RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4383
(89 letters)
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 69.9 bits (172), Expect = 8e-18
Identities = 24/40 (60%), Positives = 30/40 (75%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ LGIS+HKGY F+QF N DAR+A GE+GR + GQ L
Sbjct: 26 GKILGISLHKGYGFVQFDNEEDARAAVAGENGREIAGQKL 65
Score = 63.8 bits (156), Expect = 2e-15
Identities = 20/36 (55%), Positives = 26/36 (72%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+HKGY F+QF N DAR+A GE+GR + GQ L I+
Sbjct: 33 LHKGYGFVQFDNEEDARAAVAGENGREIAGQKLDIN 68
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 56.6 bits (136), Expect = 2e-12
Identities = 21/40 (52%), Positives = 30/40 (75%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ +G S+HKG+AF+Q+ N +AR+A GEDGR + GQ L
Sbjct: 27 GKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVL 66
Score = 52.3 bits (125), Expect = 7e-11
Identities = 19/37 (51%), Positives = 28/37 (75%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+HKG+AF+Q+ N +AR+A GEDGR + GQ L I++
Sbjct: 34 VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL 70
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 55.4 bits (133), Expect = 5e-12
Identities = 23/40 (57%), Positives = 31/40 (77%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ +G S+HKGYAF+Q+SN AR A +GE+GR + GQTL
Sbjct: 27 GRVVGCSVHKGYAFVQYSNERHARGAVIGENGRVLAGQTL 66
Score = 52.4 bits (125), Expect = 9e-11
Identities = 22/37 (59%), Positives = 29/37 (78%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+HKGYAF+Q+SN AR A +GE+GR + GQTL I+M
Sbjct: 34 VHKGYAFVQYSNERHARGAVIGENGRVLAGQTLDINM 70
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 46.9 bits (111), Expect = 1e-08
Identities = 19/40 (47%), Positives = 28/40 (70%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ +G S+HKGYAF+Q+ + AR+A GE+ R + GQ L
Sbjct: 27 GKIVGCSVHKGYAFVQYISERHARAAVAGENARIIAGQPL 66
Score = 41.9 bits (98), Expect = 9e-07
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+HKGYAF+Q+ + AR+A GE+ R + GQ L I+
Sbjct: 34 VHKGYAFVQYISERHARAAVAGENARIIAGQPLDIN 69
>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 = 40.7 bits (96), Expect = 3e-06
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A DGR + G + + + +G
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73
Score = 38.8 bits (91), Expect = 2e-05
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQ 67
G+AF++F +P DA A DGR + G
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGN 64
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+AF++F +P DA A +G+ + G+ L +S
Sbjct: 38 SKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
Score = 37.3 bits (87), Expect = 7e-05
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AF++F +P DA A +G+ + G+ L
Sbjct: 38 SKGFAFVEFESPEDAEKALEALNGKELDGRKL 69
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 38.3 bits (90), Expect = 3e-05
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+AF++F + DA A +G+ + G+ L
Sbjct: 40 SKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72
Score = 38.0 bits (89), Expect = 3e-05
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+AF++F + DA A +G+ + G+ L
Sbjct: 40 SKGFAFVEFESEEDAEKALEALNGKELDGRPL 71
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 36.1 bits (83), Expect = 2e-04
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A G DG+ + G + + + G
Sbjct: 37 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG 73
Score = 34.2 bits (78), Expect = 0.001
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLG 66
G+AF++F +P DA A G DG+ + G
Sbjct: 37 GFAFVEFEDPRDAEDAVRGLDGKVICG 63
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 35.8 bits (83), Expect = 2e-04
Identities = 11/41 (26%), Positives = 24/41 (58%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ I++ G+ F++F +P DA A +G+ + G+ ++
Sbjct: 24 GRIREINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVI 64
Score = 33.1 bits (76), Expect = 0.002
Identities = 10/40 (25%), Positives = 22/40 (55%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ G+ F++F +P DA A +G+ + G+ + + +G
Sbjct: 31 LKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 35.7 bits (83), Expect = 4e-04
Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 4/43 (9%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQ 45
KGYA I++ +A++A G +G+ +LGQT+ + +AF++
Sbjct: 48 KGYALIEYETKKEAQAAIEGLNGKELLGQTISVD----WAFVK 86
Score = 34.5 bits (80), Expect = 0.001
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYA I++ +A++A G +G+ +LGQT+
Sbjct: 48 KGYALIEYETKKEAQAAIEGLNGKELLGQTI 78
>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 = 34.5 bits (80), Expect = 6e-04
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+AF++F + DA A +G+ + G+ L
Sbjct: 38 SKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
Score = 34.5 bits (80), Expect = 6e-04
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AF++F + DA A +G+ + G+ L
Sbjct: 38 SKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 34.6 bits (80), Expect = 8e-04
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
GY F+ F +A A +G+T LG+ LV
Sbjct: 45 GYCFVTFETKEEAEKALKSLNGKTALGKKLV 75
Score = 33.0 bits (76), Expect = 0.003
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
GY F+ F +A A +G+T LG+ L
Sbjct: 45 GYCFVTFETKEEAEKALKSLNGKTALGKKL 74
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and
similar proteins. This subfamily corresponds to the
RRM of Nab3p, an acidic nuclear polyadenylated
RNA-binding protein encoded by Saccharomyces cerevisiae
NAB3 gene that is essential for cell viability. Nab3p
is predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA
processing. Nab3p contains an N-terminal
aspartic/glutamic acid-rich region, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal region rich in glutamine and proline
residues. .
Length = 71
Score = 34.3 bits (79), Expect = 0.001
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ I + Y F+QF +P +A E G+ + G+ L
Sbjct: 25 GELAQIVLKNAYGFVQFDSPESCANAINCEQGKMIRGRKL 64
Score = 30.5 bits (69), Expect = 0.022
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 5 YAFIQFSNPHDARSACLGEDGRTVLGQTL 33
Y F+QF +P +A E G+ + G+ L
Sbjct: 36 YGFVQFDSPESCANAINCEQGKMIRGRKL 64
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins.
This subgroup corresponds to the RRM1 of SF2, also
termed SR1 protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal domain rich in proline, serine
and lysine residues (PSK domain), a composition
reminiscent of histones. This PSK domain harbors a
putative phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 34.0 bits (78), Expect = 0.001
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
GYAFI+F + DA A G DG GQ L
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDFDGQRL 68
Score = 34.0 bits (78), Expect = 0.001
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
GYAFI+F + DA A G DG GQ L
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDFDGQRL 68
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Although
the cellular function of RBM23 remains unclear, it
shows high sequence homology to RBM39 and contains two
RRMs. It may possibly function as a pre-mRNA splicing
factor. .
Length = 73
Score = 33.8 bits (78), Expect = 0.001
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGY FIQF++ DA+ A
Sbjct: 40 KGYGFIQFADAEDAKKA 56
Score = 33.8 bits (78), Expect = 0.001
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 39 KGYAFIQFSNPHDARSA 55
KGY FIQF++ DA+ A
Sbjct: 40 KGYGFIQFADAEDAKKA 56
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 33.5 bits (77), Expect = 0.001
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G +I F DA A + +GR G+ +
Sbjct: 35 HKRGNVYITFERSEDAARAIVDLNGRYFDGRLV 67
Score = 33.5 bits (77), Expect = 0.001
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G +I F DA A + +GR G+ +
Sbjct: 35 HKRGNVYITFERSEDAARAIVDLNGRYFDGRLV 67
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4
is a splicing regulatory serine/arginine (SR) protein
that plays an important role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
For instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, it activates splicing of the cardiac troponin
T (cTNT) alternative exon by direct interactions with
the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between
the nucleus and cytoplasm. It contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 33.8 bits (77), Expect = 0.002
Identities = 11/41 (26%), Positives = 23/41 (56%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ L + + GY F++F + DA A +G+ + G+ ++
Sbjct: 24 GKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVI 64
Score = 30.7 bits (69), Expect = 0.021
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ GY F++F + DA A +G+ + G+ + + +G
Sbjct: 31 LKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARG 70
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the
RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. SRSF12, also
termed 35 kDa SR repressor protein (SRrp35), or
splicing factor, arginine/serine-rich 13B (SFRS13B), or
splicing factor, arginine/serine-rich 19 (SFRS19), is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice
site of the adenovirus E1A pre-mRNA in vivo. Both,
SRSF10 and SRSF12, contain a single N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a C-terminal RS domain rich in serine-arginine
dipeptides. .
Length = 84
Score = 33.5 bits (77), Expect = 0.002
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGY 41
+G+A++QF + DA A D LG+ + I +G
Sbjct: 42 RGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQGD 80
Score = 30.4 bits (69), Expect = 0.029
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+A++QF + DA A D LG+ +
Sbjct: 42 RGFAYVQFEDVRDAEDALYYLDRTRFLGREI 72
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is ubiquitously expressed Hu family member. It has
a variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the
cytoplasm, Hu proteins recognize and bind to AU-rich
RNA elements (AREs) in the 3' untranslated regions
(UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. This family
also includes the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own
pre-mRNA and promotes female-specific alternative
splicing. It contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 77
Score = 33.5 bits (77), Expect = 0.002
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
G S+ GY F+ + + +DA+ A +G + + L VSY
Sbjct: 39 GQSL--GYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSY 76
Score = 31.2 bits (71), Expect = 0.013
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
GY F+ + + +DA+ A +G + + L +S
Sbjct: 43 GYGFVDYVDENDAQKAINTLNGFEIRNKRLKVS 75
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 33.5 bits (77), Expect = 0.002
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNP 49
KG A++++ N A A L DG + +T+ +++ SNP
Sbjct: 43 KGLAYVEYENESSASQAVLKMDGTEIKEKTISVAI---------SNP 80
Score = 32.0 bits (73), Expect = 0.009
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG A++++ N A A L DG + +T+
Sbjct: 43 KGLAYVEYENESSASQAVLKMDGTEIKEKTI 73
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 32.5 bits (75), Expect = 0.003
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMH 38
G+AF++FS A A +G G+ L +
Sbjct: 20 KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
Score = 32.5 bits (75), Expect = 0.003
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
G+AF++FS A A +G G+ L V Y
Sbjct: 20 KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33
(Cyp33) and similar proteins. This subfamily
corresponds to the RRM of Cyp33, also termed
peptidyl-prolyl cis-trans isomerase E (PPIase E), or
cyclophilin E, or rotamase E. Cyp33 is a nuclear
RNA-binding cyclophilin with an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal PPIase domain. Cyp33 possesses RNA-binding
activity and preferentially binds to polyribonucleotide
polyA and polyU, but hardly to polyG and polyC. It
binds specifically to mRNA, which can stimulate its
PPIase activity. Moreover, Cyp33 interacts with the
third plant homeodomain (PHD3) zinc finger cassette of
the mixed lineage leukemia (MLL) proto-oncoprotein and
a poly-A RNA sequence through its RRM domain. It
further mediates downregulation of the expression of
MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a
proline isomerase-dependent manner. Cyp33 also
possesses a PPIase activity that catalyzes cis-trans
isomerization of the peptide bond preceding a proline,
which has been implicated in the stimulation of folding
and conformational changes in folded and unfolded
proteins. The PPIase activity can be inhibited by the
immunosuppressive drug cyclosporin A. .
Length = 73
Score = 33.0 bits (76), Expect = 0.003
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
H+G+AF++F P DA +A + + G+T+ ++
Sbjct: 39 HRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73
Score = 32.6 bits (75), Expect = 0.003
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F P DA +A + + G+T+
Sbjct: 39 HRGFAFVEFEEPEDAAAAIDNMNESELFGRTI 70
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 32.9 bits (76), Expect = 0.003
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 11/41 (26%)
Query: 21 LGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDG 61
+ E G+T KGYAF++F+ P +A+ A +G
Sbjct: 43 VDETGKT-----------KGYAFVEFATPEEAKEAVKALNG 72
Score = 32.2 bits (74), Expect = 0.006
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 3 KGYAFIQFSNPHDARSACLGEDG 25
KGYAF++F+ P +A+ A +G
Sbjct: 50 KGYAFVEFATPEEAKEAVKALNG 72
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 32.7 bits (75), Expect = 0.004
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 HKGYAFIQFSNPHDARSAC 20
KG+AFI+F P +A+ AC
Sbjct: 40 IKGFAFIEFETPEEAQKAC 58
Score = 32.7 bits (75), Expect = 0.004
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 38 HKGYAFIQFSNPHDARSAC 56
KG+AFI+F P +A+ AC
Sbjct: 40 IKGFAFIEFETPEEAQKAC 58
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 82
Score = 32.9 bits (76), Expect = 0.004
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
I+ K +AF++F +A +A L DG GQ L
Sbjct: 44 INPEKNFAFVEFRTVEEA-TAALALDGIIFKGQPL 77
Score = 31.7 bits (73), Expect = 0.008
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
K +AF++F +A +A L DG GQ L I
Sbjct: 48 KNFAFVEFRTVEEA-TAALALDGIIFKGQPLKIR 80
>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 = 33.0 bits (76), Expect = 0.004
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+GYAFI+F + D ++A DG+ + G+ ++
Sbjct: 42 PRGYAFIEFEHERDMKAAYKYADGKKIDGRRVL 74
Score = 32.6 bits (75), Expect = 0.005
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLG 30
+GYAFI+F + D ++A DG+ + G
Sbjct: 42 PRGYAFIEFEHERDMKAAYKYADGKKIDG 70
>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 = 32.6 bits (75), Expect = 0.004
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F +F + A SA +G G+ L
Sbjct: 40 KGYGFCEFEDIETAASAIRNLNGYEFNGRAL 70
Score = 32.6 bits (75), Expect = 0.004
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F +F + A SA +G G+ L
Sbjct: 40 KGYGFCEFEDIETAASAIRNLNGYEFNGRAL 70
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 32.8 bits (75), Expect = 0.004
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 5 YAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
YAF+QF+N DA++A G + G+ + K
Sbjct: 47 YAFVQFTNDDDAKNALAKGQGTILDGRHIRCERAKV 82
Score = 30.1 bits (68), Expect = 0.041
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 41 YAFIQFSNPHDARSACLGEDGRTVLGQTL 69
YAF+QF+N DA++A G + G+ +
Sbjct: 47 YAFVQFTNDDDAKNALAKGQGTILDGRHI 75
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 32.6 bits (75), Expect = 0.004
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
KG+AF+QF++ DA A G +G+ + G+ + +
Sbjct: 39 KKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAV 72
Score = 32.6 bits (75), Expect = 0.005
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AF+QF++ DA A G +G+ + G+ +
Sbjct: 39 KKGFAFVQFTSKADAEKAIKGVNGKKIKGRPV 70
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 32.2 bits (74), Expect = 0.005
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+ G+AF+ F + A +A L +G + G+ + +S+
Sbjct: 44 NNGFAFVTFKDASSAENA-LQLNGTELGGRKISVSL 78
Score = 30.3 bits (69), Expect = 0.028
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 38 HKGYAFIQFSNPHDARSA 55
+ G+AF+ F + A +A
Sbjct: 44 NNGFAFVTFKDASSAENA 61
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 33.8 bits (76), Expect = 0.005
Identities = 9/49 (18%), Positives = 22/49 (44%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNP 49
+G+AF++F + A A +G+ + G+ L + + + +
Sbjct: 155 KSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELS 203
Score = 33.0 bits (74), Expect = 0.010
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
+G+AF++F + A A +G+ + G+ L V
Sbjct: 155 KSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA 192
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 31.0 bits (71), Expect = 0.014
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+ +GYA+++F +P DA A DG + GQ + +
Sbjct: 38 LPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73
Score = 30.6 bits (70), Expect = 0.020
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ +GYA+++F +P DA A DG + GQ +
Sbjct: 38 LPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds
to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share
high sequence similarity and are expressed in a wide
variety of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains. This subfamily also
includes a yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1, termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein, which has been identified as
both a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP).
It may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. PUB1 is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it
is one of the major cellular proteins cross-linked by
UV light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there
is no strong evidence implicating PUB1 in the mechanism
of DNA replication. PUB1 contains three RRMs, and a GAR
motif (glycine and arginine rich stretch) that is
located between RRM2 and RRM3. .
Length = 73
Score = 31.1 bits (71), Expect = 0.014
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYAF++F A +A + +G ++ GQT+
Sbjct: 36 KGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66
Score = 31.1 bits (71), Expect = 0.014
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYAF++F A +A + +G ++ GQT+
Sbjct: 36 KGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 30.9 bits (70), Expect = 0.015
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + + K +AF++F + DA A G + G L
Sbjct: 25 GPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLT 65
Score = 29.0 bits (65), Expect = 0.11
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ K +AF++F + DA A G + G L
Sbjct: 32 IRKTFAFVEFEDSEDATKALEALHGSRIDGSVL 64
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 31.0 bits (71), Expect = 0.017
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTV-LGQTLGISM 37
+GYAF+ ++N A+ A + G+ LG+ +
Sbjct: 42 RGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCI 77
Score = 29.4 bits (67), Expect = 0.066
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 39 KGYAFIQFSNPHDARSA 55
+GYAF+ ++N A+ A
Sbjct: 42 RGYAFVTYTNKEAAQRA 58
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 30.7 bits (69), Expect = 0.021
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGR 62
G+ I + +G+ F++F +P DA A DG+
Sbjct: 24 GRIRDIDLKRGFGFVEFDDPRDADDAVYELDGK 56
Score = 28.8 bits (64), Expect = 0.098
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
+ +G+ F++F +P DA A DG+ + + + I
Sbjct: 31 LKRGFGFVEFDDPRDADDAVYELDGKELCNERVTI 65
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 30.6 bits (70), Expect = 0.026
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 1 MHKGYAFIQFSNPHDARSAC 20
H+GY F++F + DA A
Sbjct: 38 AHQGYGFVEFLSEEDADYAI 57
Score = 30.6 bits (70), Expect = 0.026
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 37 MHKGYAFIQFSNPHDARSAC 56
H+GY F++F + DA A
Sbjct: 38 AHQGYGFVEFLSEEDADYAI 57
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 30.2 bits (69), Expect = 0.030
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 5/33 (15%)
Query: 1 MHKGYAFIQFSNPHDARSA--CLGE---DGRTV 28
+G+AF++F++P DA +A L DGRT+
Sbjct: 36 RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68
Score = 30.2 bits (69), Expect = 0.030
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 5/33 (15%)
Query: 37 MHKGYAFIQFSNPHDARSA--CLGE---DGRTV 64
+G+AF++F++P DA +A L DGRT+
Sbjct: 36 RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 30.3 bits (68), Expect = 0.031
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGYAF++F + DA+ A
Sbjct: 38 KGYAFVEFESAEDAKEA 54
Score = 30.3 bits (68), Expect = 0.031
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 39 KGYAFIQFSNPHDARSA 55
KGYAF++F + DA+ A
Sbjct: 38 KGYAFVEFESAEDAKEA 54
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 30.2 bits (69), Expect = 0.033
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 11/37 (29%)
Query: 20 CLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSAC 56
+DGR G A+++F++P DAR A
Sbjct: 33 VYDDDGR-----------PTGEAYVEFASPEDARRAL 58
Score = 29.4 bits (67), Expect = 0.055
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 1 MHKGYAFIQFSNPHDARSAC 20
G A+++F++P DAR A
Sbjct: 39 RPTGEAYVEFASPEDARRAL 58
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation
factor (ACF). hnRNP R is a ubiquitously expressed
nuclear RNA-binding protein that specifically bind
mRNAs with a preference for poly(U) stretches and has
been implicated in mRNA processing and mRNA transport,
and also acts as a regulator to modify binding to
ribosomes and RNA translation. hnRNP Q is also a
ubiquitously expressed nuclear RNA-binding protein. It
has been identified as a component of the spliceosome
complex, as well as a component of the apobec-1
editosome, and has been implicated in the regulation of
specific mRNA transport. ACF is an RNA-binding subunit
of a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. This
family also includes two functionally unknown
RNA-binding proteins, RBM46 and RBM47. All members
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains).
Length = 72
Score = 29.9 bits (68), Expect = 0.044
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
K YAF+ F DA A +G+ + G + +S+ K
Sbjct: 35 KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAK 71
Score = 26.4 bits (59), Expect = 0.73
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K YAF+ F DA A +G+ + G +
Sbjct: 35 KDYAFVHFEERDDAVKAMEEMNGKELEGSPI 65
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 30.0 bits (68), Expect = 0.051
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGY 41
G A+ +FS+P A +G+ + L + +H Y
Sbjct: 47 GIAYAEFSSPEQAEKVVKDLNGKVFKNRKLFVKLHVPY 84
Score = 25.8 bits (57), Expect = 1.6
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYN 78
G A+ +FS+P A +G+ + L ++ +
Sbjct: 47 GIAYAEFSSPEQAEKVVKDLNGKVFKNRKL---FVKLHV 82
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). 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 polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 29.5 bits (67), Expect = 0.053
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
G A +Q +P A A +G + GQ L ++
Sbjct: 37 PGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEVNF 71
Score = 27.9 bits (63), Expect = 0.20
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G A +Q +P A A +G + GQ L
Sbjct: 37 PGTAMVQMGDPQAAERAIEYLNGVVLFGQKL 67
>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 = 31.0 bits (70), Expect = 0.058
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYAF ++ +P A +G+ L
Sbjct: 337 KGYAFCEYKDPSVTDVAIAALNGKDTGDNKL 367
Score = 31.0 bits (70), Expect = 0.058
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYAF ++ +P A +G+ L
Sbjct: 337 KGYAFCEYKDPSVTDVAIAALNGKDTGDNKL 367
>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 = 29.3 bits (66), Expect = 0.069
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+AF++F +P DA A G DG G L
Sbjct: 39 PFAFVEFEDPRDAEDAVRGRDGYDFDGYRL 68
Score = 29.3 bits (66), Expect = 0.069
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+AF++F +P DA A G DG G L
Sbjct: 39 PFAFVEFEDPRDAEDAVRGRDGYDFDGYRL 68
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 29.1 bits (65), Expect = 0.074
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ L I + GY F++F + DA A +G+ + G+ ++
Sbjct: 24 GKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVI 64
Score = 25.7 bits (56), Expect = 2.0
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ GY F++F + DA A +G+ + G+ + + +G
Sbjct: 31 LKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHARG 70
>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 = 29.2 bits (66), Expect = 0.077
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 1 MHKGYAFIQFSNPHDARSA 19
+ KGY F+ FS+ +A
Sbjct: 39 LSKGYGFVSFSSRDGLENA 57
Score = 29.2 bits (66), Expect = 0.077
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 37 MHKGYAFIQFSNPHDARSA 55
+ KGY F+ FS+ +A
Sbjct: 39 LSKGYGFVSFSSRDGLENA 57
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the
RRM of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). This
family also includes yeast eIF3-p33, a homolog of
vertebrate eIF-3G, plays an important role in the
initiation phase of protein synthesis in yeast. It
binds both, mRNA and rRNA, fragments due to an RRM near
its C-terminus. .
Length = 77
Score = 29.0 bits (66), Expect = 0.081
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGR 26
+G+AF+ F DA A +G
Sbjct: 41 RGFAFVTFHTREDAERAIEKLNGF 64
Score = 29.0 bits (66), Expect = 0.081
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGR 62
+G+AF+ F DA A +G
Sbjct: 41 RGFAFVTFHTREDAERAIEKLNGF 64
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 29.2 bits (65), Expect = 0.082
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A DGRT+ G + + + G
Sbjct: 42 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 78
Score = 28.1 bits (62), Expect = 0.27
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLG 66
G+AF++F +P DA A DGRT+ G
Sbjct: 42 GFAFVEFEDPRDAADAVRELDGRTLCG 68
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 29.2 bits (66), Expect = 0.089
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
KG+AF+ F P A A DG G+ L +
Sbjct: 41 KGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73
Score = 29.2 bits (66), Expect = 0.094
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AF+ F P A A DG G+ L
Sbjct: 41 KGFAFVSFMFPEHAVKAYSELDGSIFQGRLL 71
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 28.9 bits (65), Expect = 0.091
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQY 76
+AFI F N A+ A +G +V G + K+Q
Sbjct: 38 PHAFITFENLEAAQLAIETLNGASVDGNCI---KVQR 71
Score = 28.2 bits (63), Expect = 0.22
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+AFI F N A+ A +G +V G +
Sbjct: 38 PHAFITFENLEAAQLAIETLNGASVDGNCI 67
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 28.8 bits (64), Expect = 0.10
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 27 TVLGQTLGISM--HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSY 72
+ GQ + I + KGY+FI+FS A A + +G T+ G + Y
Sbjct: 22 SPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTIEGHVVKCY 69
Score = 25.8 bits (56), Expect = 1.5
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY+FI+FS A A + +G T+ G +
Sbjct: 36 KGYSFIRFSTHESAAHAIVSVNGTTIEGHVV 66
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM1 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two of which are followed by a glutamine-rich
stretch that may be involved in transcriptional
activity. In addition, NGR1 has an asparagine-rich
region near the carboxyl terminus which also harbors a
methionine-rich region. The subgroup also includes
NAM8, a putative RNA-binding protein that acts as a
suppressor of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 28.9 bits (65), Expect = 0.10
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 36 SMHKGYAFIQFSNPHDARSA 55
++ GY F++F +PH A++A
Sbjct: 39 GLNAGYCFVEFPSPHAAQNA 58
Score = 28.5 bits (64), Expect = 0.15
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 1 MHKGYAFIQFSNPHDARSA 19
++ GY F++F +PH A++A
Sbjct: 40 LNAGYCFVEFPSPHAAQNA 58
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 28.7 bits (65), Expect = 0.12
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQ 67
G S KGY F+ F A A +G + +
Sbjct: 40 GGS--KGYGFVHFETEEAAVRAIEKVNGMLLNDK 71
Score = 28.3 bits (64), Expect = 0.20
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQ 31
KGY F+ F A A +G + +
Sbjct: 43 KGYGFVHFETEEAAVRAIEKVNGMLLNDK 71
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 28.7 bits (64), Expect = 0.12
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 18 SACLGEDGRTVL---GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ C ++ R + G+ + K YAF+ +A +A +G+ V G+ +
Sbjct: 10 ATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEVKGRRI 64
Score = 27.9 bits (62), Expect = 0.20
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
K YAF+ +A +A +G+ V G+ + + +
Sbjct: 34 KDYAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 28.8 bits (65), Expect = 0.14
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+G+AF++++ DA A +G ++ G + +S
Sbjct: 44 RGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVS 77
Score = 28.4 bits (64), Expect = 0.18
Identities = 10/35 (28%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+G+AF++++ DA A +G ++ G + VS+
Sbjct: 44 RGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSF 78
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 28.5 bits (64), Expect = 0.17
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KG A + + +PH A +A + + +G T+ +S+
Sbjct: 48 KGEATVTYDDPHAASAAIEWFNNKDFMGNTIKVSL 82
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 28.3 bits (64), Expect = 0.18
Identities = 9/37 (24%), Positives = 20/37 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G+ F+ F + DA +A +G+ + G+ + + K
Sbjct: 43 RGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79
Score = 27.6 bits (62), Expect = 0.32
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+ F+ F + DA +A +G+ + G+ +
Sbjct: 43 RGFGFVTFESVEDADAAIRDLNGKELEGRVI 73
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 28.3 bits (64), Expect = 0.21
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ F+ F N A+ A +G+ V G+ L
Sbjct: 42 KGFGFVNFENHEAAQKAVEELNGKEVNGKKL 72
Score = 28.3 bits (64), Expect = 0.21
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ F+ F N A+ A +G+ V G+ L
Sbjct: 42 KGFGFVNFENHEAAQKAVEELNGKEVNGKKL 72
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 28.1 bits (63), Expect = 0.21
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
KG+A++ F +P DA A DG+ G+ + I
Sbjct: 44 KGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76
Score = 27.4 bits (61), Expect = 0.49
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+A++ F +P DA A DG+ G+ +
Sbjct: 44 KGFAYVLFLDPEDAVKAYKELDGKVFQGRLI 74
>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 = 28.3 bits (63), Expect = 0.22
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQ 31
+G+ F+ F NP DA+ A + +G++V G+
Sbjct: 42 RGFGFVTFENPDDAKDAMMAMNGKSVDGR 70
Score = 28.3 bits (63), Expect = 0.22
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQ 67
+G+ F+ F NP DA+ A + +G++V G+
Sbjct: 42 RGFGFVTFENPDDAKDAMMAMNGKSVDGR 70
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 28.0 bits (63), Expect = 0.23
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 2 HKGYAFIQFSNPHDARSA 19
H+G+AF++F +A++A
Sbjct: 40 HRGFAFVEFVTKQEAQNA 57
Score = 28.0 bits (63), Expect = 0.23
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 38 HKGYAFIQFSNPHDARSA 55
H+G+AF++F +A++A
Sbjct: 40 HRGFAFVEFVTKQEAQNA 57
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 27.6 bits (62), Expect = 0.29
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYN 78
+G AF+ + + +DA++AC G V + LV + YY
Sbjct: 41 RGTAFVVYEDIYDAKNACDHLSGFNVANRYLV---VLYYQ 77
Score = 26.0 bits (58), Expect = 1.2
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMH 38
+G AF+ + + +DA++AC G V + L + +
Sbjct: 41 RGTAFVVYEDIYDAKNACDHLSGFNVANRYLVVLYY 76
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 28.0 bits (63), Expect = 0.29
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 36 SMHKGYAFIQFSNPHDARSAC 56
SM GY F++F + A+ A
Sbjct: 46 SM--GYGFVEFKSKEAAQKAL 64
Score = 26.8 bits (60), Expect = 0.70
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 4 GYAFIQFSNPHDARSAC 20
GY F++F + A+ A
Sbjct: 48 GYGFVEFKSKEAAQKAL 64
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 27.6 bits (61), Expect = 0.30
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 2 HKGYAFIQFSNPHDARSA 19
++GYAF+ FSN +A++A
Sbjct: 41 NRGYAFVTFSNKQEAKNA 58
Score = 27.6 bits (61), Expect = 0.30
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 38 HKGYAFIQFSNPHDARSA 55
++GYAF+ FSN +A++A
Sbjct: 41 NRGYAFVTFSNKQEAKNA 58
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 27.9 bits (62), Expect = 0.31
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQY 76
+G+AF++FS +A +A +LG+ LV LQY
Sbjct: 41 RGFAFVEFSTAKEALNAMNALKDTHLLGRRLV---LQY 75
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 27.7 bits (61), Expect = 0.31
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+ YAF+ FSN DA A +G+ + G + +++ K
Sbjct: 44 RDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80
>gnl|CDD|188194 TIGR02018, his_ut_repres, histidine utilization repressor,
proteobacterial. This model represents a
proteobacterial histidine utilization repressor. It is
usually found clustered with the enzymes HutUHIG so that
it can regulate its own expression as well. A number of
species have several paralogs and may fine-tune the
regulation according to levels of degradation
intermediates such as urocanate. This family belongs to
the larger GntR family of transcriptional regulators
[Energy metabolism, Amino acids and amines, Regulatory
functions, DNA interactions].
Length = 230
Score = 28.4 bits (64), Expect = 0.31
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 51 DARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
DA CL RT G +V+ Y G RY
Sbjct: 191 DAGEPCLLIRRRTWSGAQVVTRARLLYPGSRY 222
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM2 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 96
Score = 28.2 bits (63), Expect = 0.32
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 12/39 (30%)
Query: 42 AFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGC 80
A IQF++ A++A L DG+ + YNGC
Sbjct: 44 ALIQFADAVSAQAAKLSLDGQNI------------YNGC 70
Score = 25.1 bits (55), Expect = 3.7
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 6 AFIQFSNPHDARSACLGEDGRTV 28
A IQF++ A++A L DG+ +
Sbjct: 44 ALIQFADAVSAQAAKLSLDGQNI 66
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 27.7 bits (61), Expect = 0.34
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
D R V G S KGY F+ F N DA +A + G+ + G+ +
Sbjct: 30 DARVVKDMATGKS--KGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 73
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 27.7 bits (62), Expect = 0.36
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 2 HKGYAFIQFSNPHDARSA 19
H+G+ F+ F DA+ A
Sbjct: 42 HRGFGFVDFITKQDAKRA 59
Score = 27.7 bits (62), Expect = 0.36
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 38 HKGYAFIQFSNPHDARSA 55
H+G+ F+ F DA+ A
Sbjct: 42 HRGFGFVDFITKQDAKRA 59
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 74
Score = 27.6 bits (62), Expect = 0.36
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLG 30
G AFI F+ DAR A + DG+T+ G
Sbjct: 39 MGEAFIAFATDEDARLA-MSRDGQTIKG 65
Score = 27.6 bits (62), Expect = 0.36
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLG 66
G AFI F+ DAR A + DG+T+ G
Sbjct: 39 MGEAFIAFATDEDARLA-MSRDGQTIKG 65
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate
nucleolin. This subfamily corresponds to the RRM4 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 78
Score = 27.6 bits (61), Expect = 0.41
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 3 KGYAFIQFSNPHDARSA 19
KG+ F+ FS+ DA++A
Sbjct: 39 KGFGFVDFSSEEDAKAA 55
Score = 27.6 bits (61), Expect = 0.41
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 39 KGYAFIQFSNPHDARSA 55
KG+ F+ FS+ DA++A
Sbjct: 39 KGFGFVDFSSEEDAKAA 55
>gnl|CDD|152044 pfam11608, Limkain-b1, Limkain b1. This family of proteins
represents Limkain b1, which is a novel human
autoantigen, localised to a subset of ABCD3 and PXF
marked peroxisomes. Limkain b1 may be a relatively
common target of human autoantibodies reactive to
cytoplasmic vesicle-like structures.
Length = 91
Score = 27.5 bits (61), Expect = 0.41
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQ-TLVSYK 73
G+ LGIS G A ++F+N A A + V G VS+
Sbjct: 32 GKVLGIS--GGSAVLRFANQEAAERAQKRMENEDVFGNRITVSFS 74
Score = 26.0 bits (57), Expect = 1.7
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
G A ++F+N A A + V G + +S
Sbjct: 40 GSAVLRFANQEAAERAQKRMENEDVFGNRITVS 72
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 27.6 bits (61), Expect = 0.43
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+G+A++QF + DA A D + + G+ + I +G
Sbjct: 42 RGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQG 79
Score = 26.1 bits (57), Expect = 1.5
Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCR 81
+G+A++QF + DA A D + + G+ + ++Q+ G R
Sbjct: 42 RGFAYVQFEDVRDAEDALHNLDRKWICGRQI---EIQFAQGDR 81
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 27.3 bits (61), Expect = 0.43
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F+ F DA +A +G+ + G+ +
Sbjct: 41 KGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71
Score = 27.3 bits (61), Expect = 0.43
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F+ F DA +A +G+ + G+ +
Sbjct: 41 KGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 27.3 bits (61), Expect = 0.43
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 35 ISMHKG--YAFIQFSNPHDARSACLGEDGRTVLGQ 67
I H YAF+++ + A +A +GR +LGQ
Sbjct: 31 IREHGNDPYAFVEYYDHRSAAAALQTMNGRLILGQ 65
Score = 26.9 bits (60), Expect = 0.62
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 5 YAFIQFSNPHDARSACLGEDGRTVLGQ 31
YAF+++ + A +A +GR +LGQ
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQ 65
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 27.2 bits (61), Expect = 0.45
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 2 HKGYAFIQFSNPHDAR 17
KGYAF++F +P A+
Sbjct: 40 SKGYAFVEFESPEVAK 55
Score = 27.2 bits (61), Expect = 0.45
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 38 HKGYAFIQFSNPHDAR 53
KGYAF++F +P A+
Sbjct: 40 SKGYAFVEFESPEVAK 55
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 27.5 bits (62), Expect = 0.46
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G F++F++ DA+ A L GR G+T+V
Sbjct: 57 GKVFVEFADVEDAQKAQLALAGRKFDGRTVV 87
Score = 26.4 bits (59), Expect = 1.3
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G F++F++ DA+ A L GR G+T+
Sbjct: 57 GKVFVEFADVEDAQKAQLALAGRKFDGRTV 86
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 27.1 bits (60), Expect = 0.47
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 5 YAFIQFSNPHDARSACLGEDG 25
+AF++F +P DA A G +G
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNG 60
Score = 27.1 bits (60), Expect = 0.47
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 41 YAFIQFSNPHDARSACLGEDG 61
+AF++F +P DA A G +G
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNG 60
>gnl|CDD|241113 cd12669, RRM1_Nop12p_like, RNA recognition motif 1 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM1 of Nop12p which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 105
Score = 27.4 bits (61), Expect = 0.52
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTL 33
A+I + P A A +G LG+ L
Sbjct: 70 AYIVYKTPALAAKAAKKLNGTVFLGRHL 97
Score = 27.4 bits (61), Expect = 0.52
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 42 AFIQFSNPHDARSACLGEDGRTVLGQTL 69
A+I + P A A +G LG+ L
Sbjct: 70 AYIVYKTPALAAKAAKKLNGTVFLGRHL 97
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 27.1 bits (60), Expect = 0.53
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
K Y FIQF NP A A + ++G+ L
Sbjct: 41 KHYGFIQFLNPEVAAIAAKSMNNYLLMGKVL 71
Score = 27.1 bits (60), Expect = 0.53
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K Y FIQF NP A A + ++G+ L
Sbjct: 41 KHYGFIQFLNPEVAAIAAKSMNNYLLMGKVL 71
>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 = 27.2 bits (61), Expect = 0.54
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 3 KGYAFIQFSNPHDARSAC 20
+GY F+ F + A AC
Sbjct: 42 RGYGFVTFKDKESAERAC 59
Score = 27.2 bits (61), Expect = 0.54
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 39 KGYAFIQFSNPHDARSAC 56
+GY F+ F + A AC
Sbjct: 42 RGYGFVTFKDKESAERAC 59
>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 = 26.9 bits (60), Expect = 0.55
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
KGY F+ +N +A SA +G + G+ L VS+K
Sbjct: 43 KGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVSFK 78
Score = 25.4 bits (56), Expect = 2.1
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KGY F+ +N +A SA +G + G+ L +S
Sbjct: 43 KGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVS 76
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 27.9 bits (62), Expect = 0.59
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+ FIQF + +A+ A +G + G+ + +
Sbjct: 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG 261
Score = 27.6 bits (61), Expect = 0.82
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
KG+ FIQF + +A+ A +G + G+ + V Y
Sbjct: 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGY 262
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 27.2 bits (60), Expect = 0.62
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 1 MHKGYAFIQFSNPHDARSACL--GEDGRTVLGQTLGISMHK 39
+ KG+A++QF + + A L + +L + L +S K
Sbjct: 39 VGKGFAYVQFKDENAVEKALLLNEKKFPPMLPRELRVSRCK 79
>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 = 26.8 bits (60), Expect = 0.63
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 2 HKGYAFIQFSNPHDARSA 19
HKGY FI++ NP A+ A
Sbjct: 41 HKGYGFIEYENPQSAQDA 58
Score = 26.8 bits (60), Expect = 0.63
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 38 HKGYAFIQFSNPHDARSA 55
HKGY FI++ NP A+ A
Sbjct: 41 HKGYGFIEYENPQSAQDA 58
>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 = 26.8 bits (60), Expect = 0.65
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 2 HKGYAFIQFSNPHDARSAC 20
+G+ ++ F+ DA+ A
Sbjct: 40 CRGFGYVTFALEEDAKRAL 58
Score = 26.8 bits (60), Expect = 0.65
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 38 HKGYAFIQFSNPHDARSAC 56
+G+ ++ F+ DA+ A
Sbjct: 40 CRGFGYVTFALEEDAKRAL 58
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins.
This subfamily includes the RRM1 and RRM2 of
RNA-binding protein 5 (RBM5 or LUCA15 or H37) and
RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). These RBMs share high sequence homology and may
play an important role in regulating apoptosis. RBM5 is
a known modulator of apoptosis. It may also act as a
tumor suppressor or an RNA splicing factor. RBM6 has
been predicted to be a nuclear factor based on its
nuclear localization signal. Both, RBM6 and RBM5,
specifically bind poly(G) RNA. RBM10 is a paralog of
RBM5. It may play an important role in mRNA generation,
processing and degradation in several cell types. The
rat homolog of human RBM10 is protein S1-1, a
hypothetical RNA binding protein with poly(G) and
poly(U) binding capabilities. All family members
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a
G-patch/D111 domain. .
Length = 84
Score = 26.7 bits (60), Expect = 0.68
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 14/48 (29%)
Query: 34 GISMHKGYAFIQFSNPHDA-----RSACLGE---DGRTVLGQTLVSYK 73
G S +G+AF++F + DA L DGR V VSY
Sbjct: 43 GTS--RGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVV----RVSYA 84
Score = 26.0 bits (58), Expect = 1.4
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 8/34 (23%)
Query: 3 KGYAFIQFSNPHDA-----RSACLGE---DGRTV 28
+G+AF++F + DA L DGR V
Sbjct: 46 RGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVV 79
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2),
TRA2-alpha, TRA2-beta (also termed SFRS10), and similar
proteins found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent
GnRH pre-mRNA splicing. TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. Both, TRA2-alpha and TRA2-beta, contains a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), flanked by the N- and C-terminal
arginine/serine (RS)-rich regions. .
Length = 78
Score = 26.8 bits (60), Expect = 0.69
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 1 MHKGYAFIQFSNPHDARSA---CLGE--DGR 26
+G+ F+ F + DA+ A G DGR
Sbjct: 39 RSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69
Score = 26.8 bits (60), Expect = 0.69
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 37 MHKGYAFIQFSNPHDARSA---CLGE--DGR 62
+G+ F+ F + DA+ A G DGR
Sbjct: 39 RSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 26.5 bits (59), Expect = 0.76
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KGYA+++F N + A L D + G+ + +S
Sbjct: 39 SKGYAYVEFENEESVQEA-LKLDRELIKGRPMFVS 72
Score = 26.1 bits (58), Expect = 1.3
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLG 66
KGYA+++F N + A L D + G
Sbjct: 39 SKGYAYVEFENEESVQEA-LKLDRELIKG 66
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM3 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 86
Score = 26.8 bits (60), Expect = 0.85
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 36 SMHKGYAFIQFSNPHDAR 53
+ GYAFI F NP A
Sbjct: 40 KCNVGYAFINFVNPEYAE 57
Score = 26.4 bits (59), Expect = 1.2
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 1 MHKGYAFIQFSNPHDAR 17
+ GYAFI F NP A
Sbjct: 41 CNVGYAFINFVNPEYAE 57
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM3 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B) and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and is a
novel component of the NXF1 pathway. It binds to NXF1
and serves as receptor for the RNA export element RTE.
It also possess mRNA export activity and can facilitate
the access of DEAD-box protein DBP5 to mRNA at the
nuclear pore complex (NPC). RNA-binding protein 15B
(RBM15B), also termed one twenty-two 3 (OTT3), is a
paralog of RBM15 and therefore has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF.
Members in this family belong to the Spen (split end)
protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 72
Score = 26.4 bits (59), Expect = 0.90
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 2 HKGYAFIQFSNPHDARSAC 20
+ YA+I++ + A++A
Sbjct: 33 GRNYAYIEYESIEAAQAAK 51
Score = 26.4 bits (59), Expect = 0.90
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 38 HKGYAFIQFSNPHDARSAC 56
+ YA+I++ + A++A
Sbjct: 33 GRNYAYIEYESIEAAQAAK 51
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 26.5 bits (59), Expect = 0.90
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KG AFI F + DA + + + G+TL S+
Sbjct: 43 KGVAFILFLDREDAHKCVKALNNKELFGRTLKCSI 77
Score = 25.0 bits (55), Expect = 2.9
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG AFI F + DA + + + G+TL
Sbjct: 43 KGVAFILFLDREDAHKCVKALNNKELFGRTL 73
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 26.3 bits (58), Expect = 0.94
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 5 YAFIQFSNPHDARSACLGEDG 25
+AF++F +P DA A G DG
Sbjct: 39 FAFVEFEDPRDAEDAVYGRDG 59
Score = 26.3 bits (58), Expect = 0.94
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 41 YAFIQFSNPHDARSACLGEDG 61
+AF++F +P DA A G DG
Sbjct: 39 FAFVEFEDPRDAEDAVYGRDG 59
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 26.6 bits (58), Expect = 0.97
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
D R V G S KGY F+ F N DA +A G+ + G+ +
Sbjct: 30 DARVVKDMATGKS--KGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 73
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 26.5 bits (59), Expect = 0.98
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+A+++F++ A + +GR G+ V
Sbjct: 42 KGFAYVEFASEAAAAAVKEKLEGREFNGKKCV 73
Score = 26.5 bits (59), Expect = 0.98
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+A+++F++ A + +GR G+ ++
Sbjct: 42 KGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVT 75
>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 = 26.6 bits (58), Expect = 1.0
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 5 YAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
Y F++F DA +A +GR +LG+ + ++
Sbjct: 41 YCFVEFYEHRDAAAALAAMNGRKILGKEVKVN 72
Score = 25.8 bits (56), Expect = 1.7
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 41 YAFIQFSNPHDARSACLGEDGRTVLGQ 67
Y F++F DA +A +GR +LG+
Sbjct: 41 YCFVEFYEHRDAAAALAAMNGRKILGK 67
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 26.3 bits (59), Expect = 1.1
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 4 GYAFIQFSNPHDARSA 19
GYA++ F NP DA A
Sbjct: 42 GYAYVNFQNPADAERA 57
Score = 26.3 bits (59), Expect = 1.1
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 40 GYAFIQFSNPHDARSA 55
GYA++ F NP DA A
Sbjct: 42 GYAYVNFQNPADAERA 57
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe
CD corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 79
Score = 26.4 bits (59), Expect = 1.1
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ F+ FS+P +A A +GR + G+ L
Sbjct: 42 KGFGFVCFSSPEEATKAVTEMNGRIIGGKPL 72
Score = 26.4 bits (59), Expect = 1.1
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ F+ FS+P +A A +GR + G+ L
Sbjct: 42 KGFGFVCFSSPEEATKAVTEMNGRIIGGKPL 72
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 26.4 bits (59), Expect = 1.1
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+G+ F++ +A +A +G G+TL
Sbjct: 41 RGFGFVEMETAEEANAAIEKLNGTDFGGRTLT 72
Score = 25.3 bits (56), Expect = 2.6
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+ F++ +A +A +G G+TL
Sbjct: 41 RGFGFVEMETAEEANAAIEKLNGTDFGGRTL 71
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 26.1 bits (58), Expect = 1.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 3 KGYAFIQFSNPHDA-------RSACLGEDGRTV 28
KG A+++F+ A CLG D + +
Sbjct: 44 KGVAYVKFAKASSAARAMEEMNGKCLGGDTKPL 76
Score = 26.1 bits (58), Expect = 1.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 39 KGYAFIQFSNPHDA-------RSACLGEDGRTV 64
KG A+++F+ A CLG D + +
Sbjct: 44 KGVAYVKFAKASSAARAMEEMNGKCLGGDTKPL 76
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 26.4 bits (59), Expect = 1.1
Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 43 FIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYN 78
F++FS+ +A A +GR G+ + + +Y+
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFGGRKVTAR---FYD 85
Score = 24.9 bits (55), Expect = 3.8
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 7 FIQFSNPHDARSACLGEDGRTVLG 30
F++FS+ +A A +GR G
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFGG 76
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 26.2 bits (58), Expect = 1.1
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARS 54
D R + +T G S +G+AF++F + +A
Sbjct: 32 DVRLMRRKTTGAS--RGFAFVEFMSLEEATR 60
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 26.2 bits (58), Expect = 1.2
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVL 65
F +F AR E GR+ +G+ ++ F +P DA+ A DG+ +
Sbjct: 19 EFEKFGTVVGARVITDRETGRS-----------RGFGYVDFESPEDAKKAIEAMDGKELD 67
Query: 66 GQTL 69
G+ +
Sbjct: 68 GRPI 71
Score = 25.4 bits (56), Expect = 2.4
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+G+ ++ F +P DA+ A DG+ + G+ + +
Sbjct: 41 RGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDF 75
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 27.2 bits (60), Expect = 1.2
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
KGY F+ +N +A A L +G T+ + L VS+K
Sbjct: 311 KGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK 346
Score = 26.4 bits (58), Expect = 2.3
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KGY F+ +N +A A L +G T+ + L +S
Sbjct: 311 KGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVS 344
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 26.2 bits (57), Expect = 1.3
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+ YAF+ F N DA +A +G+ + G ++ +++ K
Sbjct: 37 RDYAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAK 73
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 84
Score = 26.2 bits (57), Expect = 1.4
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
GY F+ + +P+DA A +G + +T+ +S
Sbjct: 46 GYGFVNYVDPNDADKAINTLNGLKLQTKTIKVS 78
Score = 25.8 bits (56), Expect = 1.7
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 28 VLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+ GQ+LG Y F+ + +P+DA A +G + +T+ VSY
Sbjct: 40 ITGQSLG------YGFVNYVDPNDADKAINTLNGLKLQTKTIKVSY 79
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 26.0 bits (58), Expect = 1.5
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 2 HKGYAFIQFSNPHDA 16
KGY F++F+N A
Sbjct: 56 SKGYGFVEFTNHEHA 70
Score = 26.0 bits (58), Expect = 1.5
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 38 HKGYAFIQFSNPHDA 52
KGY F++F+N A
Sbjct: 56 SKGYGFVEFTNHEHA 70
>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 = 25.9 bits (57), Expect = 1.5
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
HKG+AF+++ P A+ A +G + G+ + +
Sbjct: 41 HKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74
Score = 25.9 bits (57), Expect = 1.8
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
HKG+AF+++ P A+ A +G + G+ +
Sbjct: 41 HKGFAFVEYEVPEAAQLALEQMNGVMLGGRNI 72
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and
U3 small nucleolar RNAs (snoRNAs). MRD1 is essential
for the initial processing at the A0-A2 cleavage sites
in the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which may play an important structural role in
organizing specific rRNA processing events. .
Length = 84
Score = 26.0 bits (57), Expect = 1.6
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
GQTL SM G+ F+ F A++A DG + G TLV
Sbjct: 42 GQTL--SM--GFGFVGFKTKEQAQAALKAMDGFVLDGHTLV 78
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 25.8 bits (57), Expect = 1.6
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 41 YAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
+AFI+F A A E+ + +T+ V YK
Sbjct: 45 FAFIKFEREQAAARAVESENHSMLKNKTMHVQYK 78
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 25.6 bits (57), Expect = 1.7
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 3 KGYAFIQFSNPHD 15
KGY F+ FS+P+D
Sbjct: 48 KGYGFVSFSDPND 60
Score = 25.6 bits (57), Expect = 1.7
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 39 KGYAFIQFSNPHD 51
KGY F+ FS+P+D
Sbjct: 48 KGYGFVSFSDPND 60
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 25.7 bits (57), Expect = 1.8
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGYAF+++ + DA A
Sbjct: 45 KGYAFVEYEHERDALRA 61
Score = 25.7 bits (57), Expect = 1.8
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 39 KGYAFIQFSNPHDARSA 55
KGYAF+++ + DA A
Sbjct: 45 KGYAFVEYEHERDALRA 61
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 25.7 bits (56), Expect = 1.8
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+G+A+IQF + DA A + + V G+ + I +G
Sbjct: 42 RGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQG 79
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in
muscle differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 25.5 bits (56), Expect = 1.9
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
GQ+LG Y F+ + +P DA A +G + +T+ VSY
Sbjct: 40 GQSLG------YGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.7 bits (57), Expect = 2.0
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
A IQ ++P A++A +G + G+ L +++ K
Sbjct: 40 ALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSKH 74
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1),
a ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response; it binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
Meanwhile, HuR also has pro-apoptotic function by
promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Like other Hu proteins, HuR contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 81
Score = 25.4 bits (55), Expect = 2.2
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 10 FSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
FS+ + SA L D V G +LG Y F+ + N DA A +G + +T+
Sbjct: 22 FSSIGEVESAKLIRD--KVAGHSLG------YGFVNYVNAKDAERAINTLNGLRLQSKTI 73
Query: 70 -VSY 72
VSY
Sbjct: 74 KVSY 77
Score = 25.0 bits (54), Expect = 3.5
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
GY F+ + N DA A +G + +T+ +S
Sbjct: 44 GYGFVNYVNAKDAERAINTLNGLRLQSKTIKVS 76
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 26.5 bits (58), Expect = 2.2
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 2 HKGYAFIQFSNPHDARSA 19
++GYAF+ F +A+ A
Sbjct: 98 NRGYAFVTFCGKEEAKEA 115
Score = 26.5 bits (58), Expect = 2.2
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 38 HKGYAFIQFSNPHDARSA 55
++GYAF+ F +A+ A
Sbjct: 98 NRGYAFVTFCGKEEAKEA 115
Score = 25.0 bits (54), Expect = 6.9
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+ YAF+ F + DA A +G+ + G + +++ K
Sbjct: 269 RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAK 305
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types
1, 2, 3, 4 family. These eukaryotic proteins recognize
the poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are
four paralogs in Homo sapiens which are expressed in
testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4
), broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 26.3 bits (58), Expect = 2.2
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 4 GYAFIQFSNPHDARSA 19
GY ++ F NP DA A
Sbjct: 43 GYGYVNFQNPADAERA 58
Score = 26.3 bits (58), Expect = 2.2
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 40 GYAFIQFSNPHDARSA 55
GY ++ F NP DA A
Sbjct: 43 GYGYVNFQNPADAERA 58
Score = 26.3 bits (58), Expect = 2.7
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 3 KGYAFIQFSNPHDARSA 19
+G+AF+ F DA A
Sbjct: 219 RGFAFVNFEKHEDAAKA 235
Score = 26.3 bits (58), Expect = 2.7
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 39 KGYAFIQFSNPHDARSA 55
+G+AF+ F DA A
Sbjct: 219 RGFAFVNFEKHEDAAKA 235
Score = 24.8 bits (54), Expect = 7.7
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ +G+ F+ FSNP +A A GR + G+ L
Sbjct: 324 VSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPL 356
Score = 24.8 bits (54), Expect = 7.7
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ +G+ F+ FSNP +A A GR + G+ L
Sbjct: 324 VSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPL 356
>gnl|CDD|100091 cd03089, PMM_PGM, The phosphomannomutase/phosphoglucomutase
(PMM/PGM) bifunctional enzyme catalyzes the reversible
conversion of 1-phospho to 6-phospho-sugars (e.g.
between mannose-1-phosphate and mannose-6-phosphate or
glucose-1-phosphate and glucose-6-phosphate) via a
bisphosphorylated sugar intermediate. The reaction
involves two phosphoryl transfers, with an intervening
180 degree reorientation of the reaction intermediate
during catalysis. Reorientation of the intermediate
occurs without dissociation from the active site of the
enzyme and is thus, a simple example of processivity,
as defined by multiple rounds of catalysis without
release of substrate. Glucose-6-phosphate and
glucose-1-phosphate are known to be utilized for energy
metabolism and cell surface construction, respectively.
PMM/PGM belongs to the alpha-D-phosphohexomutase
superfamily which includes several related enzymes that
catalyze a reversible intramolecular phosphoryl
transfer on their sugar substrates. Other members of
this superfamily include phosphoglucosamine mutase
(PNGM), phosphoacetylglucosamine mutase (PAGM), the
bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the
phosphoglucomutases (PGM1 and PGM2). Each of these
enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 443
Score = 26.3 bits (59), Expect = 2.3
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRT 27
G AF + A+ +G DGR
Sbjct: 24 GRAFGSWLLEKGAKKVVVGRDGRL 47
Score = 26.3 bits (59), Expect = 2.3
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRT 63
G AF + A+ +G DGR
Sbjct: 24 GRAFGSWLLEKGAKKVVVGRDGRL 47
>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 = 25.7 bits (56), Expect = 2.3
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 1 MHKGYAFIQFSNPHDARS---ACLGEDG 25
KGY F+ F RS AC E+G
Sbjct: 62 HPKGYVFLLFEKERSVRSLLLACSEEEG 89
Score = 25.7 bits (56), Expect = 2.3
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 37 MHKGYAFIQFSNPHDARS---ACLGEDG 61
KGY F+ F RS AC E+G
Sbjct: 62 HPKGYVFLLFEKERSVRSLLLACSEEEG 89
>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 = 25.5 bits (56), Expect = 2.4
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 36 SMHKGYAFIQFSNPHDA 52
+ KGY F+ F DA
Sbjct: 40 GVSKGYGFVTFETQEDA 56
Score = 24.4 bits (53), Expect = 5.2
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 1 MHKGYAFIQFSNPHDA 16
+ KGY F+ F DA
Sbjct: 41 VSKGYGFVTFETQEDA 56
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 25.3 bits (56), Expect = 2.4
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
++ KG+ FI+ +A A DG G+ L
Sbjct: 33 LNKEKGFGFIRLDTRTNAEKAKAELDGIMRKGRQL 67
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 25.2 bits (55), Expect = 2.4
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTV 64
D R + G S +GY F+ F + DA +A +G+ +
Sbjct: 28 DARVMWDMKSGRS--RGYGFVSFRSQQDAENAINEMNGKWL 66
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This
subgroup corresponds to the RRM3 of the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
proteins, a family of structurally related RNA-binding
proteins involved in the regulation of pre-mRNA
splicing in the nucleus and in the control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or
NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or
ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed
BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also
termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts. .
Length = 73
Score = 24.9 bits (55), Expect = 2.8
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
K + F+ + NP A++A +G V G+ L
Sbjct: 40 KCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
Score = 24.9 bits (55), Expect = 2.8
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K + F+ + NP A++A +G V G+ L
Sbjct: 40 KCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 24.9 bits (55), Expect = 3.0
Identities = 10/29 (34%), Positives = 12/29 (41%)
Query: 42 AFIQFSNPHDARSACLGEDGRTVLGQTLV 70
AF F N A A +LG+ LV
Sbjct: 41 AFATFDNEQAASQALSRLHQLKILGKRLV 69
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 25.3 bits (55), Expect = 3.0
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 2 HKGYAFIQFSNPHDARSA 19
++GYAF+ ++ H+A+ A
Sbjct: 41 NRGYAFVMYTQKHEAKRA 58
Score = 25.3 bits (55), Expect = 3.0
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 38 HKGYAFIQFSNPHDARSA 55
++GYAF+ ++ H+A+ A
Sbjct: 41 NRGYAFVMYTQKHEAKRA 58
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 25.0 bits (54), Expect = 3.4
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 3 KGYAFIQFSNPHDA-RSACLGEDGRTVLGQTLGISMH 38
+G+AF++F++ DA R + +LGQ +SMH
Sbjct: 45 RGFAFVEFNHLQDATRWMEANQHSLMILGQK--VSMH 79
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 24.9 bits (55), Expect = 3.6
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQT 32
KGY F+ F +P A A G +GR V Q
Sbjct: 42 KGYGFVDFDSPEAALKAIEGLNGRGVQAQF 71
Score = 24.9 bits (55), Expect = 3.6
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
KGY F+ F +P A A G +GR V Q
Sbjct: 42 KGYGFVDFDSPEAALKAIEGLNGRGVQAQF 71
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 24.6 bits (53), Expect = 4.0
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSY 72
KGY+F++F++ A A + +G T+ G + Y
Sbjct: 36 KGYSFVRFNSHESAAHAIVSVNGTTIEGHVVKCY 69
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 24.5 bits (54), Expect = 4.3
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F+++++ A A DG+ + G+ L
Sbjct: 41 KGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
Score = 24.5 bits (54), Expect = 4.3
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F+++++ A A DG+ + G+ L
Sbjct: 41 KGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 24.6 bits (54), Expect = 4.4
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG F+QF + A +A G + G + +S
Sbjct: 37 KGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLS 70
Score = 23.4 bits (51), Expect = 9.9
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
KG F+QF + A +A G + G
Sbjct: 37 KGCGFVQFVHRAAAEAAIQQLQGTIIGGSR 66
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 24.6 bits (54), Expect = 4.7
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF++F + DA A DG+ + G+ L
Sbjct: 40 RGFAFVRFYDKRDAEDAMDAMDGKELDGREL 70
Score = 24.6 bits (54), Expect = 4.7
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA A DG+ + G+ L
Sbjct: 40 RGFAFVRFYDKRDAEDAMDAMDGKELDGREL 70
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 24.1 bits (53), Expect = 6.1
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNP 49
+ + ++QF++P A +A + LG+ + ++ S+P
Sbjct: 40 TRRFCYVQFTSPESAAAA-VALLNGK-LGEGYKLV-------VKISDP 78
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 24.4 bits (54), Expect = 6.1
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 14/40 (35%)
Query: 42 AFIQFSNPHDARSACLGEDGRTVL-GQTLVSYKLQYYNGC 80
A +QF + A +A + L G+ Y+GC
Sbjct: 42 ALVQFDSVESAENA------KKALNGR-------NIYDGC 68
Score = 24.0 bits (53), Expect = 6.8
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSN 48
A +QF + A +A +GR + + IQFS
Sbjct: 42 ALVQFDSVESAENAKKALNGRNIYDGCCTLD-------IQFSR 77
>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 = 24.1 bits (53), Expect = 7.1
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGYAF ++ +P A G +G + + L
Sbjct: 42 KGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLT 73
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 24.2 bits (53), Expect = 7.7
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 24 DGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
+ VL Q G S +GY F++FS+ + + A
Sbjct: 31 GAKVVLDQ-NGNS--RGYGFVRFSDESEQKRA 59
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.137 0.427
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,400,348
Number of extensions: 335735
Number of successful extensions: 753
Number of sequences better than 10.0: 1
Number of HSP's gapped: 752
Number of HSP's successfully gapped: 261
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.3 bits)