RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16913
(81 letters)
>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 = 106 bits (266), Expect = 3e-32
Identities = 52/70 (74%), Positives = 54/70 (77%), Gaps = 14/70 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MFLPFGNVIS+KVF+DRATNQSKCFG FVSFDNPASA AIQAMNGF
Sbjct: 24 MFLPFGNVISAKVFVDRATNQSKCFG--------------FVSFDNPASAQAAIQAMNGF 69
Query: 61 QIGMKRLKVQ 70
QIGMKRLKVQ
Sbjct: 70 QIGMKRLKVQ 79
>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 = 102 bits (254), Expect = 2e-30
Identities = 51/80 (63%), Positives = 59/80 (73%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF+PFGNV+S+KVFID+ TN SKCFG FVS+DNP SA AIQAMNGF
Sbjct: 27 MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQAMNGF 72
Query: 61 QIGMKRLKVQLKRPKDAARP 80
QIGMKRLKVQLKR K+ ++P
Sbjct: 73 QIGMKRLKVQLKRSKNDSKP 92
>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 = 99.2 bits (248), Expect = 2e-29
Identities = 42/70 (60%), Positives = 49/70 (70%), Gaps = 14/70 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFGNVIS+KVF+D+ T QSKCFG FVS+DNP SA AI+AMNGF
Sbjct: 18 LFAPFGNVISAKVFVDKNTGQSKCFG--------------FVSYDNPESAQAAIKAMNGF 63
Query: 61 QIGMKRLKVQ 70
Q+G KRLKVQ
Sbjct: 64 QVGGKRLKVQ 73
>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 = 86.6 bits (214), Expect = 3e-24
Identities = 46/69 (66%), Positives = 49/69 (71%), Gaps = 14/69 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
FLPFGNVIS+KVFID+ TN SKCFG FVS+DNP SA AIQAMNGFQ
Sbjct: 25 FLPFGNVISAKVFIDKQTNLSKCFG--------------FVSYDNPDSAQAAIQAMNGFQ 70
Query: 62 IGMKRLKVQ 70
IG KRLKVQ
Sbjct: 71 IGTKRLKVQ 79
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 54.5 bits (132), Expect = 7e-12
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG V S ++ D+ T +SK F FV F++ A A++A+NG
Sbjct: 19 LFSKFGKVESVRLVRDKETGKSKGFA--------------FVEFESEEDAEKALEALNGK 64
Query: 61 QIGMKRLKV 69
++ + LKV
Sbjct: 65 ELDGRPLKV 73
>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 = 54.3 bits (131), Expect = 1e-11
Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ DR T QS +G FV + + A AI +NGF
Sbjct: 20 LFEAIGPIESCKIVRDRITGQSLGYG--------------FVDYVDENDAQKAINTLNGF 65
Query: 61 QIGMKRLKV 69
+I KRLKV
Sbjct: 66 EIRNKRLKV 74
>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 = 51.9 bits (125), Expect = 1e-10
Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 16/63 (25%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN--GFQ 61
PFG +IS+K +D+ TN KC K +GFV FD+P +A AI+ +N G Q
Sbjct: 23 PFGKIISTKAILDKKTN--KC------------KGYGFVDFDSPEAALKAIEGLNGRGVQ 68
Query: 62 IGM 64
Sbjct: 69 AQF 71
>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 = 51.8 bits (125), Expect = 1e-10
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 14/73 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V S++V DR T +S+ G FGFV + A+ AI+ +NG
Sbjct: 20 FGQFGEVTSARVITDRETGRSR--G------------FGFVEMETAEEANAAIEKLNGTD 65
Query: 62 IGMKRLKVQLKRP 74
G + L V RP
Sbjct: 66 FGGRTLTVNEARP 78
>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 = 50.9 bits (122), Expect = 3e-10
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+FL G V + K+ D+ T S +G FGFV + + A AI+ +NG
Sbjct: 20 LFLAVGPVKNCKIVRDKRTGYS--YG------------FGFVDYQSAEDAQRAIRTLNGL 65
Query: 61 QIGMKRLKVQLKRP 74
Q+ KR+KV RP
Sbjct: 66 QLQNKRIKVAYARP 79
>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 = 50.2 bits (121), Expect = 4e-10
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 15/69 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FGN++S KV D SK G +GFV F+ +A AI+ +NG
Sbjct: 22 TFSAFGNILSCKVATD-ENGGSK--G------------YGFVHFETEEAAVRAIEKVNGM 66
Query: 61 QIGMKRLKV 69
+ K++ V
Sbjct: 67 LLNDKKVFV 75
>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 = 52.9 bits (127), Expect = 8e-10
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 15/79 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S+KV +D S+ FG FV F NP A+ A+ M+G
Sbjct: 305 LFSECGEITSAKVMLD-EKGVSRGFG--------------FVCFSNPEEANRAVTEMHGR 349
Query: 61 QIGMKRLKVQLKRPKDAAR 79
+G K L V L + K+ R
Sbjct: 350 MLGGKPLYVALAQRKEQRR 368
Score = 42.9 bits (101), Expect = 2e-06
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FGN++S KV AT++ G+ + +GFV F+ SA AIQ +NG
Sbjct: 108 TFSKFGNILSCKV----ATDE---NGK--------SRGYGFVHFEKEESAKAAIQKVNGM 152
Query: 61 QIGMKRLKVQLKRPK 75
+ K + V K
Sbjct: 153 LLNDKEVYVGRFIKK 167
Score = 40.2 bits (94), Expect = 2e-05
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 19/79 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG + S+ V D + + F FV+F+ A A++ MNG +
Sbjct: 199 FAKFGEITSAAVMKDGSGRS---------------RGFAFVNFEKHEDAAKAVEEMNGKK 243
Query: 62 IGM----KRLKVQLKRPKD 76
IG+ K+L V + +
Sbjct: 244 IGLAKEGKKLYVGRAQKRA 262
Score = 37.9 bits (88), Expect = 1e-04
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG V+S +V D T +S +G +V+F NPA A A++ MN +
Sbjct: 21 FKPFGPVLSVRVCRDSVTRRSLGYG--------------YVNFQNPADAERALETMNFKR 66
Query: 62 IGMKRLKV 69
+G K +++
Sbjct: 67 LGGKPIRI 74
>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 = 46.1 bits (110), Expect = 2e-08
Identities = 27/71 (38%), Positives = 32/71 (45%), Gaps = 15/71 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F PFG + S+KV D +SK FG FV F +P A A+ MNG
Sbjct: 21 EFSPFGTITSAKVMTD-EKGRSKGFG--------------FVCFSSPEEATKAVTEMNGR 65
Query: 61 QIGMKRLKVQL 71
IG K L V L
Sbjct: 66 IIGGKPLYVAL 76
>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 = 45.4 bits (108), Expect = 3e-08
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 15/70 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + S ++ D+ K F FV F++P A A++A+NG
Sbjct: 18 LFSKFGEIESVRIVRDK---------------DGKSKGFAFVEFESPEDAEKALEALNGK 62
Query: 61 QIGMKRLKVQ 70
++ ++LKV
Sbjct: 63 ELDGRKLKVS 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 = 45.5 bits (108), Expect = 3e-08
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 14/70 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V+ ++V DR T +S+ FG +V F++P A AI+AM+G +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFG--------------YVDFESPEDAKKAIEAMDGKE 65
Query: 62 IGMKRLKVQL 71
+ + + V
Sbjct: 66 LDGRPINVDF 75
>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 = 45.0 bits (107), Expect = 5e-08
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 14/72 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG V + KV D TN KC K +GFV+ N A++AI ++NG+
Sbjct: 21 LFSPFGAVTNVKVIRDLTTN--KC------------KGYGFVTMTNYEEAYSAIASLNGY 66
Query: 61 QIGMKRLKVQLK 72
++G + L+V K
Sbjct: 67 RLGGRVLQVSFK 78
>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 = 44.7 bits (106), Expect = 7e-08
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 14/67 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D T +SK +G FVSF A AIQ+MNG
Sbjct: 20 FAPFGEISDARVVKDMQTGKSKGYG--------------FVSFVKKEDAENAIQSMNGQW 65
Query: 62 IGMKRLK 68
+G + ++
Sbjct: 66 LGGRAIR 72
>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 = 44.6 bits (106), Expect = 8e-08
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++ D T +SK +G F+ F + A A++ +NGF+
Sbjct: 19 FEPFGEIEFVQLQRDPETGRSKGYG--------------FIQFADAEDAKKALEQLNGFE 64
Query: 62 IGMKRLKV 69
+ + +KV
Sbjct: 65 LAGRPIKV 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 = 44.5 bits (106), Expect = 9e-08
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V + D T +S+ G FGFV+F++ A AI+ +NG +
Sbjct: 22 FSKFGRVEEVLLMKDPETGESR--G------------FGFVTFESVEDADAAIRDLNGKE 67
Query: 62 IGMKRLKVQLKR 73
+ + +KV+ +
Sbjct: 68 LEGRVIKVEKAK 79
>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 = 46.5 bits (110), Expect = 1e-07
Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG V + K+ D TNQ C K +GFVS N A AI ++NG+
Sbjct: 289 LFGPFGAVQNVKIIRDLTTNQ------C--------KGYGFVSMTNYDEAAMAILSLNGY 334
Query: 61 QIGMKRLKVQLKRPK 75
+G + L+V K K
Sbjct: 335 TLGNRVLQVSFKTNK 349
Score = 39.2 bits (91), Expect = 5e-05
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS G +GFV++ P A A+ ++NG
Sbjct: 23 LFTSIGEIESCKLVRDKVTGQS--LG------------YGFVNYVRPEDAEKAVNSLNGL 68
Query: 61 QIGMKRLKVQLKRPKDAA 78
++ K +KV RP +
Sbjct: 69 RLQNKTIKVSYARPSSDS 86
Score = 37.2 bits (86), Expect = 2e-04
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F PFG +I+S++ D T S K GF+ FD A AI+ +NG
Sbjct: 109 IFSPFGQIITSRILSDNVTGLS--------------KGVGFIRFDKRDEADRAIKTLNG 153
>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 = 43.4 bits (103), Expect = 2e-07
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 15/68 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + S ++ D T +SK F FV F++ A A++A+NG
Sbjct: 18 LFSKFGPIESIRIVRD-ETGRSKGFA--------------FVEFEDEEDAEKALEALNGK 62
Query: 61 QIGMKRLK 68
++G + L+
Sbjct: 63 ELGGRELR 70
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 42.9 bits (102), Expect = 3e-07
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + S+KV D K FGFV+F+N +A A++ +NG
Sbjct: 21 LFGKYGKITSAKVMKDD---------------EGKSKGFGFVNFENHEAAQKAVEELNGK 65
Query: 61 QIGMKRLKV 69
++ K+L V
Sbjct: 66 EVNGKKLYV 74
>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 = 43.1 bits (101), Expect = 3e-07
Identities = 30/75 (40%), Positives = 38/75 (50%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF PFG V + KV D TN KC G FGFV+ N A AI ++NG+
Sbjct: 21 MFGPFGAVTNVKVIRDFNTN--KCKG------------FGFVTMTNYEEAAMAIASLNGY 66
Query: 61 QIGMKRLKVQLKRPK 75
++G K L+V K K
Sbjct: 67 RLGDKILQVSFKTSK 81
>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 = 43.2 bits (102), Expect = 3e-07
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS G +GFV++ +P A AI +NG
Sbjct: 21 LFSSIGEIESCKLIRDKVTGQS--LG------------YGFVNYVDPEDAEKAINTLNGL 66
Query: 61 QIGMKRLKV 69
++ K +KV
Sbjct: 67 RLQNKTIKV 75
>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 = 42.6 bits (101), Expect = 4e-07
Identities = 15/33 (45%), Positives = 24/33 (72%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +GF+ ++NP SA AI +MN F +G ++L+V
Sbjct: 42 KGYGFIEYENPQSAQDAIASMNLFDLGGQQLRV 74
>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 = 42.8 bits (100), Expect = 5e-07
Identities = 29/75 (38%), Positives = 38/75 (50%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF PFG V + KV D TN KC G FGFV+ N A AI ++NG+
Sbjct: 23 MFGPFGAVTNVKVIRDFNTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 68
Query: 61 QIGMKRLKVQLKRPK 75
++G + L+V K K
Sbjct: 69 RLGDRVLQVSFKTNK 83
>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 = 42.5 bits (99), Expect = 6e-07
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 14/71 (19%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
P+G ++S+K +D+ TN KC G +GFV FD+PA+A A+ A+ +
Sbjct: 30 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPAAAQKAVSALKASGVQ 75
Query: 64 MKRLKVQLKRP 74
+ K Q + P
Sbjct: 76 AQMAKQQEQDP 86
>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 = 42.4 bits (99), Expect = 6e-07
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG V + KV D TN KC G FGFV+ N A AI ++NG+
Sbjct: 21 LFGPFGAVTNVKVIRDFTTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 66
Query: 61 QIGMKRLKVQLKRPK 75
++G + L+V K K
Sbjct: 67 RLGDRVLQVSFKTSK 81
>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 = 42.1 bits (99), Expect = 7e-07
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + V DR T +S+ FG FV+F+NP A A+ AMNG
Sbjct: 21 FSKYGQISEVVVVKDRETQRSRGFG--------------FVTFENPDDAKDAMMAMNGKS 66
Query: 62 IGMKRLKV 69
+ ++++V
Sbjct: 67 VDGRQIRV 74
>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 = 41.8 bits (99), Expect = 9e-07
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 18/62 (29%)
Query: 1 MFLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
+F PFG + S+V++ D+ T QS+ F FV+F A AI+ +N
Sbjct: 19 LFRPFGPI--SRVYLAKDKETGQSRGFA--------------FVTFHTREDAERAIEKLN 62
Query: 59 GF 60
GF
Sbjct: 63 GF 64
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 42.7 bits (100), Expect = 1e-06
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 14/77 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG+V+ +KV +DR T +S+ FG FV+F++ +A AI M+G +
Sbjct: 55 FAHFGDVVDAKVIVDRETGRSRGFG--------------FVNFNDEGAATAAISEMDGKE 100
Query: 62 IGMKRLKVQLKRPKDAA 78
+ + ++V + +A
Sbjct: 101 LNGRHIRVNPANDRPSA 117
>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 = 40.9 bits (95), Expect = 3e-06
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 16/65 (24%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQ 61
P+G ++S+K +D+ TN KC G +GFV FD+P++A A+ A+ +G Q
Sbjct: 24 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPSAAQKAVTALKASGVQ 69
Query: 62 IGMKR 66
M +
Sbjct: 70 AQMAK 74
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic
RNA-binding protein 25 and similar proteins. This
subfamily corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or
protein S164, or RNA-binding region-containing protein
7, an evolutionary-conserved splicing coactivator
SRm160 (SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif.
It localizes to the nuclear speckles and associates
with multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors.
It can activate proapoptotic Bcl-xS 5'ss by binding to
the exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 40.7 bits (96), Expect = 3e-06
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FGF F++P A A++ +NG ++G K+L V+
Sbjct: 44 FGFCEFEDPEGALRALRLLNGLELGGKKLLVK 75
>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 = 40.4 bits (95), Expect = 3e-06
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 14/61 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F P+G +I+S++ D T S R V GF+ FD A AI+A+NG
Sbjct: 20 LFSPYGRIITSRILCDNVTGLS-------RGV-------GFIRFDKRIEAERAIKALNGT 65
Query: 61 Q 61
Sbjct: 66 I 66
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 41.9 bits (97), Expect = 6e-06
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 14/80 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG V ++ DR T +S+ F FV F++ SA AI+ +NG
Sbjct: 135 LFKKFGPVKRVRLVRDRETGKSRGFA--------------FVEFESEESAEKAIEELNGK 180
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++ + L+VQ +P R
Sbjct: 181 ELEGRPLRVQKAQPASQPRS 200
>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 = 39.7 bits (92), Expect = 9e-06
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 14/75 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG V + KV D TN KC G FGFV+ N A AI ++NG+
Sbjct: 23 LFGPFGAVNNVKVIRDFNTN--KCKG------------FGFVTMTNYDEAAMAIASLNGY 68
Query: 61 QIGMKRLKVQLKRPK 75
++G + L+V K K
Sbjct: 69 RLGDRVLQVSFKTNK 83
>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 = 1e-05
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+ FG + + + D AT SK G + F + +P+ AI +NG
Sbjct: 20 LLESFGKLKAFNLVKDSATGLSK--G------------YAFCEYLDPSVTDQAIAGLNGM 65
Query: 61 QIGMKRLKVQ 70
Q+G K+L VQ
Sbjct: 66 QLGDKKLTVQ 75
>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 = 38.8 bits (91), Expect = 1e-05
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 14/64 (21%)
Query: 6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK 65
G V+S ++ DR T + K +G F F++ +A +AI+ +NG++ +
Sbjct: 23 GPVVSFRLVTDRDTGKPKGYG--------------FCEFEDIETAASAIRNLNGYEFNGR 68
Query: 66 RLKV 69
L+V
Sbjct: 69 ALRV 72
>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 = 38.7 bits (91), Expect = 1e-05
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 14/58 (24%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
+G V + IDR N + G + +V F++P A AI+ M+G QI
Sbjct: 22 YGTVKDVDLPIDREVNLPR--G------------YAYVEFESPEDAEKAIKHMDGGQI 65
>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 = 38.6 bits (90), Expect = 2e-05
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S + D T + K F FV ++ P +A A++ MNG
Sbjct: 21 FSPFGPIKSIDMSWDPVTMK--------------HKGFAFVEYEVPEAAQLALEQMNGVM 66
Query: 62 IGMKRLKV 69
+G + +KV
Sbjct: 67 LGGRNIKV 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 = 38.4 bits (90), Expect = 2e-05
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 23 KCFGECNRKVSV---NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FG V V K GFV F + A+A AIQ + G IG R+++
Sbjct: 20 SLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLS 70
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 20/68 (29%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + +VF D K + FV FD +A TAI A+NG
Sbjct: 21 FSPFGAIEEVRVFKD--------------------KGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 62 IGMKRLKV 69
I + +K
Sbjct: 61 INGQTVKC 68
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It 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. RBMS3 contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 80
Score = 38.7 bits (89), Expect = 2e-05
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 14/67 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
P+G ++S+K +D+ TNQ K +GFV FD+PA+A A+ ++ +
Sbjct: 27 PYGKIVSTKAILDKNTNQC--------------KGYGFVDFDSPAAAQKAVASLKANGVQ 72
Query: 64 MKRLKVQ 70
+ K Q
Sbjct: 73 AQMAKQQ 79
>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 = 37.6 bits (88), Expect = 3e-05
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ P A AI MN +
Sbjct: 19 FIPFGDIKDIQIPLDYETQK--------------HRGFAFVEFEEPEDAAAAIDNMNESE 64
Query: 62 IGMKRLKV 69
+ + ++V
Sbjct: 65 LFGRTIRV 72
>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 = 37.7 bits (88), Expect = 4e-05
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 2 FLPFGNVISS-KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG ++ + K+ D T SK F F+S+D+ ++ AI+AMNG
Sbjct: 22 FSAFGVILQTPKIMRDPDTGNSKGFA--------------FISYDSFEASDAAIEAMNGQ 67
Query: 61 QIGMKRLKVQLKRPKD 76
+ + + V KD
Sbjct: 68 YLCNRPITVSYAFKKD 83
>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 = 37.8 bits (87), Expect = 4e-05
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS G +GFV++ +P A AI +NG
Sbjct: 24 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYIDPKDAEKAINTLNGL 69
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 70 RLQTKTIKVSYARP 83
>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 = 37.7 bits (88), Expect = 5e-05
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 14/76 (18%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHT----AIQAM 57
F PFG + S++ +D T QS G C V F P++AH A+ +
Sbjct: 19 FRPFGEIEESELKLDPRTGQS--LGIC----RV---TFR-GDPLRPSAAHEAAKAAVDGL 68
Query: 58 NGFQIGMKRLKVQLKR 73
NG +IG KR++V+L R
Sbjct: 69 NGRRIGGKRVRVELDR 84
>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 = 36.7 bits (86), Expect = 5e-05
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 24 CFGECNR-KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
FG + K+ + F FV F +A A+Q +NG G + L+V
Sbjct: 7 PFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
>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 = 37.4 bits (86), Expect = 6e-05
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS G +GFV++ +P A AI +NG
Sbjct: 23 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYVDPNDADKAINTLNGL 68
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 69 KLQTKTIKVSYARP 82
>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 = 36.9 bits (86), Expect = 7e-05
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 20/72 (27%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFGN+I+ + +++ N GFV+F+ SA AI +NG
Sbjct: 23 FSPFGNIIN--ISMEKEKNC------------------GFVTFEKMESADRAIAELNGTT 62
Query: 62 IGMKRLKVQLKR 73
+ +LKV L R
Sbjct: 63 VQGVQLKVSLAR 74
>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 = 36.4 bits (85), Expect = 8e-05
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
F FV F++P A A++A++G +I R++V+L R
Sbjct: 38 FAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73
>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 = 37.0 bits (85), Expect = 9e-05
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 14/67 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AIQ M G
Sbjct: 22 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 67
Query: 62 IGMKRLK 68
+G ++++
Sbjct: 68 LGGRQIR 74
>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 = 36.6 bits (84), Expect = 1e-04
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS G +GFV++ +P A AI +NG
Sbjct: 22 LFGSIGEIESCKLVRDKITGQS--LG------------YGFVNYIDPKDAEKAINTLNGL 67
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 68 RLQTKTIKVSYARP 81
>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 = 36.4 bits (85), Expect = 1e-04
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F +G + +V D+ T +S+ FG FV F++ A A + +NG +
Sbjct: 20 FSRYGPIEKVQVVYDQKTGRSRGFG--------------FVYFESVEDAKEAKERLNGME 65
Query: 62 IGMKRLKV 69
I +R++V
Sbjct: 66 IDGRRIRV 73
>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 = 36.5 bits (84), Expect = 1e-04
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
MF FG +I+S+V +D+AT S R V+ F+ FD + A AI + NG
Sbjct: 20 MFSRFGRIINSRVLVDQATGLS-------RGVA-------FIRFDKRSEAEEAITSFNG 64
>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 = 36.1 bits (84), Expect = 1e-04
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG + S +V D+ T S + F+ F+ A M+
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDS--------------LQYAFIEFETKEDCEEAYFKMDNVL 69
Query: 62 IGMKRLKV 69
I +R+ V
Sbjct: 70 IDDRRIHV 77
>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 = 35.8 bits (83), Expect = 2e-04
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 16/70 (22%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + V D+ T +SK G +V F +SA A++ MNG
Sbjct: 23 FAPFGEIQDIWVVKDKQTKESK--GVA------------YVKFAKASSAARAMEEMNGKC 68
Query: 62 IG--MKRLKV 69
+G K LKV
Sbjct: 69 LGGDTKPLKV 78
>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 = 35.8 bits (82), Expect = 2e-04
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V S+K+ D KV+ + +GFV++ N A AI +NG
Sbjct: 21 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVNAKDAERAINTLNGL 66
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 67 RLQSKTIKVSYARP 80
>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 = 35.3 bits (82), Expect = 2e-04
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 15/69 (21%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F GNV+ + V D N S K FG V F++P A AI+ NG+
Sbjct: 18 LFRECGNVLRADVKTD------------NDGRS---KGFGTVLFESPEDAQRAIEMFNGY 62
Query: 61 QIGMKRLKV 69
+ + L+V
Sbjct: 63 DLEGRELEV 71
>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 = 35.3 bits (82), Expect = 2e-04
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F+ A A++ MNG ++ ++V L +P
Sbjct: 37 YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72
>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 = 37.2 bits (86), Expect = 3e-04
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 14/67 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
FG++ + + D AT SK + F + +P+ AI A+NG G
Sbjct: 318 SFGDLKAFNLIKDIATGLSKGYA--------------FCEYKDPSVTDVAIAALNGKDTG 363
Query: 64 MKRLKVQ 70
+L VQ
Sbjct: 364 DNKLHVQ 370
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 35.4 bits (82), Expect = 3e-04
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+ FV + + SA A+Q MNG I + +KV
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQEIKV 69
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 35.0 bits (81), Expect = 3e-04
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 16/62 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-- 59
F FG + + +D+ T +SK F FVSF P A A ++G
Sbjct: 20 FEAFGEISEVHLPLDKETKRSKGFA--------------FVSFMFPEHAVKAYSELDGSI 65
Query: 60 FQ 61
FQ
Sbjct: 66 FQ 67
>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 = 35.1 bits (81), Expect = 4e-04
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
F +F +P A T ++A+NG++I +RL+V+ KR
Sbjct: 47 FANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 35.2 bits (82), Expect = 4e-04
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 16/60 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSK-CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +GN+ + D+ T QSK C FV F + A AI+A++G
Sbjct: 19 LFEEYGNIEEVTIIRDKDTGQSKGC---------------AFVKFSSREEAQKAIEALHG 63
>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 = 35.2 bits (81), Expect = 4e-04
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 31 KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
K + N K +GF+ F NP A A ++MN + + K L+V
Sbjct: 35 KKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVH 74
>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 = 35.0 bits (81), Expect = 4e-04
Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V+ +K+ + + + +CFGFV+ + A IQ ++
Sbjct: 19 LFSKYGKVVGAKIVTNARSPGA--------------RCFGFVTMASVEEAAKCIQHLHRT 64
Query: 61 QIGMKRLKVQ 70
++ + + V+
Sbjct: 65 ELHGRVISVE 74
>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 = 34.8 bits (81), Expect = 5e-04
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 14/57 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
F P G V+S +V D T +S G + +V+F NPA A A+ +N
Sbjct: 20 FSPAGPVLSIRVCRDLITRRS--LG------------YAYVNFQNPADAERALDTLN 62
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 36.4 bits (84), Expect = 5e-04
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG++ ++ D T +SK FG F+ F + A A++ MNGF
Sbjct: 206 IFEPFGDIEDVQLHRDPETGRSKGFG--------------FIQFHDAEEAKEALEVMNGF 251
Query: 61 QIGMKRLKV 69
++ + +KV
Sbjct: 252 ELAGRPIKV 260
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 34.6 bits (80), Expect = 6e-04
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
K F FV+F + S AIQ +NG ++ + L+++
Sbjct: 40 KPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75
>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 = 34.6 bits (79), Expect = 6e-04
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 14/71 (19%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
F I++++ DR T SK FG FV F + A A +AM +I
Sbjct: 21 FDGSIAARIVTDRDTGSSKGFG--------------FVDFSSEEDAKAAKEAMEDGEIDG 66
Query: 65 KRLKVQLKRPK 75
++ + +PK
Sbjct: 67 NKVTLDFAKPK 77
>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 = 34.2 bits (79), Expect = 6e-04
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +G+ + + SA AI ++G ++ +LKV
Sbjct: 35 KNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67
>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 = 34.6 bits (80), Expect = 6e-04
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 14/65 (21%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
+ +V +KV +D T +SK +G FV F + A+ MNG
Sbjct: 26 YPSVRGAKVVMDPVTGRSKGYG--------------FVRFGDEDERDRALTEMNGVYCSS 71
Query: 65 KRLKV 69
+ ++V
Sbjct: 72 RPMRV 76
>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 = 34.3 bits (79), Expect = 7e-04
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 17/72 (23%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG V+ +++ D T +S + FGFV+FD+ ++ + + +
Sbjct: 20 FSQFGKVVDAQLMQDHDTGRS--------------RGFGFVTFDSESAVE-RVFSAGMLE 64
Query: 62 IGMKRLKVQLKR 73
+G K +V++KR
Sbjct: 65 LGGK--QVEVKR 74
>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 = 34.2 bits (79), Expect = 9e-04
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 14/55 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
F +GNV S ++ D+ T + ++ F FV+FD+ +
Sbjct: 20 FSQYGNVESVEIVTDKETGK--------------KRGFAFVTFDDYDPVDKIVLQ 60
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 34.3 bits (78), Expect = 9e-04
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 14/67 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AI M G
Sbjct: 22 FAPFGKISDARVVKDMATGKSKGYG--------------FVSFYNKLDAENAIVHMGGQW 67
Query: 62 IGMKRLK 68
+G ++++
Sbjct: 68 LGGRQIR 74
>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 = 34.1 bits (79), Expect = 0.001
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 14/69 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F + + +KV D+ T +SK +G FVSF +P A++ MNG
Sbjct: 27 FSKYPSFQKAKVVRDKRTGKSKGYG--------------FVSFSDPNDYLKAMKEMNGKY 72
Query: 62 IGMKRLKVQ 70
+G + +K++
Sbjct: 73 VGNRPIKLR 81
>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 = 33.8 bits (78), Expect = 0.001
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
FGFV F++P A A+ +NG ++ +R+ V+ R
Sbjct: 35 FGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
>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 = 33.8 bits (78), Expect = 0.001
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 14/67 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
PFG V + +T +SK G +GFV + + ASA A ++G QIG
Sbjct: 22 PFGAVERCFLVYSESTGESK--G------------YGFVEYASKASALKAKNQLDGKQIG 67
Query: 64 MKRLKVQ 70
++L+V
Sbjct: 68 GRKLQVD 74
>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 = 35.0 bits (80), Expect = 0.001
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F + A + AI+ +NG + KRLKV RP
Sbjct: 151 YAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP 186
>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 = 35.0 bits (80), Expect = 0.001
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 14/79 (17%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S + D AT + K F FV ++ P +A A++ MNG
Sbjct: 128 FDPFGPIKSINMSWDPATGK--------------HKGFAFVEYEVPEAAQLALEQMNGQM 173
Query: 62 IGMKRLKVQLKRPKDAARP 80
+G + +KV A+P
Sbjct: 174 LGGRNIKVGRPSNMPQAQP 192
Score = 31.2 bits (70), Expect = 0.035
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +GF+ ++N S AI +MN F +G + L+V
Sbjct: 245 HKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278
Score = 25.8 bits (56), Expect = 2.6
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
FV F + A A++G G + + +
Sbjct: 569 FVEFSDSMEVDRAKAALDGRFFGGRTVVAEA 599
>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 = 33.3 bits (77), Expect = 0.001
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 14/55 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
F +G V+ + D T +S+ G FGFV+F +P+S + A
Sbjct: 19 FSKYGEVVDCVIMKDPITGRSR--G------------FGFVTFADPSSVDKVLAA 59
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 33.5 bits (77), Expect = 0.002
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
K +V ++N +SA A+ M+G +I K + V + P
Sbjct: 43 KGLAYVEYENESSASQAVLKMDGTEIKEKTISVAISNP 80
>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 = 33.5 bits (77), Expect = 0.002
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 18/70 (25%)
Query: 1 MFLPFGNVISSK-VFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
MF FG ++ + +F +R + K FGFV+F N A A A + ++G
Sbjct: 20 MFGQFGPILDVEIIFNERGS-----------------KGFGFVTFANSADADRAREKLHG 62
Query: 60 FQIGMKRLKV 69
+ ++++V
Sbjct: 63 TVVEGRKIEV 72
>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 = 33.3 bits (77), Expect = 0.002
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
+ FGFV F + A A++ N I ++ V+L
Sbjct: 41 RRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVEL 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 = 33.1 bits (76), Expect = 0.002
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
F FV F++P A A++ +G+ RL+V+
Sbjct: 40 FAFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 72
>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 = 32.9 bits (76), Expect = 0.003
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 25 FGECNRKVSV--------NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
F + +S+ + F +V F +P SA A+ +NG +L V++ P
Sbjct: 21 FEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVKISDP 78
>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 = 32.6 bits (75), Expect = 0.003
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +GFV FDN A A+ NG +I ++L +
Sbjct: 35 KGYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67
>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 = 32.9 bits (75), Expect = 0.003
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
FGFV F A A++AM+GF + L V+
Sbjct: 49 FGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83
>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 = 32.7 bits (75), Expect = 0.003
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 8 VISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRL 67
V S K F +A +SK G +V F + A+A + + G + K+
Sbjct: 27 VKSIKFFEHKANGKSK--GFA------------YVEFASEAAAAAVKEKLEGREFNGKKC 72
Query: 68 KVQL 71
V
Sbjct: 73 VVTY 76
>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 = 32.5 bits (74), Expect = 0.004
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+GFV + A A+Q +NG QI ++V
Sbjct: 41 YGFVEYHQSHDAEIALQTLNGRQIENNEIRV 71
>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 = 32.5 bits (74), Expect = 0.004
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
F FV F++P A A+ NG+ G RL+V+
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVE 71
>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 = 32.3 bits (74), Expect = 0.005
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGM-KRLKV 69
K F +V++ NPASA A + +NGF+ RLKV
Sbjct: 41 KGFAYVTYSNPASAIYAKEKLNGFEYPPGNRLKV 74
>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 = 0.006
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 15/60 (25%)
Query: 12 KVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K++ D+ T GE V++D+P++A AI+ NG++ ++KV L
Sbjct: 37 KIYTDKETEPK---GEAT------------VTYDDPSAAQAAIEWFNGYEFRGNKIKVSL 81
>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 = 32.1 bits (73), Expect = 0.006
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 18/71 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM---- 57
F +G + V +D T +S+ FG F++F + A A++A
Sbjct: 23 FTRYGKLTECVVMVDPNTKRSRGFG--------------FITFSSADEADEAMEAQPHSI 68
Query: 58 NGFQIGMKRLK 68
+G QI +KR K
Sbjct: 69 DGNQIELKRAK 79
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 31.7 bits (73), Expect = 0.007
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FV F + SA A++A+ GF K +++Q
Sbjct: 46 FVVFKDVESATNALRALQGFPFYDKPMRIQ 75
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 31.8 bits (73), Expect = 0.007
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 29 NRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
++ +N F FV+F + +SA A+Q +NG ++G +++ V L
Sbjct: 38 EKQGRLN-NGFAFVTFKDASSAENALQ-LNGTELGGRKISVSL 78
>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 = 32.0 bits (73), Expect = 0.008
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
FV F P+ A AIQA+NG G +++K +L
Sbjct: 56 FVEFSLPSEAEKAIQALNGRWFGGRKVKAEL 86
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 31.4 bits (72), Expect = 0.009
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 16/68 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F P+G V ++ ++ + F FV F +P A A++ +NG
Sbjct: 18 FFSPYGKVEGVRLVRNKDRP----------------RGFAFVEFASPEDAEAALKKLNGL 61
Query: 61 QIGMKRLK 68
+ + L+
Sbjct: 62 VLDGRTLR 69
>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 = 31.5 bits (71), Expect = 0.009
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 25 FGECNRKVSVN-------QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
F EC + + K G V F++P A A + MNG+++ + + V++ R
Sbjct: 20 FNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRIDR 75
>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 = 31.3 bits (71), Expect = 0.009
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F F + ++V D + +S+ +G FVSF + A AI MNG
Sbjct: 20 FSAFPSCSDARVMWDMKSGRSRGYG--------------FVSFRSQQDAENAINEMNGKW 65
Query: 62 IGMKRLKV 69
+G + ++
Sbjct: 66 LGSRPIRC 73
>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 = 31.6 bits (71), Expect = 0.010
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ +D+ T S + GF+ FD A AI+ +NG
Sbjct: 22 LFSQYGRIITSRILVDQVTGVS--------------RGVGFIRFDKRIEAEEAIKGLNG 66
>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 = 31.4 bits (72), Expect = 0.010
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQI 62
+GFV F + +A A++ + G +
Sbjct: 49 YGFVEFKSKEAAQKALKRLQGTVL 72
>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 = 31.2 bits (70), Expect = 0.012
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
G V FD+P SA A + MNG +I + + V+L R
Sbjct: 42 GTVRFDSPESAEKACRLMNGIKINGREIDVRLDR 75
>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 = 31.1 bits (70), Expect = 0.013
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ +D+ T S+ G F+ FD A AI+ +NG
Sbjct: 21 LFSQYGRIITSRILVDQVTGISRGVG--------------FIRFDKRIEAEEAIKGLNG 65
>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 = 30.9 bits (70), Expect = 0.013
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 31 KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K+ + F+ F++ A AI+ +G+ +RL+V+L
Sbjct: 32 KLPPRPPGYAFIEFEDARDAEDAIRGRDGYDFDGQRLRVEL 72
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 31.0 bits (71), Expect = 0.017
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 13/55 (23%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+G V++ V + E + V + FV F + A A++A+NG
Sbjct: 30 YGKVLNVIVHEVAS-------SEADDAVRI------FVEFSDADEAIKAVRALNG 71
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 30.7 bits (70), Expect = 0.018
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
F +FDN +A A+ ++ +I KRL V+
Sbjct: 42 FATFDNEQAASQALSRLHQLKILGKRLVVE 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 = 30.6 bits (70), Expect = 0.019
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 31 KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+V+ + +GFV F + A AI+ MN ++ K ++V
Sbjct: 34 RVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 30.7 bits (69), Expect = 0.019
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ D+ T S R V GF+ FD A AI+ +NG
Sbjct: 20 LFSQYGRIITSRILRDQLTGVS-------RGV-------GFIRFDKRIEAEEAIKGLNG 64
>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 = 30.5 bits (69), Expect = 0.023
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
F FV F++P A A+ +G+ RL+V+ R
Sbjct: 39 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 73
>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 = 30.1 bits (68), Expect = 0.026
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+GFV FD+P S AI G I ++L +++ +P
Sbjct: 36 YGFVQFDSPESCANAINCEQGKMIRGRKLHLEVSKP 71
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 30.5 bits (68), Expect = 0.027
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ +D+ T S + GF+ FD A AI+ +NG
Sbjct: 25 LFSQYGRIITSRILVDQVTGVS--------------RGVGFIRFDKRIEAEEAIKGLNG 69
>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 = 30.3 bits (68), Expect = 0.027
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
++ FGFV FD+P A A+ ++G ++ +R+ ++ R
Sbjct: 32 KRGFGFVEFDDPRDADDAVYELDGKELCNERVTIEHAR 69
>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 = 30.2 bits (69), Expect = 0.027
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQI 62
K + FV F P A A++A+NG+++
Sbjct: 50 KGYAFVEFATPEEAKEAVKALNGYKL 75
>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 = 30.2 bits (69), Expect = 0.028
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 34 VNQKCFGFVSFDNPASAHTAIQAMNGFQI 62
V ++ FV F+ A A+QA+ GF+I
Sbjct: 35 VPRRGIAFVEFETEEQATVALQALQGFKI 63
>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 = 30.4 bits (69), Expect = 0.029
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQ-IGMKRLKVQLKRPK 75
N + +GFV F + + A+ M G +G K ++V L PK
Sbjct: 41 NSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIPK 82
>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 = 30.0 bits (68), Expect = 0.036
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 18/71 (25%)
Query: 2 FLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
F +G V V+I DR T +S+ F FV F + A A+ AM+G
Sbjct: 19 FEKYGEV--GDVYIPRDRYTRESRGFA--------------FVRFYDKRDAEDAMDAMDG 62
Query: 60 FQIGMKRLKVQ 70
++ + L+VQ
Sbjct: 63 KELDGRELRVQ 73
>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 = 29.9 bits (68), Expect = 0.043
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
F FV+F + A++ ++GF+ + L +L +P
Sbjct: 44 FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79
>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 = 29.8 bits (68), Expect = 0.046
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 41 FVSFDNPASAHTAIQAMNGFQI--GMKRLKVQLKRPKD 76
V FD+ SA A +A+NG I G L +Q R K+
Sbjct: 43 LVQFDSVESAENAKKALNGRNIYDGCCTLDIQFSRLKE 80
>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 = 29.6 bits (66), Expect = 0.049
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
+GFV FD+ A A+ +NG + +R+ V+
Sbjct: 35 YGFVEFDDLRDADDAVYELNGKDLCGERVIVE 66
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 29.6 bits (66), Expect = 0.053
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
FG+ R + K + FV F+ +A A+ MNG +I + +++ L +P
Sbjct: 25 FGKLERVKKL--KDYAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLAKP 72
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate
RNA-binding protein 11 (RBM11). This subfamily
corresponds to the RRM or RBM11, a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. RBM11 is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. RBM11 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a region
lacking known homology at the C-terminus. The RRM of
RBM11 is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 29.2 bits (65), Expect = 0.062
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
K FGFV F + S AI +NG ++ + +KV
Sbjct: 40 KPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIKVH 75
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 30.5 bits (69), Expect = 0.068
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
V+++ GF+S PA +H+ I +G +IG
Sbjct: 316 GVSRRRVGFISSGAPARSHSEILDESGEKIG 346
>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 = 29.2 bits (66), Expect = 0.068
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 15/72 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
M P+G VIS+++ D +R V GF ++ I NG
Sbjct: 20 MLKPYGQVISTRILRDSKGQ--------SRGV-------GFARMESREKCEDIISKFNGK 64
Query: 61 QIGMKRLKVQLK 72
+ + + +K
Sbjct: 65 YLKGEGEPLLVK 76
>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 = 29.2 bits (66), Expect = 0.071
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
+ FV+F+ A A++++NG K+L V+
Sbjct: 46 YCFVTFETKEEAEKALKSLNGKTALGKKLVVRWAH 80
>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 = 29.3 bits (66), Expect = 0.072
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 18/75 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG-F 60
F FG ++ +V D T QS K FGFV F A ++ ++
Sbjct: 20 FSTFGELLMVQVKKDPKTGQS--------------KGFGFVRF---ADYEDQVKVLSQRH 62
Query: 61 QIGMKRLKVQLKRPK 75
I + V++ K
Sbjct: 63 MIDGRWCDVKIPNSK 77
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 28.7 bits (64), Expect = 0.089
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K + FV + A AI+A+NG ++ +R+ V+L
Sbjct: 34 KDYAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
>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 = 28.8 bits (64), Expect = 0.090
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 32 VSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
++ N F FV F++P A A++ ++G I R++V+L
Sbjct: 31 IARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVEL 70
>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 = 29.0 bits (65), Expect = 0.094
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+S ++ DR T + K +G F + + +A +A++ +NG+
Sbjct: 18 IFSEVGPVVSFRLVYDRETGKPKGYG--------------FCEYKDQETALSAMRNLNGY 63
Query: 61 QIGMKRLKV 69
++ ++L+V
Sbjct: 64 ELNGRQLRV 72
>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 = 29.1 bits (66), Expect = 0.096
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 17/57 (29%)
Query: 16 DRATNQSKCFGECNRKVSVNQKCFGFVSFDNP---ASAHTAIQAMNGFQIGMKRLKV 69
D+ T S+ F FV F + A+ ++ F I + ++V
Sbjct: 39 DKLTGTSRGFA--------------FVEFPSLEDATQWMDALNNLDPFVIDGRVVRV 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 = 28.6 bits (64), Expect = 0.097
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
N++ F+ F + SA A++A+N +I KR+K++
Sbjct: 36 NKRHHKFIEFYDVRSAEAALKALNRSEIAGKRIKLE 71
>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 = 28.3 bits (64), Expect = 0.11
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
K +GFV + A AI+A+NG++ KR+ V+
Sbjct: 33 KNYGFVHMEEEEDAEDAIKALNGYEFMGKRINVE 66
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 28.7 bits (65), Expect = 0.11
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 15/69 (21%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F G+V + ++ DR T K G FG+V F S A++ +NG +
Sbjct: 20 FEDCGDVEAVRIVRDRKTGIGK--G------------FGYVLFKTKDSVALALK-LNGIK 64
Query: 62 IGMKRLKVQ 70
+ ++++V+
Sbjct: 65 LKGRKIRVK 73
>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 = 28.8 bits (65), Expect = 0.11
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 22 SKCFGECNRKVSV-------NQKC--FGFVSFDNPASAHTAIQAMNGFQI 62
F EC SV K +GFV F +A A+Q++NG I
Sbjct: 17 YSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66
>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 = 28.5 bits (64), Expect = 0.12
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 32 VSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
V V + + FV + + A AI+ +NG + K ++V+ PK
Sbjct: 29 VLVKKGGYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPK 72
>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 = 28.2 bits (63), Expect = 0.12
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 39 FGFVSFDNPASAHTAIQAMNGF 60
F FV F++ SA A +++G
Sbjct: 35 FAFVEFESLESAIRAKDSVHGK 56
>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 = 28.5 bits (64), Expect = 0.13
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 14/72 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FGNV+ ++ SK FGFV FD+P + + +
Sbjct: 24 FKEFGNVLEVRI-------NSK-------GGGGRLPNFGFVVFDDPEAVQKILANKPIYF 69
Query: 62 IGMKRLKVQLKR 73
G RL V+ K+
Sbjct: 70 RGDHRLNVEEKK 81
>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 = 28.7 bits (64), Expect = 0.13
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
VS+++P SA A++ +G +LKV L
Sbjct: 53 ATVSYEDPPSAKAAVEWFDGKDFQGSKLKVSL 84
>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 = 28.4 bits (64), Expect = 0.15
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 25 FGECNRKVSV--------NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
F EC V V K FG V F A A+ +G ++ + ++V L +
Sbjct: 20 FKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EKSGEELLGREIRVDLATER 77
>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 = 0.17
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFG-FVSFDNPASAHTAIQAMNGFQIG 63
+G + K+ I+R T+ + +V++ A IQA++GF +
Sbjct: 32 YGKIK--KIVINRNTSYN----------GSQGPSASAYVTYSRKEDALRCIQAVDGFYLD 79
Query: 64 MKRLKVQL 71
+ LK
Sbjct: 80 GRLLKASF 87
>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 = 27.9 bits (63), Expect = 0.17
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 25 FGECNR------KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FG R K + K + FV F++P A + MN + + + LK +
Sbjct: 23 FGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74
>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 = 28.2 bits (63), Expect = 0.17
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 16/63 (25%)
Query: 11 SKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLK 68
K+++ D+ T + K GE V++D+P +A AI+ N +K
Sbjct: 34 PKIWLYKDKDTGEPK--GEAT------------VTYDDPHAASAAIEWFNNKDFMGNTIK 79
Query: 69 VQL 71
V L
Sbjct: 80 VSL 82
>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 = 28.2 bits (63), Expect = 0.18
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
G V F + S A++ MN +++ ++L V+
Sbjct: 44 GVVEFKDKESVQKALETMNRYELKGRKLVVK 74
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2,
Smad3 and Smad4, and stimulates Smad-mediated
transactivation. Cpo may play an important role in
regulating normal function of the nervous system,
whereas mutations in Mec-8 affect mechanosensory and
chemosensory neuronal function. All members contain a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). Some uncharacterized family members contain
two RRMs; this subfamily includes their RRM1. Their
RRM2 shows high sequence homology to the RRM of yeast
proteins scw1, Whi3, and Whi4.
Length = 79
Score = 28.0 bits (63), Expect = 0.18
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQ 61
GFV F + A A+ A+ G++
Sbjct: 46 GFVDFSSAQCAAAAMDALQGYR 67
>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 = 28.3 bits (63), Expect = 0.18
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 14/68 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
F + S+K+ D T S + +GFV F + A+ M G G
Sbjct: 25 RFPSCKSAKIMTDPVTGVS--------------RGYGFVRFSDENDQQRALIEMQGVYCG 70
Query: 64 MKRLKVQL 71
+ +++
Sbjct: 71 GRPMRIST 78
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 28.0 bits (63), Expect = 0.19
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 24 CFGECNR-KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
+G+ R K+ N+K + +P A TA+ +NG ++ K+L+V L +
Sbjct: 23 VYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSK 73
>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 = 28.3 bits (64), Expect = 0.19
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 41 FVSFDNPASAHTAIQAMNG 59
+V F +A IQA+NG
Sbjct: 53 YVKFKTVEAAQKCIQALNG 71
>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 = 27.8 bits (62), Expect = 0.21
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 19/63 (30%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECN--RKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
+F PFG + EC R N K FV F + A A AI A++
Sbjct: 21 LFEPFGTI-----------------EECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
Query: 59 GFQ 61
G Q
Sbjct: 64 GSQ 66
>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 = 28.8 bits (64), Expect = 0.23
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
+ FV F++ A A+ +NG ++ ++V L +P D
Sbjct: 271 YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD 308
>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 = 28.0 bits (63), Expect = 0.23
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 12/62 (19%)
Query: 14 FIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
F+ + KC + FG+V+F A A++ + G +++ V+ +
Sbjct: 30 FVVKDKGSKKC------------RGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAK 77
Query: 74 PK 75
K
Sbjct: 78 KK 79
>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 = 28.1 bits (62), Expect = 0.24
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
+ FV F N A A+ A+NG I ++V L +P D
Sbjct: 46 YAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKPVD 83
>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 = 27.9 bits (62), Expect = 0.25
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 14/54 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQ 55
F +G V+ + D+ TN+S + FGFV F +P T +
Sbjct: 20 FSQYGEVVDCVIMKDKTTNRS--------------RGFGFVKFKDPNCVGTVLA 59
>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 = 27.6 bits (62), Expect = 0.26
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 16/68 (23%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG+V K+ DRA G K +GFV+F+ A I AM
Sbjct: 23 FSRFGSVKDVKIITDRA-------GVS--------KGYGFVTFETQEDA-EKILAMGNLN 66
Query: 62 IGMKRLKV 69
K+L +
Sbjct: 67 FRGKKLNI 74
>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 = 27.6 bits (62), Expect = 0.29
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
F FG + + + +DR T K G + + ++ A AI+ +NG
Sbjct: 26 KFAEFGEIKNLHLNLDRRTGFVK--G------------YALIEYETKKEAQAAIEGLNGK 71
Query: 61 QIGMKRLKV 69
++ + + V
Sbjct: 72 ELLGQTISV 80
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La)
family. It is expressed predominantly in neurons and
muscle in vertebrates. LARP6 functions as a key
regulatory protein that may play a role in mediating a
variety of developmental and homeostatic processes in
animals, including myogenesis, neurogenesis and
possibly metastasis. LARP6 binds to
Ca2+/calmodulin-dependent serine protein kinase (CASK),
and forms a complex with inhibitor of differentiation
transcription factors. It is structurally related to
the La autoantigen and contains a La motif (LAM),
nuclear localization and export (NLS and NES) signals,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 93
Score = 27.6 bits (62), Expect = 0.35
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K + +R + K V F+ +A A++ ++ +KV L
Sbjct: 45 KRYS--SRHPQLGTKECAVVEFEKLEAARKAVEELSARDDWRDGIKVVL 91
>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 = 27.2 bits (61), Expect = 0.36
Identities = 9/33 (27%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGM--KRLKV 69
+ ++ +++ +A A +A+ GF +G +RL+V
Sbjct: 36 YAYIEYESIEAAQAAKEALRGFPLGGPGRRLRV 68
>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 = 27.2 bits (60), Expect = 0.36
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRL 67
N + + FV+F N A AI+ +N ++I RL
Sbjct: 40 NNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 72
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 27.3 bits (61), Expect = 0.37
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLK 72
F F+ F+ +A A+++ N + K + VQ K
Sbjct: 45 FAFIKFEREQAAARAVESENHSMLKNKTMHVQYK 78
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 27.3 bits (61), Expect = 0.37
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 22 SKCFGECNRKVSV---------NQKCFGFVSFDNPASAHTAIQAMNGFQI 62
+ FGE SV K FG+V F + +A A+ A+ G +
Sbjct: 16 YEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDL 65
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 27.3 bits (61), Expect = 0.40
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ F +P A ++ +NG ++L V+L P
Sbjct: 49 AYAEFSSPEQAEKVVKDLNGKVFKNRKLFVKLHVP 83
>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 = 27.2 bits (61), Expect = 0.41
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+ F FV + A A QA+NG + ++V
Sbjct: 44 RGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>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 = 27.2 bits (61), Expect = 0.42
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 19/75 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN--- 58
F FG V +++ D+ T SK G FV F SA ++A +
Sbjct: 21 FSQFGEVKYARIVKDKLTGHSK--GT------------AFVKFKTKESAQKCLEAADNAE 66
Query: 59 --GFQIGMKRLKVQL 71
G + +RL V L
Sbjct: 67 DSGLSLDGRRLIVTL 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 = 27.2 bits (61), Expect = 0.44
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
F FV F + A A AI+ +NG +I + + V
Sbjct: 42 FAFVQFTSKADAEKAIKGVNGKKIKGRPVAV 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 = 26.9 bits (60), Expect = 0.46
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 15 IDRATNQ---SKCFGECNRKVSVNQ----KCFGFVSFDNPASAHTAIQAMNGFQIGMKRL 67
+ + + F E S++ C +V + AH A+Q + ++ K++
Sbjct: 10 LSKKVTEEDLKNLFEEYGEIQSIDMIPPRGC-AYVCMETRQDAHRALQKLRNVKLAGKKI 68
Query: 68 KV 69
KV
Sbjct: 69 KV 70
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 27.0 bits (60), Expect = 0.49
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F FG + V ID+ + +S K F +V F +P A A + ++G
Sbjct: 22 LFSKFGELSEVHVAIDKKSGKS--------------KGFAYVLFLDPEDAVKAYKELDG- 66
Query: 61 QIGMKRL 67
++ RL
Sbjct: 67 KVFQGRL 73
>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 = 26.8 bits (59), Expect = 0.57
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 14/48 (29%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPAS 49
F FG V V D AT +S + FGF++F P S
Sbjct: 19 FGQFGEVTDCTVMRDSATGRS--------------RGFGFLTFKKPKS 52
>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 = 26.8 bits (60), Expect = 0.57
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNG 59
K + FVS+ + A A A+NG
Sbjct: 38 GKPYCFVSYSSIEDAAAAYDALNG 61
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and
similar proteins. This subfamily corresponds to the
RRM of Acinus, a caspase-3-activated nuclear factor
that induces apoptotic chromatin condensation after
cleavage by caspase-3 without inducing DNA
fragmentation. It is essential for apoptotic chromatin
condensation and may also participate in nuclear
structural changes occurring in normal cells. Acinus
contains a P-loop motif and an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which indicates Acinus
might have ATPase and DNA/RNA-binding activity. .
Length = 90
Score = 26.8 bits (60), Expect = 0.57
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 41 FVSFDNPASAHTAIQAMNGFQ---IGMKRLKVQLKRPKDAAR 79
+V++ A +A++G Q KRLKV ++
Sbjct: 43 YVTYSTVEEAVATREALHGLQWPSSNPKRLKVDFVPQEELEE 84
>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 = 26.4 bits (58), Expect = 0.66
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 17 RATNQSKCFGECNRKVSVNQK-CFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
R + + FG + + ++ K +GFV F++ A A+ +NG + +R+ V+ R
Sbjct: 12 REKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHAR 69
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 26.5 bits (59), Expect = 0.67
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V+ + D+ T +SK F+ F + AH ++A+N
Sbjct: 21 IFSKYGKVVKVTIVKDKETRKSKGVA--------------FILFLDREDAHKCVKALNNK 66
Query: 61 QIGMKRLKV 69
++ + LK
Sbjct: 67 ELFGRTLKC 75
>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 = 26.8 bits (59), Expect = 0.70
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+GF+ F+N AH A AM+G + +K+
Sbjct: 47 TSTYGFLKFENLDMAHRAKLAMSGKVLRRNPIKI 80
>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 = 26.5 bits (59), Expect = 0.72
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 20/69 (28%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V S+VF+++ +K FGF+ D +A A ++G
Sbjct: 21 LFSKYGEV--SEVFLNK------------------EKGFGFIRLDTRTNAEKAKAELDGI 60
Query: 61 QIGMKRLKV 69
++L+V
Sbjct: 61 MRKGRQLRV 69
>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 = 26.4 bits (59), Expect = 0.73
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
V F+ A AI+ NG + + ++V+L
Sbjct: 44 ADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 75
>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 = 26.8 bits (60), Expect = 0.77
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
V F P A I+A+NG ++L+ +
Sbjct: 55 VKFKEPEEADRCIEALNGRWFAGRQLEAER 84
>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 = 26.6 bits (58), Expect = 0.82
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 20/61 (32%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG ++ +VF D+ + FV F++ SA AI ++NG
Sbjct: 21 FSPFGQIMEVRVFPDKG--------------------YSFVRFNSHESAAHAIVSVNGTT 60
Query: 62 I 62
I
Sbjct: 61 I 61
>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 = 26.2 bits (58), Expect = 0.86
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+ FV F N AH A AM+G IG ++K+
Sbjct: 45 YAFVKFLNLDMAHRAKVAMSGQYIGRNQIKI 75
>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 = 26.3 bits (58), Expect = 0.90
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
FV F + A A++AMNG +I K + ++
Sbjct: 42 FVEFFDVRDAAKALRAMNGKEISGKPVVIE 71
>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 = 26.2 bits (58), Expect = 0.92
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+ F+ + + AS A++ M+G +G R+K+
Sbjct: 43 YAFIQYADIASVVKAMRKMDGEYLGNNRVKL 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 = 26.1 bits (58), Expect = 1.2
Identities = 8/35 (22%), Positives = 19/35 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
+ F+ F++ A + +G +I +R+ V ++R
Sbjct: 45 YAFIEFEHERDMKAAYKYADGKKIDGRRVLVDVER 79
>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 = 25.9 bits (57), Expect = 1.2
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 17 RATNQSKCFGECNRKVSVNQKC-FGFVSFDNPASAHTAIQAMNGFQIGM--KRLKVQ 70
R + + FG+ R V+ K F FV ++ A AI+ ++ F+ G +RL+V+
Sbjct: 13 RQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDAEDAIRGLDNFEFGRQRRRLRVE 69
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing (RBP-MS).
This subfamily corresponds to the RRM of RBP-MS, also
termed heart and RRM expressed sequence (hermes), an
RNA-binding proteins found in various vertebrate
species. It contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). RBP-MS physically interacts
with Smad2, Smad3 and Smad4 and plays a role in
regulation of Smad-mediated transcriptional activity.
In addition, RBP-MS may be involved in regulation of
mRNA translation and localization during Xenopus laevis
development. .
Length = 76
Score = 25.8 bits (56), Expect = 1.3
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQ 61
GFVSFD+ + A A A+NG +
Sbjct: 42 GFVSFDSRSEAEAAKNALNGIR 63
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 25.9 bits (57), Expect = 1.3
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 18/70 (25%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V + +R V F++F+N +A AI+ +NG
Sbjct: 19 LFETCGPVRKVTML--------------SRTVQP----HAFITFENLEAAQLAIETLNGA 60
Query: 61 QIGMKRLKVQ 70
+ +KVQ
Sbjct: 61 SVDGNCIKVQ 70
>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 = 25.6 bits (57), Expect = 1.4
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
+QK FV F + +A A+ A+NG RLKV+
Sbjct: 39 SQK---FVEFYDIRAAEAALDALNGRPFLGGRLKVK 71
>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 = 25.7 bits (57), Expect = 1.5
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
F VS+ + +A A +A+ G ++G ++L + PKD
Sbjct: 40 FIMVSYYDIRAARRAKRALQGTELGGRKLDIHFSIPKD 77
>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 = 25.8 bits (57), Expect = 1.5
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
F FV F + SA +A+ ++G +G L+V
Sbjct: 42 FAFVEFADAESALSAL-NLSGTLLGGHPLRV 71
>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 = 25.6 bits (56), Expect = 1.5
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
K F FV+F + S A+ +NG ++ + L +Q
Sbjct: 41 PKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPLNIQ 75
>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 = 25.7 bits (57), Expect = 1.6
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 15/70 (21%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FG + + V DR T +S+ +G FV+F + SA A + N
Sbjct: 21 FSQFGEIEEAVVITDRQTGKSRGYG--------------FVTFKDKESAERACKDPNPI- 65
Query: 62 IGMKRLKVQL 71
I ++ V L
Sbjct: 66 IDGRKANVNL 75
>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 = 25.4 bits (55), Expect = 1.7
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F N A A+ MNG I ++V L +P
Sbjct: 39 YAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAKP 74
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 25.5 bits (56), Expect = 1.9
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKV 69
V+FD A A++ +NG IG +++K+
Sbjct: 47 VAFDTHREAMAAVRELNGRPIGTRKVKL 74
>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 = 25.3 bits (56), Expect = 1.9
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 32 VSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
N+ C GFV+F N A A A+ ++G + LK+
Sbjct: 42 RRRNRNC-GFVAFMNRADAERALDELDGKDVMGYELKL 78
>gnl|CDD|117519 pfam08952, DUF1866, Domain of unknown function (DUF1866). This
domain, found in Synaptojanin, has no known function.
Length = 145
Score = 25.8 bits (57), Expect = 1.9
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
V+F + SA A+ +G ++ ++L ++LK P
Sbjct: 74 VTFRDGESALAALS-KDGIKVLGRQLNIRLKSP 105
>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 = 25.2 bits (56), Expect = 2.1
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQI 62
F FV + A A++ +NG ++
Sbjct: 42 FCFVEYYTREDAENAVKYLNGTKL 65
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 25.4 bits (56), Expect = 2.2
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
V++++P A A+ +NG + +LKV
Sbjct: 43 NVTYESPEQAQQAVNKLNGHEYEGSKLKV 71
>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 = 25.2 bits (55), Expect = 2.3
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +GN++ + D++T + FV +D A AI ++NG
Sbjct: 20 IFEAYGNIVQCNLLRDKSTGLPRGVA--------------FVRYDKREEAQAAISSLNG 64
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 25.2 bits (56), Expect = 2.5
Identities = 10/32 (31%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGM-KRLKV 69
+ FV++ N +A A++ ++ ++I KRL V
Sbjct: 44 YAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGV 75
>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 = 24.7 bits (54), Expect = 2.7
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
++ FGFV+F+N + + N I R++V
Sbjct: 36 KRMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69
>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 = 25.4 bits (55), Expect = 2.7
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
S + F FV F+N A A + NG ++ +R++V
Sbjct: 47 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 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 = 25.0 bits (54), Expect = 2.8
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 16/69 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G S K+ +D A N CF V F A ++ AMNG
Sbjct: 19 LFSQIGPCKSCKMIMDTAGNDPYCF----------------VEFFEHRHAAASLAAMNGR 62
Query: 61 QIGMKRLKV 69
+I K +KV
Sbjct: 63 KIMGKEVKV 71
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 25.0 bits (55), Expect = 2.9
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
FGFV + A A++ N I ++ V++
Sbjct: 43 FGFVGYKTEEEAQKALKHFNNSFIDTSKITVEI 75
>gnl|CDD|119337 cd06569, GH20_Sm-chitobiase-like, The chitobiase of Serratia
marcescens is a beta-N-1,4-acetylhexosaminidase with a
glycosyl hydrolase family 20 (GH20) domain that
hydrolyzes the beta-1,4-glycosidic linkages in oligomers
derived from chitin. Chitin is degraded by a two step
process: i) a chitinase hydrolyzes the chitin to
oligosaccharides and disaccharides such as
di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase
then further degrades these oligomers into monomers. The
GH20 hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself.
Length = 445
Score = 25.7 bits (57), Expect = 2.9
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 43 SFDNPASAHTAIQAMN 58
D P A AI+AM
Sbjct: 116 EIDMPGHARAAIKAME 131
>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 = 24.9 bits (55), Expect = 3.1
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM 57
+G+ + K FV + ASA A +AM
Sbjct: 29 WGDIEDIRVLPSKGIAFVRYKYRASAEFAKEAM 61
>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 = 24.9 bits (55), Expect = 3.1
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 25 FGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+G V Q+ V FD +A A+ M G ++G ++L+V
Sbjct: 31 YGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMKGRKLGGRKLQV 75
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding
protein with multiple splicing (RBP-MS). The biological
function of RBP-MS2 remains unclear. Like RBP-MS,
RBP-MS2 contains an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 25.0 bits (54), Expect = 3.2
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQ 61
GFV+FD+ A A A A+NG +
Sbjct: 42 GFVTFDSRAGAEAAKNALNGIR 63
>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 = 24.8 bits (54), Expect = 3.3
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA 77
F FV+ +A A++ NG +I + + V K+
Sbjct: 44 FAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWAVQKNR 82
>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 = 24.8 bits (54), Expect = 3.4
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
+ F FV A+A AI+ +NG ++ ++L V+
Sbjct: 34 RQFAFVHLRGEAAADRAIEELNGRELHGRKLVVEH 68
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B"), a unique protein that comprises the U2
snRNP. It was initially identified to bind to stem-loop
IV (SLIV) at the 3' end of U2 snRNA. Additional
research indicates U2B" binds to U1 snRNA stem-loop II
(SLII) as well and shows no preference for SLIV or SLII
on the basis of binding affinity. U2B" does not require
an auxiliary protein for binding to RNA and its nuclear
transport is independent of U2 snRNA binding. U2B"
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). It also contains a nuclear localization
signal (NLS) in the central domain. However, nuclear
import of U2B'' does not depend on this NLS. The
N-terminal RRM is sufficient to direct U2B" to the
nucleus. .
Length = 80
Score = 25.0 bits (54), Expect = 3.4
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 41 FVSFDNPASAHTAIQAMNGFQI 62
FV F+N A A A A+ GF+I
Sbjct: 46 FVEFENEAQAGAARDALQGFKI 67
>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 = 24.8 bits (54), Expect = 3.6
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 17/63 (26%)
Query: 1 MFLPFGNVISSKVFIDRATNQSK-CFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
MF PFG++ V D QS+ C FV+F + A AI+AM+
Sbjct: 21 MFAPFGSIEECTVLRD-QNGQSRGC---------------AFVTFASRQCALNAIKAMHH 64
Query: 60 FQI 62
Q
Sbjct: 65 SQT 67
>gnl|CDD|190398 pfam02714, DUF221, Domain of unknown function DUF221. This
family consists of hypothetical transmembrane proteins
none of which have any function, the aligned region is
at 538 residues at maximum length.
Length = 325
Score = 25.2 bits (56), Expect = 3.7
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 40 GFVSFDNPASAHTAIQA 56
FV+F + A+A A QA
Sbjct: 1 AFVTFKSQAAAQMAAQA 17
>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 = 24.6 bits (53), Expect = 3.8
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F + A A+ +NG ++ ++V L +P
Sbjct: 39 YAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAKP 74
>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 = 24.5 bits (53), Expect = 4.0
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 14/57 (24%)
Query: 13 VFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
++ DR T + K GE VSFD+P SA AI +G + +KV
Sbjct: 42 LYTDRETGKLK--GEAT------------VSFDDPPSAKAAIDWFDGKEFSGNPIKV 84
>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 = 24.6 bits (53), Expect = 4.1
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 23 KCFGECNRKVSVNQ-KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
K FG+ + V + K + F+ FD A A++ MNG ++ + +++ +P
Sbjct: 20 KAFGQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKELEGENIEIVFAKP 72
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 25.2 bits (55), Expect = 4.3
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
F + P HTA QA++ FQ R
Sbjct: 274 FSKPERPPEIHTAFQALDQFQEKYSRKPN 302
>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 = 24.5 bits (54), Expect = 4.5
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 30 RKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
+K + + F FV F A A++A+ + + L ++
Sbjct: 34 KKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLE 74
>gnl|CDD|216016 pfam00602, Flu_PB1, Influenza RNA-dependent RNA polymerase subunit
PB1. Two GTP binding sites exist in this protein.
Length = 740
Score = 25.2 bits (55), Expect = 4.6
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 23 KCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKD 76
+ + +C ++CF S NP + +AM RLK + R
Sbjct: 685 QIYQKCCNLF---ERCFESASIRNPVGPGSMKEAMKRRLREDARLKGESGRITK 735
>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 = 24.5 bits (54), Expect = 4.6
Identities = 8/33 (24%), Positives = 20/33 (60%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K F F+++++ S A+ +NG ++ + ++V
Sbjct: 51 KGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
>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 = 24.6 bits (54), Expect = 4.6
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQI 62
+ FV F + A+A + +NG I
Sbjct: 44 YCFVEFADEATAERCLHKLNGKPI 67
>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 = 24.2 bits (53), Expect = 5.1
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 25 FGECNRKVSVNQKCF---------GFVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
F C ++ F F++F +A A+ A++G +G + LKV+
Sbjct: 19 FSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-ALDGEDMGGRFLKVE 72
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 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 = 92
Score = 24.4 bits (54), Expect = 5.1
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIG-MKRLKVQ 70
N K + S AIQ ++G +IG ++KV+
Sbjct: 48 NLKGDALCCYLKEESVELAIQLLDGTEIGRGYKMKVE 84
>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 = 24.2 bits (53), Expect = 5.1
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 37 KCFGFVSFDNPASAHTAIQAMN 58
K F F+ F+ P A A + +N
Sbjct: 41 KGFAFIEFETPEEAQKACKHLN 62
>gnl|CDD|131505 TIGR02452, TIGR02452, TIGR02452 family protein. Members of this
uncharacterized protein family are found in
Streptomyces, Nostoc sp. PCC 7120, Clostridium
acetobutylicum, Lactobacillus johnsonii NCC 533,
Deinococcus radiodurans, and Pirellula sp. for a broad
but sparse phylogenetic distibution that at least
suggests lateral gene transfer.
Length = 266
Score = 24.8 bits (54), Expect = 5.1
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 2/52 (3%)
Query: 6 GNVISSKVFIDRATNQSKCFGECNRKV--SVNQKCFGFVSFDNPASAHTAIQ 55
+ F DRA +K + +V + N ++ H A++
Sbjct: 20 TEKVDIATFTDRAIQGTKLYDPQEEEVLFLYPAHHRTELKVVNESTLHAAVR 71
>gnl|CDD|237666 PRK14296, PRK14296, chaperone protein DnaJ; Provisional.
Length = 372
Score = 24.9 bits (54), Expect = 5.4
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 3 LPFGNVISSKVFIDRATNQSKCFG---ECNRKVSVNQKCFG 40
L FG + + +D TN SKCFG E N + + C G
Sbjct: 136 LLFG--VDKIIELDLLTNCSKCFGSGAESNSDIHICNNCHG 174
>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 = 24.2 bits (52), Expect = 5.5
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K F FV + N +A A+ +G I + L + L
Sbjct: 35 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL 70
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both nuclear
and cytoplasmic roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 86
Score = 24.2 bits (53), Expect = 5.8
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 42 VSFDNPASAHTAIQAMNGFQI--GMKRLKVQLKRP 74
V FD+ SA A A+NG I G LK++ +P
Sbjct: 45 VEFDSVDSAQRAKAALNGADIYAGCCTLKIEYAKP 79
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A
or U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding
protein associated with the U1 snRNP, a small
RNA-protein complex involved in pre-mRNA splicing. U1A
binds with high affinity and specificity to stem-loop
II (SLII) of U1 snRNA. It is predominantly a nuclear
protein that shuttles between the nucleus and the
cytoplasm independently of interactions with U1 snRNA.
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins, including polypyrimidine tract binding
protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and it may be free for binding other proteins.
U1A also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 24.3 bits (52), Expect = 5.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 40 GFVSFDNPASAHTAIQAMNGFQI 62
FV FDN A A +A+ GF+I
Sbjct: 45 AFVEFDNEVQAGAAREALQGFKI 67
>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 = 24.5 bits (54), Expect = 5.9
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 41 FVSFDNPASAHTAIQAMNGFQIGMKRLKVQ 70
+V + + A A + NG K+L +
Sbjct: 73 YVQYQSEEEALAAFKMFNGRWYAGKQLTCE 102
>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 = 24.2 bits (53), Expect = 5.9
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 26 GECNR------KVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
G NR K + K F ++ F + +S A+ +N + +++KV
Sbjct: 24 GTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRGRQIKV 72
>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 = 24.2 bits (52), Expect = 6.2
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
+ F+ F N AH A AM+G IG +K+
Sbjct: 51 YAFLKFQNLDMAHRAKVAMSGRVIGRNPIKI 81
>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 = 24.2 bits (53), Expect = 6.8
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
V FD+ SA ++ +N + K +KV L
Sbjct: 49 VVFDSVKSAKRCVEKLNQTSVMGKIIKVFL 78
>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 = 24.1 bits (53), Expect = 8.0
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 12 KVFIDRATNQSKCFGECN------RKVSVNQ---KCFGFVSFDNPASAHTAIQAMN 58
K +RA + + R + K +GFV F N A A++A+N
Sbjct: 23 KAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALN 78
>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 = 23.5 bits (51), Expect = 8.9
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 39 FGFVSFDNPAS 49
FGFV+F +PAS
Sbjct: 42 FGFVTFSDPAS 52
>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 = 23.9 bits (51), Expect = 9.5
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 32 VSVNQKCFG--FVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
VS + K G FV F +SA A+++M GF K +++Q +
Sbjct: 39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 82
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
0.325 0.136 0.412
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,776,981
Number of extensions: 263878
Number of successful extensions: 644
Number of sequences better than 10.0: 1
Number of HSP's gapped: 568
Number of HSP's successfully gapped: 249
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)