRV
Sbjct: 58 EPQHTLNGHRLRV 70
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 26.2 bits (57), Expect = 3.6
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDA 71
GMVS K +D+R +F G++ + I R SRG AFV F + A+ A
Sbjct: 7 GMVSKKC-------NENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 58
Query: 72 LDAM 75
+ AM
Sbjct: 59 IKAM 62
>gnl|CDD|215979 pfam00534, Glycos_transf_1, Glycosyl transferases group 1.
Mutations in this domain of human PIGA lead to disease
(Paroxysmal Nocturnal haemoglobinuria). Members of this
family transfer activated sugars to a variety of
substrates, including glycogen, Fructose-6-phosphate and
lipopolysaccharides. Members of this family transfer
UDP, ADP, GDP or CMP linked sugars. The eukaryotic
glycogen synthases may be distant members of this
family.
Length = 158
Score = 26.9 bits (60), Expect = 3.6
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 62 FFDKRDAEDALDAMDGRMLDGRELRVQMARYGR 94
D DAE +A++ ++L ELR ++ R
Sbjct: 125 LVDPGDAEALAEAIE-KLLKDEELRERLGENAR 156
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 27.7 bits (62), Expect = 3.7
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 94 RPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSR 132
+P R R ++ RRDR+ RD R R+R +R
Sbjct: 599 KPERQQDRRKPR-QNNRRDRNERRDTRDNRTRREGRENR 636
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 77
Score = 26.1 bits (57), Expect = 3.8
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 28 DDLRRVF---ERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRE 84
++L R F ERC ++ T S+G+ FV + K A A + G+ L R
Sbjct: 17 EELVRPFGNLERC------FLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGSRT 70
Query: 85 LRVQ 88
L V
Sbjct: 71 LYVH 74
>gnl|CDD|215334 PLN02623, PLN02623, pyruvate kinase.
Length = 581
Score = 27.6 bits (61), Expect = 3.8
Identities = 16/79 (20%), Positives = 28/79 (35%)
Query: 74 AMDGRMLDGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRS 133
++D +L V + +S+ G R RRR R R RS S +
Sbjct: 10 SIDSSILSSSSGSVSLDLLSPLSFASKVLGSEARARRRVAVRRRAVTAASLRSKSQETEV 69
Query: 134 GSKSPRKARSKSIDRDNKH 152
SP + ++ + +
Sbjct: 70 IPVSPEDGGANFVEDNEEV 88
>gnl|CDD|179402 PRK02265, PRK02265, acetoacetate decarboxylase; Provisional.
Length = 246
Score = 26.8 bits (60), Expect = 4.6
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 2 SYGRPPPRI---EGMVSLKVDNLTYRTTPDDLRRV 33
+Y P R E + +TYRT PD LR V
Sbjct: 19 AYPPGPYRFVNREYL------IITYRTDPDALRAV 47
>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast
sporulation-specific protein 2 (Ssp2) and similar
protein. This subfamily corresponds to the RRM of the
lineage specific yeast sporulation-specific protein 2
(Ssp2) and similar proteins. Ssp2 is encoded by a
sporulation-specific gene necessary for outer spore
wall assembly in the yeast Saccharomyces cerevisiae. It
localizes to the spore wall and may play an important
role after meiosis II and during spore wall formation.
Ssp2 contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 25.8 bits (57), Expect = 4.6
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 29 DLRRVFERCGEVGDIYIPRDRFTRESRGFAF-VRFFDKRDAEDALDAMDGR 78
+L+ F GE+ DI SR + F D R A A + ++ +
Sbjct: 10 ELKDDFTVFGEIVDISPI------ISRKLCVSIFFADIRSAIRAKETLEDK 54
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 27.0 bits (59), Expect = 4.7
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 59 FVRFFDKRDAEDALDAMDGRMLDGRELRVQMARYG 93
++ + K DA + +DG +LDGR L+ A YG
Sbjct: 169 YITYSTKEDAARCIAEVDGSLLDGRVLK---ATYG 200
>gnl|CDD|218612 pfam05501, DUF755, Domain of unknown function (DUF755). This
family is predominated by ORFs from Circoviridae. The
function of this family remains to be determined.
Length = 122
Score = 26.2 bits (58), Expect = 4.7
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 97 SSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKS 137
+SR R ++ ++ R R + S S SS S S S+S
Sbjct: 81 KRKKSRHVSSRSAKKISAKKRRRSSSSSSSSSSSSSSSSES 121
>gnl|CDD|223692 COG0619, CbiQ, ABC-type cobalt transport system, permease component
CbiQ and related transporters [Inorganic ion transport
and metabolism].
Length = 252
Score = 26.9 bits (60), Expect = 5.1
Identities = 22/106 (20%), Positives = 32/106 (30%), Gaps = 37/106 (34%)
Query: 21 LTYRTTPDDLRRVFERCG----EVGDI------YIP--RDRFTR-----ESRGF------ 57
LT T P +L ER E+ + +IP + R +RG
Sbjct: 121 LTLTTPPLELTSALERLLVPLVELALLLSLALRFIPLLLEELQRIRRAQRARGLDLSSGK 180
Query: 58 ------------AFVRFFDKRDAEDALDAMDGRMLDGRELRVQMAR 91
+R R AE+ AM+ R G + R
Sbjct: 181 RRIKSLGALIIPLLIRSL--RRAEELAIAMEARGFRGNKRRTSYRE 224
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 27.1 bits (60), Expect = 5.2
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGR-ELRVQMAR 91
F +R + R+ ED L +L+GR EL + R
Sbjct: 165 FVLMARVYK--HMAAARETEDKLQNDYQTILEGRKELTLNRER 205
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed
RNA-binding motif, single-stranded-interacting protein
4, an RNA-binding protein that is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. For instance, DND1
binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and
cell cycle regulator and tumor suppressor, LATS2 (large
tumor suppressor, homolog 2 of Drosophila). It helps
maintain their protein expression through blocking the
inhibitory function of microRNAs (miRNA) from these
transcripts. DND1 may also impose another level of
translational regulation to modulate expression of
critical factors in embryonic stem (ES) cells. DND1
interacts specifically with apolipoprotein B editing
complex 3 (APOBEC3), a multi-functional protein
inhibiting retroviral replication. The DND1-APOBEC3
interaction may play a role in maintaining viability of
germ cells and for preventing germ cell tumor
development. DND1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 78
Score = 25.5 bits (56), Expect = 5.7
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 50 FTRESRGFAFVRFFDKRDAEDALDAMDG-RMLDGRELRV 87
F+ +RGFA+ ++ D+R A A+ + + +G L V
Sbjct: 37 FSGLNRGFAYAKYSDRRGASAAIATLHNYELPEGCCLLV 75
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 25.6 bits (57), Expect = 5.7
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 54 SRGFAFVRFFDKRDAEDALDAM 75
S+G+ FV F + E AL A+
Sbjct: 56 SKGYGFVEF---TNHEHALKAL 74
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 25.4 bits (55), Expect = 5.9
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 26 TPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDA 74
T D+R + G + ++ + R++ + +SRGFAFV F +DA ++A
Sbjct: 15 TETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEA 64
>gnl|CDD|222340 pfam13718, GNAT_acetyltr_2, GNAT acetyltransferase 2. This
domain has N-acetyltransferase activity. It has a
GCN5-related N-acetyltransferase (GNAT) fold.
Length = 169
Score = 26.3 bits (59), Expect = 6.1
Identities = 6/10 (60%), Positives = 9/10 (90%)
Query: 23 YRTTPDDLRR 32
YRT+P+DL+
Sbjct: 11 YRTSPNDLQL 20
>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subgroup corresponds to the RRM2 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, an essential splicing
regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 25.3 bits (55), Expect = 6.4
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAM 75
L V+NL+ R + DL+ + GEV ++R + F D + AL+ +
Sbjct: 3 LIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERANE-----GVIEFRSYSDMKRALEKL 57
Query: 76 DGRMLDGRELRV 87
DG ++GR++R+
Sbjct: 58 DGTEINGRKIRL 69
>gnl|CDD|202795 pfam03880, DbpA, DbpA RNA binding domain. This RNA binding
domain is found at the C-terminus of a number of DEAD
helicase proteins. It is sufficient to confer
specificity for hairpin 92 of 23S rRNA, which is part
of the ribosomal A-site. However, several members of
this family lack specificity for 23S rRNA. These can
proteins can generally be distinguished by a basic
region that extends beyond this domain [Karl Kossen,
unpublished data].
Length = 74
Score = 25.1 bits (56), Expect = 7.3
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 38 GEVGDIYIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRV 87
++G I I D F+ F V + A+ L A+ + GR+L++
Sbjct: 31 DDIGKIDI-FDNFS-----FVEV---PEDMADKVLKALKKGKIKGRKLKI 71
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM1 of RBM5, also termed protein
G15, or putative tumor suppressor LUCA15, or renal
carcinoma antigen NY-REN-9, a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor. RBM5 shows high sequence
similarity to RNA-binding protein 6 (RBM6 or NY-LU-12
or g16 or DEF-3). Both, RBM5 and RBM6, specifically
bind poly(G) RNA. They contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), two C2H2-type zinc
fingers, a nuclear localization signal, and a
G-patch/D111 domain. .
Length = 87
Score = 25.3 bits (55), Expect = 7.8
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 49 RFTRESRGFAFVRFFDKRDAEDALDA 74
R T SRGFAFV F+ +DA ++A
Sbjct: 42 RKTGVSRGFAFVEFYHLQDATSWMEA 67
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 26.4 bits (58), Expect = 7.8
Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 4/65 (6%)
Query: 94 RPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHE 153
PSS S + + + R S SS S S + ++S S + K E
Sbjct: 805 PSPSSPLS----SSSPKPEHPSRKRPRRQEDTSSSSGPFSASSTKSSSKSSSTSKHRKTE 860
Query: 154 RNGRS 158
G S
Sbjct: 861 GKGSS 865
>gnl|CDD|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM1 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 70
Score = 24.9 bits (54), Expect = 8.1
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 37 CGEVGDI---YIPRDRFTRESRGFAFVRFFDKRDAEDALDAMDGRMLDGRELRVQM 89
EV D+ Y + + ++ AFV + A+DA+ + G+++ VQ+
Sbjct: 13 NQEVHDLLKDYELKYCYVDRNKRTAFVTLLNGEQAQDAIRTFHQTSVRGKDINVQL 68
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 26.3 bits (58), Expect = 8.5
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 81 DGRELRVQMARYGRPPSSSRSRGGRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRK 140
+ RE + R G+P + + R R R D Y + + + PR
Sbjct: 4 NDRE---PIGRKGKPSRPVKQKVSR-RRYRDDDDYDDYDDYEDEEPMPRKGKGKGRKPRG 59
Query: 141 AR 142
R
Sbjct: 60 KR 61
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 26.3 bits (58), Expect = 9.7
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 104 GRDRDRRRDRSRSRDRRYTRSRSFSSRSRSGSKSPRKARSKSIDRDNKHERNGR 157
GR R + R RS+SR R RS + SR+ + NK++ N R
Sbjct: 17 GRSRSKSRARSQSRGRG--RSVKITVNSRNKGRRQN--------GRNKYQSNQR 60
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
0.321 0.136 0.396
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: 8,384,676
Number of extensions: 788651
Number of successful extensions: 2382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1838
Number of HSP's successfully gapped: 582
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.1 bits)