RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3698
(534 letters)
>gnl|CDD|241169 cd12725, RRM2_CPEB1, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 86
Score = 156 bits (396), Expect = 2e-46
Identities = 58/86 (67%), Positives = 74/86 (86%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSD 175
+P KT+FVGALHG L A+AL ++MNDLFG VVYAGIDTDK+KYPIGSGR+TF + R+Y
Sbjct: 1 DPSKTVFVGALHGMLNAEALAHIMNDLFGGVVYAGIDTDKYKYPIGSGRVTFNNQRSYMK 60
Query: 176 AIRAAFIEVKSGRICKKLQIDPYLED 201
A++AAF+E+K+ + KK+QIDPYLED
Sbjct: 61 AVKAAFVEIKTPKFTKKVQIDPYLED 86
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 89.3 bits (222), Expect = 6e-22
Identities = 32/81 (39%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 119 KTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHK-YPIGSGRITFGSTRAYSDAI 177
+T+FVG L LTA L ++ L+G V Y IDTD+ YP G R+TF + ++Y A+
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
Query: 178 RAAFIEVKSGRICKKLQIDPY 198
F+E+ I K+++I PY
Sbjct: 61 SEVFVELPFNDINKRVRIRPY 81
>gnl|CDD|241170 cd12726, RRM2_CPEB2_like, RNA recognition motif 2 found in
cytoplasmic polyadenylation element-binding protein
CPEB-2, CPEB-3, CPEB-4 and similar protiens. This
subgroup corresponds to the RRM2 of the paralog proteins
CPEB-2, CPEB-3 and CPEB-4, all well conserved in both,
vertebrates and invertebrates. Due to the high sequence
similarity, members in this family may share similar
expression patterns and functions. CPEB-2 is an
RNA-binding protein that is abundantly expressed in
testis and localized in cytoplasm in transfected HeLa
cells. It preferentially binds to poly(U) RNA oligomers
and may regulate the translation of stored mRNAs during
spermiogenesis. Moreover, CPEB-2 impedes target RNA
translation at elongation; it directly interacts with
the elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 81
Score = 84.5 bits (209), Expect = 3e-20
Identities = 37/81 (45%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 119 KTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTD-KHKYPIGSGRITFGSTRAYSDAI 177
KTIFVG + L A L +M+ L+G V YAGIDTD + KYP G+GR+ F + ++Y AI
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAI 60
Query: 178 RAAFIEVKSGRICKKLQIDPY 198
A F++++ G I K++++ PY
Sbjct: 61 SARFVQLQHGDIDKRVEVKPY 81
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 64.0 bits (156), Expect = 9e-13
Identities = 36/100 (36%), Positives = 45/100 (45%), Gaps = 18/100 (18%)
Query: 23 LSNKIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTPESPTAPKAISLDVISEL---VL 79
S K+F+GGVPWD E L+ F FG V VEWP + P P + +I E V
Sbjct: 1 YSCKVFLGGVPWDITEAGLINTFKPFGSVSVEWPGKDGKHPRHPPKGYVYLIFESEKSVK 60
Query: 80 ILGQWATEGNLCGR---------------VEVVPWAISDS 104
L Q T L G V+V+PW +SDS
Sbjct: 61 ALLQACTHDFLNGGEYYFKISSRRMRSKEVQVIPWVLSDS 100
Score = 43.2 bits (102), Expect = 2e-05
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 490 LSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
S K+F+GGVPWD E L+ F FG V
Sbjct: 1 YSCKVFLGGVPWDITEAGLINTFKPFGSVS 30
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate
their translation. CPEB proteins are well conserved in
both, vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The
second subfamily includes CPEB-2, CPEB-3, CPEB-4, and
related protiens. Due to high sequence similarity,
members in this subfamily may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. CPEB-2 impedes target RNA translation
at elongation; it directly interacts with the
elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a Zn-finger motif. CPEB-2, -3, and -4 have
conserved nuclear export signals that are not present
in CPEB-1. .
Length = 112
Score = 48.0 bits (114), Expect = 5e-07
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTPESPTAP 66
K+F+GG+PWD E +L F +FG ++V+WP E +
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDS 42
Score = 36.9 bits (85), Expect = 0.004
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGP 517
K+F+GG+PWD E +L F +FG
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGS 26
>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 = 45.7 bits (109), Expect = 1e-06
Identities = 16/31 (51%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV-KAVV 522
KIF+GG+P+ T + L FSQFG + +AVV
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVV 32
Score = 43.8 bits (104), Expect = 6e-06
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+P+ T + L FSQFG +
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEI 27
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 44.1 bits (105), Expect = 5e-06
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+G +P DT E L +FS+FG V++V + R
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVR 33
Score = 40.7 bits (96), Expect = 8e-05
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G +P DT E L +FS+FG V+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVE 27
>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 = 42.6 bits (101), Expect = 2e-05
Identities = 20/40 (50%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRAEMS 529
N+IF+GG+P DT E L FS+FG VK V + +RA +S
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVS 42
Score = 39.6 bits (93), Expect = 2e-04
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
N+IF+GG+P DT E L FS+FG VK
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVK 30
Score = 30.7 bits (70), Expect = 0.31
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 5/78 (6%)
Query: 120 TIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRA 179
IFVG + T + L + + FG V I TD+ G G +TF + +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSR-FGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62
Query: 180 AFIEVKSGRICKKLQIDP 197
+ + KKL I P
Sbjct: 63 GNLNFRG----KKLNIGP 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 = 41.1 bits (97), Expect = 6e-05
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+G +P DT E L +FS+FG +++V + R
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVR 32
Score = 37.3 bits (87), Expect = 0.001
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G +P DT E L +FS+FG ++
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIE 26
Score = 36.5 bits (85), Expect = 0.002
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 121 IFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+FVG L T + L + + FG++ I DK G + F S DA +A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSK-FGEIESVRIVRDKDGKSKGFAFVEFES---PEDAEKA 55
>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 = 40.7 bits (96), Expect = 7e-05
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+F+G +P DT E L +FS+FGP++++ +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRI 30
Score = 38.3 bits (90), Expect = 5e-04
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G +P DT E L +FS+FGP++
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIE 26
Score = 31.4 bits (72), Expect = 0.13
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 121 IFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+FVG L T + L ++ + FG + I D+ G + F A+ A
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSK-FGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEA 58
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
K+FIGG+ +DT E L VFS++G + VV+
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVV 32
Score = 37.1 bits (86), Expect = 0.002
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ +DT E L VFS++G +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQI 27
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 40.2 bits (94), Expect = 2e-04
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRAEMS 529
N+IF+GG+ + T E L FSQ+G VK V V +RA +S
Sbjct: 3 NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVS 42
Score = 32.9 bits (75), Expect = 0.052
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
N+IF+GG+ + T E L FSQ+G VK
Sbjct: 3 NRIFVGGIDFKTNENDLRKFFSQYGTVK 30
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 38.5 bits (90), Expect = 4e-04
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
KIF+GG+ +T E + F +FG + + +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIEL 31
Score = 38.1 bits (89), Expect = 7e-04
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK-VEWP 56
KIF+GG+ +T E + F +FG + +E P
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELP 32
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. Moreover, CPEB-2 impedes target RNA
translation at elongation; it directly interacts with
the elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a Zn-finger
motif. In addition, they do have conserved nuclear
export signals that are not present in CPEB-1. .
Length = 92
Score = 39.0 bits (91), Expect = 5e-04
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTPES 62
K+F+GG+P D E + F +FGP+ V+WP ES
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPH-KAES 37
Score = 29.7 bits (67), Expect = 0.97
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV 518
K+F+GG+P D E + F +FGP+
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPL 27
>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 = 38.0 bits (89), Expect = 8e-04
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+FIGG+ WDT E L FS++G V V+M
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIM 31
Score = 34.5 bits (80), Expect = 0.012
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+FIGG+ WDT E L FS++G V
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEV 25
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.0 bits (86), Expect = 0.002
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ KIF+GG+P + E L FSQFG V VV+
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVV 34
Score = 32.0 bits (73), Expect = 0.11
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ KIF+GG+P + E L FSQFG V
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTV 29
>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 = 35.7 bits (83), Expect = 0.004
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+F+G +P+D E L+ +FS+ GPV + +
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRL 30
Score = 35.3 bits (82), Expect = 0.007
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G +P+D E L+ +FS+ GPV
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVV 26
>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 = 35.9 bits (83), Expect = 0.006
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA 526
+K+F+ G+P+ + L +F + G VK+V V NR+
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS 39
Score = 31.6 bits (72), Expect = 0.17
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+K+F+ G+P+ + L +F + G VK
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVK 30
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 35.1 bits (81), Expect = 0.008
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ G T E L+ FS FGPV V+M++
Sbjct: 3 RSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDK 36
>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 = 34.9 bits (81), Expect = 0.008
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA 526
K+F+GG+ D E L FSQ+G V++V V ++
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE 36
Score = 34.2 bits (79), Expect = 0.015
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV-KVE 54
K+F+GG+ D E L FSQ+G V VE
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVE 30
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 34.7 bits (80), Expect = 0.011
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
KIF+GG+ +T E + FSQFG V+ ++
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAML 31
Score = 34.3 bits (79), Expect = 0.013
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
KIF+GG+ +T E + FSQFG V+
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVE 27
>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 = 34.8 bits (80), Expect = 0.011
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
K+F+GG+ W+T + L FSQ+G V V+M
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIM 32
Score = 33.6 bits (77), Expect = 0.032
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+GG+ W+T + L FSQ+G V
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEV 26
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 34.6 bits (80), Expect = 0.011
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+F+G +PW L FSQFG VK
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVK 27
Score = 34.6 bits (80), Expect = 0.011
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK 519
K+F+G +PW L FSQFG VK
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVK 27
>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 = 34.9 bits (81), Expect = 0.012
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 17 QFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
Q+ D S I+IGG+P++ E +L VFSQ+G +
Sbjct: 5 QYKD---SAYIYIGGLPYELTEGDILCVFSQYGEI 36
Score = 34.9 bits (81), Expect = 0.012
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 484 QFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
Q+ D S I+IGG+P++ E +L VFSQ+G +
Sbjct: 5 QYKD---SAYIYIGGLPYELTEGDILCVFSQYGEI 36
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 34.5 bits (79), Expect = 0.014
Identities = 16/30 (53%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV-KVE 54
K+F+GG+ D E L FSQFGPV K E
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAE 30
Score = 34.5 bits (79), Expect = 0.017
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
K+F+GG+ D E L FSQFGPV+
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKA 29
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 33.9 bits (78), Expect = 0.020
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+ + GVP D L +F + G VK +
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVKGI 31
Score = 32.7 bits (75), Expect = 0.054
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + GVP D L +F + G VK
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVK 29
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 34.3 bits (79), Expect = 0.020
Identities = 17/58 (29%), Positives = 22/58 (37%)
Query: 393 SNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGG 450
S V A + + S + + + G GG GGGG G GGG GG
Sbjct: 21 SEVAAADLSNTEKSESENEVQDDKYGGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGG 78
Score = 30.9 bits (70), Expect = 0.32
Identities = 14/23 (60%), Positives = 14/23 (60%)
Query: 428 GGYYGGGGGGQYLHNGDGGGQGG 450
GGYYGGGGG G GG GG
Sbjct: 63 GGYYGGGGGYGGGGGGYPGGGGG 85
Score = 28.9 bits (65), Expect = 1.5
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 425 PSNGGYYGGGGGGQYLHNGDGGGQGG 450
GG YGGGGGG G G G GG
Sbjct: 66 YGGGGGYGGGGGGYPGGGGGGYGGGG 91
>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 = 33.7 bits (78), Expect = 0.021
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRA 526
NKIFIGG+P E + + FG +KA +V + A
Sbjct: 1 NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSA 37
Score = 30.3 bits (69), Expect = 0.46
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
NKIFIGG+P E + + FG +K
Sbjct: 1 NKIFIGGLPNYLSEDQVKELLESFGKLK 28
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 33.9 bits (78), Expect = 0.022
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGP-VKAVVM 523
K+FIGG+ ++T + L FSQ+G VVM
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVM 32
Score = 30.8 bits (70), Expect = 0.28
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ ++T + L FSQ+G +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEI 26
>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 = 33.4 bits (77), Expect = 0.026
Identities = 26/70 (37%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 121 IFVGALHGRLTAQALYNVMNDLF---GDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAI 177
IFV L +T Q L DLF G+V+ A + TD G G + F S DA
Sbjct: 1 IFVRNLPFSVTWQDL----KDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPE---DAQ 53
Query: 178 RAAFIEVKSG 187
RA IE+ +G
Sbjct: 54 RA--IEMFNG 61
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 33.7 bits (78), Expect = 0.028
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRAEMSS 530
+F+ +P+DT + L FS+ GP+K VV ++
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKC 40
Score = 33.4 bits (77), Expect = 0.037
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ +P+DT + L FS+ GP+K
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIK 27
>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 = 33.5 bits (77), Expect = 0.034
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
KIF+GG+P D E FSQFG V A +M
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLM 32
Score = 32.7 bits (75), Expect = 0.062
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+P D E FSQFG V
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKV 26
>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 = 33.3 bits (77), Expect = 0.036
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA 526
+FI +P+D E L +FSQFG VK V ++
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKL 37
Score = 31.4 bits (72), Expect = 0.17
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+FI +P+D E L +FSQFG VK
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVK 28
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 36.1 bits (82), Expect = 0.036
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+N +F+G +P+D E L +F +FGPVK V + R
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVR 149
Score = 31.8 bits (71), Expect = 0.90
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+N +F+G +P+D E L +F +FGPVK
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVK 143
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 33.0 bits (75), Expect = 0.043
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
KIF+GG+ DT E+ L F Q+G ++V
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEV 29
Score = 32.7 bits (74), Expect = 0.069
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
KIF+GG+ DT E+ L F Q+G ++ +
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVI 30
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 33.1 bits (75), Expect = 0.048
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
K+FIGG+ W T + L F QFG VK ++ R
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMR 34
Score = 31.9 bits (72), Expect = 0.11
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+FIGG+ W T + L F QFG VK
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVK 28
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 32.5 bits (74), Expect = 0.058
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+F+GG+ WDT + L FS+FG V
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEV 25
Score = 32.5 bits (74), Expect = 0.058
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPV 518
+F+GG+ WDT + L FS+FG V
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEV 25
>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 = 32.6 bits (75), Expect = 0.069
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNR 525
NK+F+ G+ T E L +FS+FG V+ V + +
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDP 37
Score = 31.0 bits (71), Expect = 0.27
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
NK+F+ G+ T E L +FS+FG V+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVE 29
>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 = 32.6 bits (75), Expect = 0.074
Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNR 525
+++G +P++ E L +F QFG V + V+ +R
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDR 35
Score = 30.7 bits (70), Expect = 0.35
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
+++G +P++ E L +F QFG V
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEV 26
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 32.8 bits (75), Expect = 0.077
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 495 FIGGVPWDTPEYLLLTVFSQFGPVKAVVMN 524
F+ GV D PEY + F QFG K+V++N
Sbjct: 6 FLFGVEDDLPEYKIRDYFEQFGKSKSVIVN 35
>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 = 32.2 bits (74), Expect = 0.092
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGP---VKVEWPQGTPE 61
+++G + E +L F +FGP VK+ WP+ E
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEE 41
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 31.9 bits (73), Expect = 0.099
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA 526
S + + GVP PE L Q+G V+AV M+
Sbjct: 1 SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAM 36
>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 = 32.2 bits (74), Expect = 0.10
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+F+ + +DT E L F ++GP+K + +
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRL 33
Score = 30.3 bits (69), Expect = 0.58
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ + +DT E L F ++GP+K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIK 29
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 32.2 bits (73), Expect = 0.11
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMN 524
S +F GGV ++ EY L + F +FG V++ ++N
Sbjct: 3 SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILN 36
>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 = 31.9 bits (73), Expect = 0.12
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
N+I++ V D E + +VF FG +K+ +
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSL 32
Score = 31.1 bits (71), Expect = 0.19
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
N+I++ V D E + +VF FG +K
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIK 28
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 32.0 bits (73), Expect = 0.12
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMN 524
S+++F+G +P D E L F +FG V V +N
Sbjct: 3 SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRIN 36
Score = 30.1 bits (68), Expect = 0.52
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S+++F+G +P D E L F +FG V
Sbjct: 3 SHQLFVGNLPHDITEDELKEFFKEFGNVL 31
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 31.9 bits (72), Expect = 0.13
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
KIF+GG+ DT EY L F ++G ++ +
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETI 30
Score = 30.7 bits (69), Expect = 0.30
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
KIF+GG+ DT EY L F ++G ++
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIE 28
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 31.5 bits (71), Expect = 0.13
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
KIF+GG+ DTPE + F FG V+++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESI 29
Score = 30.7 bits (69), Expect = 0.33
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK-VEWP 56
KIF+GG+ DTPE + F FG V+ +E P
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELP 32
>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 = 31.4 bits (71), Expect = 0.15
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+FIGG+ W+T + L F QFG V
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEV 25
Score = 31.4 bits (71), Expect = 0.15
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPV 518
+FIGG+ W+T + L F QFG V
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEV 25
>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 = 31.2 bits (71), Expect = 0.16
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
++++G + ++ E + FS FGP+K++ M
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDM 32
Score = 29.7 bits (67), Expect = 0.70
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK---VEWPQGT 59
++++G + ++ E + FS FGP+K + W T
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVT 38
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 31.6 bits (71), Expect = 0.16
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAEMSSD 531
+++G + D E L+L +FSQ GP K+ M S+D
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND 39
Score = 28.5 bits (63), Expect = 2.2
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++G + D E L+L +FSQ GP K
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCK 27
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 31.5 bits (71), Expect = 0.17
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+GG+ WDT + L F++FG V
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEV 26
Score = 31.5 bits (71), Expect = 0.17
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV 518
K+F+GG+ WDT + L F++FG V
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEV 26
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 31.0 bits (71), Expect = 0.17
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+++ +P E L FS +G V+ V + R
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR 32
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 31.1 bits (70), Expect = 0.24
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ WDT + L S+FG V
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEV 26
Score = 31.1 bits (70), Expect = 0.24
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV 518
K+FIGG+ WDT + L S+FG V
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEV 26
>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 = 31.0 bits (71), Expect = 0.27
Identities = 8/40 (20%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNRAEMSS 530
K+F+G +P E + +F ++G ++ ++ ++ S
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQS 40
Score = 29.8 bits (68), Expect = 0.68
Identities = 7/27 (25%), Positives = 16/27 (59%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+F+G +P E + +F ++G ++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIE 27
>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 = 30.8 bits (69), Expect = 0.30
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++G + D E L+L +FSQ GP K+ M
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKM 31
Score = 29.2 bits (65), Expect = 0.86
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++G + D E L+L +FSQ GP K
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCK 27
>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 = 30.2 bits (69), Expect = 0.37
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+F+G +P+D E L F G V+AV
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAV 29
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 30.3 bits (68), Expect = 0.38
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+FIGG+ WDT + L FS+FG V
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEV 25
Score = 30.3 bits (68), Expect = 0.38
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPV 518
+FIGG+ WDT + L FS+FG V
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEV 25
>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 = 30.2 bits (69), Expect = 0.45
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++G + + T E + +FS+ G +K ++M
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIM 30
>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 = 30.1 bits (68), Expect = 0.48
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+FIGG+ W T L FS+FG +K +VM
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVM 31
Score = 27.8 bits (62), Expect = 3.0
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+FIGG+ W T L FS+FG +K
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIK 26
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 30.3 bits (69), Expect = 0.49
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+F+G +P T + L +F QFGP+++V
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESV 30
Score = 29.5 bits (67), Expect = 0.89
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+F+G +P T + L +F QFGP+
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPI 27
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 31.5 bits (72), Expect = 0.58
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 416 RSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQS 453
R+S GG+ GGGGG G GGG GG
Sbjct: 119 RASRGGGGGGGGGGFGGGGGGSGG---GGGGGGGGGAP 153
>gnl|CDD|238126 cd00207, fer2, 2Fe-2S iron-sulfur cluster binding domain.
Iron-sulfur proteins play an important role in electron
transfer processes and in various enzymatic reactions.
The family includes plant and algal ferredoxins, which
act as electron carriers in photosynthesis and
ferredoxins, which participate in redox chains (from
bacteria to mammals). Fold is ismilar to thioredoxin.
Length = 84
Score = 30.1 bits (68), Expect = 0.61
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 9/33 (27%)
Query: 213 PYFCREGICYRYFCRSCWLKVHI--GEYSQHDP 243
PY CR G C +C KV + GE Q DP
Sbjct: 32 PYSCRAGA-----CGTC--KVEVVEGEVDQSDP 57
>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 = 29.8 bits (67), Expect = 0.62
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV 51
+F+G +P++ E L +FS+ GPV
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPV 25
Score = 29.8 bits (67), Expect = 0.62
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPV 518
+F+G +P++ E L +FS+ GPV
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPV 25
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 32.3 bits (73), Expect = 0.62
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 397 ANGTAGSVPSPHTSPLN------SPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGG 450
ANG +VP+ + P N + G G YGG G + G GGG+G
Sbjct: 481 ANGKGNNVPAKKSRPSNDQKQYVNKSGEGISKV----GQSYGGRGRTRGRGRGGGGGRGR 536
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 30.7 bits (69), Expect = 0.63
Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNRA 526
+F+ +P+D E L FS+FG V+ V++++
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKS 38
Score = 29.5 bits (66), Expect = 1.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ +P+D E L FS+FG V+
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVR 29
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 31.9 bits (73), Expect = 0.75
Identities = 23/50 (46%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 414 SPRSSGARHSPPSNGGYYGGGGGG---QYLHNGDG-GGQGGLQSTLDIAA 459
S SS R S P GGYYG GGG +L G GG GGL L + A
Sbjct: 17 SRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGGLFGLLILMA 66
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 29.7 bits (66), Expect = 0.82
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
K+FIGG+ W T L FS+FG ++ ++ R
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMR 33
Score = 28.1 bits (62), Expect = 2.2
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+FIGG+ W T L FS+FG ++
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIR 27
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 29.3 bits (65), Expect = 1.1
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
K+F+GG+ DT E+ L F ++G + +
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTI 30
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 28.9 bits (65), Expect = 1.1
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+I++G +P D E + +F ++GP+KA+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAI 29
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in Fab1,
YOTB, Vac1, and EEA1;.
Length = 57
Score = 28.6 bits (64), Expect = 1.2
Identities = 12/55 (21%), Positives = 14/55 (25%), Gaps = 14/55 (25%)
Query: 200 EDNVCSECQTHSGPYF--------CREGICYRYFCRSCWLKVHIGEYSQHDPIVR 246
+ + C C F CR C R FC C VR
Sbjct: 1 DASSCMGCGKP----FTLTRRRHHCR--NCGRIFCSKCSSNRIPLPSMGGGKPVR 49
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 30.4 bits (68), Expect = 1.3
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 465 SANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
S+N +P + G L L +S K+FIGG+ W T + L F+ FG V
Sbjct: 16 SSNGNVPVTSMLGSLRL--------MSTKLFIGGLSWGTDDASLRDAFAHFGDV 61
Score = 30.0 bits (67), Expect = 1.4
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S ++S K+FIGG+ W T + L F+ FG V
Sbjct: 29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDV 61
Score = 29.2 bits (65), Expect = 2.8
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 406 SPHTSPLNSPRSSGARHSPPSNGGYYGGGGGG 437
+P ++PR+ G GG YGGGG G
Sbjct: 109 NPANDRPSAPRAYGGGGGYSGGGGGYGGGGDG 140
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 28.4 bits (64), Expect = 1.5
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
K+F+G + D E L FSQFG V V +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI 32
Score = 27.6 bits (62), Expect = 3.4
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+G + D E L FSQFG V
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEV 27
>gnl|CDD|206611 pfam14445, Prok-RING_2, Prokaryotic RING finger family 2. RING
finger family found sporadically in bacteria and
archaea, and associated with other components of the
ubiquitin-based signaling and degradation system,
including ubiquitin and the E1 and E2 proteins. The
bacterial versions contain transmembrane helices.
Length = 57
Score = 28.2 bits (63), Expect = 1.7
Identities = 10/31 (32%), Positives = 12/31 (38%), Gaps = 5/31 (16%)
Query: 203 VCSECQT---HSGPYFCREGICYRYFCRSCW 230
C C T C C R+ CR+CW
Sbjct: 9 RCDLCLTSAEQVDLRQC--VHCGRWQCRACW 37
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM1 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 28.3 bits (63), Expect = 1.7
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+G +P + E + ++F Q+G V
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKV 27
Score = 28.3 bits (63), Expect = 1.7
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV 518
K+F+G +P + E + ++F Q+G V
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKV 27
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a major
component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 30.2 bits (68), Expect = 1.8
Identities = 18/65 (27%), Positives = 20/65 (30%)
Query: 389 NTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQ 448
NTG S G+ G P G P G GGG H G G
Sbjct: 11 NTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQG 70
Query: 449 GGLQS 453
GG +
Sbjct: 71 GGTHN 75
>gnl|CDD|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other
protein.
Length = 63
Score = 28.1 bits (63), Expect = 1.9
Identities = 7/23 (30%), Positives = 9/23 (39%), Gaps = 2/23 (8%)
Query: 204 CSECQTHSGPYFCREGICYRYFC 226
CSEC + + C C C
Sbjct: 1 CSECGSTENLWLC--LTCGHVGC 21
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 28.3 bits (64), Expect = 2.1
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA------EMSSDDVR 534
+ + +P D E L+ + S FG V V++ R EM D V
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEM--DSVE 46
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 28.4 bits (64), Expect = 2.1
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
K+++G + + L F ++GP+++V
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSV 29
Score = 28.0 bits (63), Expect = 2.4
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKVEW 55
K+++G + + L F ++GP++ W
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVW 30
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 28.5 bits (64), Expect = 2.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+F+G +P + E L +F QFG +
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIY 33
Score = 28.5 bits (64), Expect = 2.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK 519
K+F+G +P + E L +F QFG +
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIY 33
>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 = 30.2 bits (68), Expect = 3.0
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRAEMSS 530
++I+IG +P E + + FG +KA ++ + A S
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLS 336
>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 = 27.6 bits (62), Expect = 3.4
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
S +F+ + + + L +F QFG ++ +
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFGDIRTL 31
>gnl|CDD|221868 pfam12938, M_domain, M domain of GW182.
Length = 238
Score = 29.5 bits (66), Expect = 4.4
Identities = 20/80 (25%), Positives = 26/80 (32%), Gaps = 7/80 (8%)
Query: 386 SLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSG------ARHSPPSNGGYYGGGGGGQY 439
NN G G G +P+ + L+S S G PP G G GG
Sbjct: 33 LPNNLGGG-GGGPGGGGGGNNPNLASLSSLTSQGLGKILSGLQPPPLGNGGGSGAGGPGP 91
Query: 440 LHNGDGGGQGGLQSTLDIAA 459
+ G G G + A
Sbjct: 92 VGGGGGPGVAPNNIQPNAQA 111
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 29.1 bits (66), Expect = 5.0
Identities = 13/26 (50%), Positives = 14/26 (53%)
Query: 425 PSNGGYYGGGGGGQYLHNGDGGGQGG 450
GGY GGG GG + DG G GG
Sbjct: 67 MVKGGYNGGGDGGNDNSSNDGSGSGG 92
>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 = 27.3 bits (61), Expect = 5.3
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
IF+ +P D E LL +FS FG V V
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNV 31
>gnl|CDD|233386 TIGR01378, thi_PPkinase, thiamine pyrophosphokinase. This model
has been revised. Originally, it described strictly
eukaryotic thiamine pyrophosphokinase. However, it is
now expanded to include also homologous enzymes,
apparently functionally equivalent, from species that
rely on thiamine pyrophosphokinase rather than
thiamine-monophosphate kinase (TIGR01379) to produce the
active TPP cofactor. This includes the thiamine
pyrophosphokinase from Bacillus subtilis, previously
designated YloS [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 205
Score = 28.8 bits (65), Expect = 5.5
Identities = 21/85 (24%), Positives = 30/85 (35%), Gaps = 10/85 (11%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRIT 166
Q L PGK G +L D+ G+ T KYP+ + +
Sbjct: 126 DEQNVIRLLLPGKYQIFKEPKGTYI--SLLPFGGDV------HGLTTKGLKYPLNNADLK 177
Query: 167 FGSTRAYSDAIRAAF--IEVKSGRI 189
FG TR S+ + V SG +
Sbjct: 178 FGGTRGISNEFIGNKATVSVDSGIL 202
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 29.4 bits (66), Expect = 5.7
Identities = 21/72 (29%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 384 SLSLNNTGQSNVRANGTAGSVPSPHTSPLNS-----PRSSGARHSPPSNGGYYGGGGGGQ 438
S S + +S RA+ S + +S S + S GGGGGG
Sbjct: 28 SRSPQSATRSP-RASSIKCSASASASSSATSSSASLVANGAVALLSASAISGGGGGGGGG 86
Query: 439 YLHNGDGGGQGG 450
+ G GGG GG
Sbjct: 87 FGGFGGGGGGGG 98
Score = 29.1 bits (65), Expect = 7.7
Identities = 17/58 (29%), Positives = 26/58 (44%)
Query: 393 SNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGG 450
A+ +A S + ++ L + + + +GG GGGGG G GGG GG
Sbjct: 43 IKCSASASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGG 100
Score = 29.1 bits (65), Expect = 7.9
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 397 ANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGG 450
A ++ S+ + L S + GG +GG GGG G GGG GG
Sbjct: 55 ATSSSASLVANGAVALLSASAISGGGGG--GGGGFGGFGGG-----GGGGGGGG 101
>gnl|CDD|185134 PRK15212, PRK15212, virulence protein SpvA; Provisional.
Length = 255
Score = 29.0 bits (64), Expect = 5.8
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 259 PHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLT 295
PH + L+ LN S EDI + S+ PWF S LT
Sbjct: 138 PHDQ-VELSLLNTDVSLEDIISESSIDWPWFLSNSLT 173
>gnl|CDD|224480 COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism].
Length = 212
Score = 28.8 bits (65), Expect = 6.5
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 157 KYPIGSGRITFGSTRAYSDAIRA--AFIEVKSGRI 189
KYP+ + + FGS+R+ S+ + +KSG +
Sbjct: 169 KYPLKNADLPFGSSRSISNEFIGDPVTVSLKSGIV 203
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 28.7 bits (64), Expect = 7.3
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 383 ASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHN 442
LS+ +S R G + PS ++ + SG +S GGY GGG G ++
Sbjct: 39 PPLSVAAAARSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYS---GGGYSGGGFGFPFIIP 95
Query: 443 GDGGGQGGL 451
G GGG G
Sbjct: 96 GGGGGGGFG 104
>gnl|CDD|220749 pfam10428, SOG2, RAM signalling pathway protein. SOG2 proteins in
Saccharomyces cerevisiae are involved in cell separation
and cytokinesis.
Length = 419
Score = 28.9 bits (65), Expect = 7.5
Identities = 26/147 (17%), Positives = 40/147 (27%), Gaps = 25/147 (17%)
Query: 245 VRNVRKSPPSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRS 304
+RN S P H + ++ A ++P D +TP R
Sbjct: 141 LRNAWSSLG--PPLQHRKRD--------AVTASPSSMIARNTPISDRLRPRSVTPTRGRR 190
Query: 305 PFESNSYAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYY-----------QTGGSTDY 353
P S + ++ P PPY S T S +
Sbjct: 191 PSSSPRSLSNPTTLESPSNLQVTTDVPPPYSNGTSRSSTMSSSANLSIISSLATPRSGES 250
Query: 354 FSYNNAPSHLNLNGSMTDSSNLDNIED 380
F + S+ S LD E+
Sbjct: 251 FRSTPTSG----SSSINPVSGLDEAEE 273
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 29.0 bits (65), Expect = 8.6
Identities = 30/141 (21%), Positives = 40/141 (28%), Gaps = 15/141 (10%)
Query: 281 SSATSSPWFDSPLLTPMTPQIVRSPFESNSYAIHGSSHSPPFGSHSMESCSPPYLTDEGD 340
+S TS+P S L P SP S S + S S S + + P
Sbjct: 122 ASKTSTPMNTSEPLVPGHSSFSDSPSRSASPSRKFSPSSTIQQSPQLTPSNKPASPSSSY 181
Query: 341 YSPYYQT---------GGSTDYFSYNNAPSHLNLNGSMTDSSNLDNI------EDLLASL 385
SP Y + S S S + TD L+ E + +
Sbjct: 182 QSPSYSSSLGPVNSSGNRSNLRSSPWALRSSGDKKDITTDEKYLETFLAEVDEEQHMITS 241
Query: 386 SLNNTGQSNVRANGTAGSVPS 406
S N S PS
Sbjct: 242 SAGKNATPPETINSFGSSSPS 262
>gnl|CDD|119376 cd06414, GH25_LytC-like, The LytC lysozyme of Streptococcus
pneumoniae is a bacterial cell wall hydrolase that
cleaves the beta1-4-glycosydic bond located between the
N-acetylmuramoyl-N-glucosaminyl residues of the cell
wall polysaccharide chains. LytC is composed of a
C-terminal glycosyl hydrolase family 25 (GH25) domain
and an N-terminal choline-binding module (CBM)
consisting of eleven homologous repeats that
specifically recognizes the choline residues of
pneumococcal lipoteichoic and teichoic acids. This
domain arrangement is the reverse of the major
pneumococcal autolysin, LytA, and the CPL-1-like lytic
enzymes of the pneumococcal bacteriophages, in which the
CBM (consisting of six repeats) is at the C-terminus.
This model represents the C-terminal catalytic domain of
the LytC-like enzymes.
Length = 191
Score = 27.9 bits (63), Expect = 9.5
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 150 GIDTDKHKYPIGSGRITFGSTRAYSDAIRAAFIEVKSGRICKKLQIDPYLEDNV--CSEC 207
GID + + G I + + + + A I G +LQ D Y E+N+
Sbjct: 3 GIDVSEWQ-----GDIDW--KKVKASGVDFAIIRAGYGGY-GELQEDKYFEENIKGAKAA 54
Query: 208 QTHSGPYF 215
G YF
Sbjct: 55 GIPVGVYF 62
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
0.314 0.133 0.413
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: 27,224,835
Number of extensions: 2609721
Number of successful extensions: 2242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2157
Number of HSP's successfully gapped: 181
Length of query: 534
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 433
Effective length of database: 6,457,848
Effective search space: 2796248184
Effective search space used: 2796248184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.2 bits)