RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3994
(282 letters)
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including SCAF4,
SCAF8 and similar proteins. The biological role of SCAF4
remains unclear, but it shows high sequence similarity
to SCAF8 (also termed CDC5L complex-associated protein
7, or RNA-binding motif protein 16, or CTD-binding
SR-like protein RA8). SCAF8 is a nuclear matrix protein
that interacts specifically with a highly
serine-phosphorylated form of the carboxy-terminal
domain (CTD) of the largest subunit of RNA polymerase II
(pol II). The pol II CTD plays a role in coupling
transcription and pre-mRNA processing. In addition,
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 77
Score = 141 bits (357), Expect = 5e-43
Identities = 52/77 (67%), Positives = 62/77 (80%)
Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
CSTTLWIGHLSK V EE+L + F EYG++ SI++IPPRGCA+VCM RQDA +AL KL+N
Sbjct: 1 CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRN 60
Query: 217 TKLQGKTITLAWAPGKG 233
KL GK I +AWAP KG
Sbjct: 61 VKLAGKKIKVAWAPNKG 77
>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
present in several RNA-processing factors such as Pcf11
and Nrd1. Pcf11 is a conserved and essential subunit of
the yeast cleavage factor IA, which is required for
polyadenylation-dependent 3'-RNA processing and
transcription termination. Nrd1 is implicated in
polyadenylation-independent 3'-RNA processing. CID binds
tightly to the carboxy-terminal domain (CTD) of RNA
polymerase (Pol) II. During transcription, Pol II
synthesizes eukaryotic messenger RNA. Transcription is
coupled to RNA processing through the CTD, which
consists of up to 52 repeats of the sequence Tyr 1-Ser
2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
alpha-helices in a right-handed superhelical
arrangement, which closely resembles that of the VHS
domains and ARM (Armadillo) repeat proteins, except for
its two amino-terminal helices.
Length = 114
Score = 117 bits (296), Expect = 2e-33
Identities = 35/121 (28%), Positives = 61/121 (50%), Gaps = 7/121 (5%)
Query: 4 IKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPAL 63
+ +N L L K S+ I +T+ AI K K +V+ +EK I KC PE K+P L
Sbjct: 1 VFDYNALLEKLTFNK--NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLL 58
Query: 64 YVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFT 123
Y++DS+V+ ++ K+ F ++ + + + K+ R+LN+W++ VF
Sbjct: 59 YLLDSIVKNVGRKY--KEFFSEFLVPLFLDAYE---KVDEKTRKKLERLLNIWEERFVFG 113
Query: 124 P 124
Sbjct: 114 S 114
>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in
regulation of nuclear pre-mRNA.
Length = 124
Score = 111 bits (279), Expect = 1e-30
Identities = 41/130 (31%), Positives = 68/130 (52%), Gaps = 10/130 (7%)
Query: 6 TFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYV 65
F Q+L SL S+ I +T+ AI K +V+ EK+I K K+P LY+
Sbjct: 1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYL 55
Query: 66 IDSLVRQSRHQF--QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFT 123
+DS+V+ S+ ++ + D GP F L+ + E K KI R+LN+W++ +F
Sbjct: 56 LDSIVQNSKRKYGSEFGDELGPVFQDALRRVLGAAPE---ELKKKIRRLLNIWEERGIFP 112
Query: 124 PDIIHPLFDM 133
P+++ PL +
Sbjct: 113 PEVLRPLREK 122
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form of
the carboxy-terminal domain (CTD) of the largest subunit
of RNA polymerase II (pol II). The pol II CTD plays a
role in coupling transcription and pre-mRNA processing.
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 92.8 bits (230), Expect = 4e-24
Identities = 41/79 (51%), Positives = 56/79 (70%), Gaps = 2/79 (2%)
Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
CSTTLW+G + K +++L++ F E+G + SIN+IPPRGCA+VCM RQDA +AL KL +
Sbjct: 1 CSTTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSS 60
Query: 217 T--KLQGKTITLAWAPGKG 233
K+ K I +AWA KG
Sbjct: 61 GSYKIGSKVIKIAWALNKG 79
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 that interacts
specifically with a highly serine-phosphorylated form of
the carboxy-terminal domain (CTD) of the largest subunit
of RNA polymerase II (pol II) and may play a direct role
in coupling with both, transcription and pre-mRNA
processing, processes. SCAF4 and SCAF8 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 81
Score = 90.9 bits (225), Expect = 2e-23
Identities = 39/81 (48%), Positives = 56/81 (69%), Gaps = 2/81 (2%)
Query: 155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
++CSTTLW+G L K +++++ E+G + SIN+IPPRGCA++ M RQDA +AL KL
Sbjct: 1 SVCSTTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKL 60
Query: 215 K--NTKLQGKTITLAWAPGKG 233
N K+ K+I +AWA KG
Sbjct: 61 SRGNVKVNQKSIKIAWALNKG 81
>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain. This domain
binds to the phosphorylated C-terminal domain (CTD) of
RNA polymerase II.
Length = 64
Score = 69.6 bits (171), Expect = 1e-15
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 59 KVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQC-PPEDKSKIIRVLNLWQ 117
K+P LY+ + +V+ S+H+ +KD F F+ L F H+Y+ E K KI R+LN+W+
Sbjct: 1 KLPLLYLANDVVQNSKHK--NKDEFVKAFSPVLPDAFAHVYKEGDEEVKKKIRRLLNIWE 58
Query: 118 KNEVF 122
+ VF
Sbjct: 59 ERNVF 63
>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 = 67.7 bits (166), Expect = 6e-15
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
TT+++G L V E+EL FG +G++V + + P +GC FV R A A+ +L+ T
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61
Query: 219 LQGKTITLAW 228
+ G I L+W
Sbjct: 62 IGGSRIRLSW 71
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 66.5 bits (163), Expect = 2e-14
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
TL++G+L EEEL + F ++G V S+ L+ +G AFV +DA KAL
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 214 LKNTKLQGKTITL 226
L +L G+ + +
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 65.8 bits (161), Expect = 4e-14
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
L++G+L EE+L + F ++G++ S+ ++ +G AFV +DA KAL L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 216 NTKLQGKTITL 226
+L G+ + +
Sbjct: 61 GKELDGRKLKV 71
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 65.4 bits (160), Expect = 4e-14
Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
TTL++G L + V E++L D F ++G++ SI ++P + CAFV R+ A KA +L N K
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFN-K 60
Query: 219 L--QGKTITLAWA 229
L G+ + L W
Sbjct: 61 LIINGRRLKLKWG 73
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 61.9 bits (151), Expect = 1e-12
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG---------CAFVCMNRRQDAA 208
+T L++G+L+ V EE L FG +G + S+ ++ PR C FV R DA
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60
Query: 209 KALYKLKNTKLQGKTITLAWA 229
+AL +L + G + L W
Sbjct: 61 RALDELDGKDVMGYELKLGWG 81
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 60.7 bits (148), Expect = 3e-12
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
L++G+L V EE+L D FG++G+V S +I RG FV M ++A A+ K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 214 LKNTKLQGKTIT 225
L T G+T+T
Sbjct: 61 LNGTDFGGRTLT 72
>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 = 59.9 bits (146), Expect = 5e-12
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
L++G+L EE+L D F ++G + SI ++ +G AFV +DA KAL L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 216 NTKLQGKTIT 225
+L G+ +
Sbjct: 61 GKELGGRELR 70
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 54.9 bits (132), Expect = 4e-10
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
T L++ +L + + E+EL F YG++V NL+ PRG AFV ++R++A A+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 213 KLKNTKLQGKTITLA 227
L T G T+ L+
Sbjct: 61 SLNGTIPPGSTMPLS 75
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 58.9 bits (142), Expect = 6e-10
Identities = 32/94 (34%), Positives = 53/94 (56%), Gaps = 10/94 (10%)
Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMN 202
AR G E++ T L++ +L + + +++L FG+YG +V N++ PRG AFV N
Sbjct: 184 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN 243
Query: 203 RRQDAAKALYKLKNTKLQGK----TITLAWAPGK 232
+R++A +A+ L N +G T+ LA GK
Sbjct: 244 KREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK 277
>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 = 54.2 bits (131), Expect = 6e-10
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
TT+++G+L + EEEL TF +G + + + +G AFV + + AA A+ + T
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 219 LQGKTITLAWAPGK 232
+ G+T+ +W GK
Sbjct: 61 INGQTVKCSW--GK 72
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 53.0 bits (128), Expect = 2e-09
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
L++ LS E+EL F ++G V + L+ RG FV +DA A+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 213 KLKNTKLQGKTITLAWA 229
L +L+G+ I + A
Sbjct: 62 DLNGKELEGRVIKVEKA 78
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 52.7 bits (127), Expect = 2e-09
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKALYKL 214
LW+ LS + +L F +YG VV ++ P C FV M ++AAK + L
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 215 KNTKLQGKTIT 225
T+L G+ I+
Sbjct: 62 HRTELHGRVIS 72
>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 = 51.3 bits (123), Expect = 9e-09
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKL 214
L++ L V +EEL F ++G V S+ L+ P+G A+V A++A+ K+
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 215 KNTKLQGKTITLA 227
T+++ KTI++A
Sbjct: 64 DGTEIKEKTISVA 76
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 50.9 bits (122), Expect = 1e-08
Identities = 18/70 (25%), Positives = 37/70 (52%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
TT+++G++ + +L F +G ++ P RG AFV ++ + AA A+ +L+
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFP 60
Query: 219 LQGKTITLAW 228
+ G+ + W
Sbjct: 61 VHGRPLRCGW 70
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---------PPRGCAFVCMNRRQDAAKA 210
LWIG+L + E L F +YG + + + PRG FV +++A KA
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 211 LYKLKNTKLQGKTITLAWA 229
L L GK + + WA
Sbjct: 61 LKSLNGKTALGKKLVVRWA 79
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 50.5 bits (121), Expect = 1e-08
Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
S ++IG++ + EE+L + F +YG++ S+N + + CAFV +A KA+ +K+
Sbjct: 3 SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVKSH 62
Query: 218 KL 219
L
Sbjct: 63 PL 64
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 166 LSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKL 219
L E +L F +G V + IP +G AFV + DA KA+ + K+
Sbjct: 7 LPFKCTEADLKKLFSPFGFVWEVT-IPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKI 65
Query: 220 QGKTITLAWA 229
+G+ + + WA
Sbjct: 66 KGRPVAVDWA 75
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYKLK 215
++++G LS V +EEL++ F +G ++ +NLI AF+ R Q AA+A+
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64
Query: 216 NTKLQGKTI 224
++ L+ KT+
Sbjct: 65 HSMLKNKTM 73
>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 = 49.1 bits (118), Expect = 5e-08
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L +G L++ V ++ L + F YG V ++L PRG A+V +DA KA+ +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 215 KNTKLQGKTIT 225
++ G+ +T
Sbjct: 61 DGGQIDGQEVT 71
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 48.4 bits (116), Expect = 6e-08
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L EEL F +YG V +++ + FV M +DA A+ L +
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEEEDAEDAIKALNGYEFM 59
Query: 221 GKTIT 225
GK I
Sbjct: 60 GKRIN 64
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 47.9 bits (115), Expect = 1e-07
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
L++G L K EE++ F EYG++ + +I +GCAFV + R++A KA+ L
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61
Query: 215 KNTK 218
Sbjct: 62 HGKV 65
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 51.5 bits (122), Expect = 1e-07
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 146 EIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFV 199
E + TL++G+L V EE+L + F ++G V + L+ RG AFV
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162
Query: 200 CMNRRQDAAKALYKLKNTKLQGKTI 224
+ A KA+ +L +L+G+ +
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPL 187
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 47.3 bits (112), Expect = 1e-07
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 2/64 (3%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
T L +G++S +EL F EYG V+ +++ + AFV M R +DA +A+ L NT+
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTE 58
Query: 219 LQGK 222
QGK
Sbjct: 59 FQGK 62
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 46.0 bits (110), Expect = 4e-07
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 175 LSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
L F +G+V I L+ + G AFV + + A KA+ L G+ + + ++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 46.0 bits (110), Expect = 4e-07
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYKLKN 216
L++ +L V EE+L + F YG V + L+ PRG AFV +DA AL KL
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 217 TKLQGKTI 224
L G+T+
Sbjct: 61 LVLDGRTL 68
>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 = 46.3 bits (110), Expect = 5e-07
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + ++E+ F G++ S LI + G FV +DA KA+
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 213 KLKNTKLQGKTITLAWA 229
L +LQ KTI +++A
Sbjct: 62 TLNGLRLQNKTIKVSYA 78
>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 = 45.7 bits (109), Expect = 5e-07
Identities = 19/64 (29%), Positives = 36/64 (56%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L + EEE + F +YG+V + L +G F+ ++ R +A KA +L +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRK 63
Query: 221 GKTI 224
G+ +
Sbjct: 64 GRQL 67
>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 = 45.4 bits (107), Expect = 8e-07
Identities = 17/70 (24%), Positives = 37/70 (52%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
T++ G ++ + E+ + TF +G ++ + + P +G +FV N + AA A+ + T +
Sbjct: 2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTI 61
Query: 220 QGKTITLAWA 229
+G + W
Sbjct: 62 EGHVVKCYWG 71
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 45.3 bits (108), Expect = 1e-06
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 160 TLWIGHL----SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK 215
TL++G + + EE L FGE+GD+ I ++P +G AFV R A A +
Sbjct: 3 TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEAMA 62
Query: 216 NTKLQGKT-ITLAWA 229
+ L G + + WA
Sbjct: 63 DQSLDGGEVLNVRWA 77
>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 = 45.4 bits (108), Expect = 1e-06
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
T+L++ +++ + ++L FG+YG +V + IP PRG A+V +DA AL
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVY-IPLDFYTRRPRGFAYVQFEDVRDAEDAL 59
Query: 212 YKLKNTKLQGKTITLAWAPG 231
Y L T+ G+ I + +A G
Sbjct: 60 YYLDRTRFLGREIEIQFAQG 79
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 44.9 bits (107), Expect = 1e-06
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
TLW+G L + E + F E G+V S+ +I G FV + A +AL
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
Query: 214 LKNTKLQGKTIT--LAWA 229
L + L WA
Sbjct: 61 LNGKPIPNTQQRFRLNWA 78
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 44.9 bits (106), Expect = 2e-06
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
L++ L K + ++EL F +YG +++ ++ RG F+ ++R +A +A+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 213 KLKNTKLQGKT 223
L K +G +
Sbjct: 61 GLNGQKPEGAS 71
>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 = 44.5 bits (106), Expect = 2e-06
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 173 EELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT 225
+EL + F +G V S+ L P RG AFV +Q+A A+ LK+T L G+ +
Sbjct: 15 KELRELFSPFGQVKSVRL--PKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLV 72
Query: 226 LAWA 229
L +A
Sbjct: 73 LEYA 76
>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 = 44.1 bits (105), Expect = 2e-06
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKALYK 213
L++G L++ V E+ L F +GD+ I IP RG AFV +DAA A+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQ-IPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59
Query: 214 LKNTKLQGKTIT 225
+ ++L G+TI
Sbjct: 60 MNESELFGRTIR 71
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 43.8 bits (104), Expect = 4e-06
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR----------GCAFVCMNRRQDAAKA 210
+++ +L + E++L F ++G+V SI IP + G AFV A A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIR-IPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 211 LYKLKNTKLQGKTITLA 227
L +L T+L G+ I+++
Sbjct: 62 L-QLNGTELGGRKISVS 77
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 43.4 bits (103), Expect = 4e-06
Identities = 22/72 (30%), Positives = 33/72 (45%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
T + + +L EEEL + F ++G + + L P R A V DA KA L +
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60
Query: 219 LQGKTITLAWAP 230
+ + L WAP
Sbjct: 61 FKHVPLYLEWAP 72
>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 = 43.7 bits (104), Expect = 4e-06
Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYK 213
T +++ +L + + +E+L + FG+YG + S ++ +G FV + A KA+ +
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61
Query: 214 LKNTKLQGKTI 224
L ++ GK +
Sbjct: 62 LNGKEVNGKKL 72
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 43.1 bits (102), Expect = 5e-06
Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L+IG+LS V E +L F E+ VS L+ G AFV + A KA+ KL LQ
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQ 60
Query: 221 GKTITLAWA-PGK 232
GK I + + P K
Sbjct: 61 GKVIEVEHSVPKK 73
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 43.3 bits (103), Expect = 5e-06
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
T+ + +LS+ E++L + F +G + + L RG AFV + R+DA +A+ K
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 214 LK 215
L
Sbjct: 61 LN 62
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 43.3 bits (102), Expect = 6e-06
Identities = 24/76 (31%), Positives = 36/76 (47%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
S TL+ G ++ + E +L FG +G+V S L + AFV M R+DA A ++
Sbjct: 3 SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAREAMEQY 62
Query: 218 KLQGKTITLAWAPGKG 233
K + W G G
Sbjct: 63 KSGDMQLRTRWGVGFG 78
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 43.2 bits (101), Expect = 6e-06
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKAL 211
LW+ LS + +L + F +YG VV ++ P C FV M+ ++A K +
Sbjct: 1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60
Query: 212 YKLKNTKLQGKTITL 226
L T+L G+ I++
Sbjct: 61 NHLHRTELHGRMISV 75
>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 = 43.1 bits (102), Expect = 6e-06
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
TL++G+LS V +E L F ++G VV +I RG +V +DA KA+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 214 LKNTKLQGKTITL 226
+ +L G+ I +
Sbjct: 61 MDGKELDGRPINV 73
>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 = 42.7 bits (100), Expect = 7e-06
Identities = 16/70 (22%), Positives = 37/70 (52%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
T++ G ++ + E+ + TF +G ++ I + P +G +F+ + + AA A+ + T +
Sbjct: 2 TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTI 61
Query: 220 QGKTITLAWA 229
+G + W
Sbjct: 62 EGHVVKCYWG 71
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 42.6 bits (101), Expect = 7e-06
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 170 VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
+ EE L F +G++++I++ + C FV + + A +A+ +L T +QG + ++ A
Sbjct: 14 LTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLA 73
>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 = 41.8 bits (98), Expect = 1e-05
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
+++G++S +EL F E+G VV + + + AFV M R ++A A+ L +
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--KDYAFVHMEREEEALAAIEALNGKE 58
Query: 219 LQGKTI 224
++G+ I
Sbjct: 59 VKGRRI 64
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM3
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 72
Score = 41.6 bits (98), Expect = 2e-05
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC-AFVCMNRRQDAAKALYKLKNT 217
TT+ + + EEL D F +G + + L+PP G A V Q A A L
Sbjct: 1 TTILVKNFPYGTTAEELRDLFEPHGKLTRV-LMPPAGTIAIVEFANPQQARLAFKALAYR 59
Query: 218 KLQGKTITLAWAP 230
+ + + L P
Sbjct: 60 RFKDSILYLEKGP 72
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 41.7 bits (98), Expect = 2e-05
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
TL++ +L+ V +E+L+D F + + ++ RG FV +DA +AL K
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 214 LKNTKLQGKTITLAWA 229
LKN KL G+ + L A
Sbjct: 61 LKNKKLHGRILRLDIA 76
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI----NLIPPR--GCAFVCMNRRQDAAKALYKL 214
L++G L V E L + F G V+SI +LI R G A+V DA +AL L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 215 KNTKLQGKTITLAW 228
++GK I + W
Sbjct: 62 NFDVIKGKPIRIMW 75
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 171 QEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
QEE++ D F E+G++ +++L R G A + +++A A+ L +L G+TI
Sbjct: 19 QEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTI 78
Query: 225 TLAWA 229
++ WA
Sbjct: 79 SVDWA 83
>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 = 45.2 bits (107), Expect = 2e-05
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL----IPPR--GCAFVCMNRRQDAAKALYK 213
+L++G L V E +L D F +G V+S+ + + R G +V DA +AL
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 214 LKNTKLQGKTITLAW 228
+ +L GK I + W
Sbjct: 62 MNFKRLGGKPIRIMW 76
Score = 36.7 bits (85), Expect = 0.011
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYK 213
T L++ +L V E++L + F ++G++ S ++ RG AFV + +DAAKA+ +
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238
Query: 214 LKNTKLQG 221
+ K+
Sbjct: 239 MNGKKIGL 246
Score = 36.3 bits (84), Expect = 0.016
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLK 215
L++ +L V +E+L + F E G++ S ++ RG FVC + ++A +A+ ++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347
Query: 216 NTKLQGKTITLAWA 229
L GK + +A A
Sbjct: 348 GRMLGGKPLYVALA 361
Score = 31.7 bits (72), Expect = 0.40
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 150 RNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRR 204
R+GV N +++ +L K V + L DTF ++G+++S + RG FV +
Sbjct: 85 RSGVGN-----IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKE 139
Query: 205 QDAAKALYKLKNTKLQGKTITLA 227
+ A A+ K+ L K + +
Sbjct: 140 ESAKAAIQKVNGMLLNDKEVYVG 162
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++ +L EE+L + F EYG+V + I + AFV R DA KA+ ++ +L+
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELE 61
Query: 221 GKTITLAWA 229
G I ++ A
Sbjct: 62 GSPIEVSLA 70
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 41.0 bits (96), Expect = 4e-05
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 158 STTLWIGHLS-----KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
S ++IG++S + + E+EL +YG++ SI ++ + CAF+ +A AL
Sbjct: 2 SRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQ 61
Query: 213 KLKNTKL 219
L K
Sbjct: 62 TLNGKKP 68
>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 = 40.5 bits (95), Expect = 5e-05
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 171 QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
+EE++ F +G +V ++ + AFV +DA KAL L +++ G +T+ +
Sbjct: 13 REEDIEKLFEPFGPLVRCDI--RKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFV 69
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 40.4 bits (95), Expect = 5e-05
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L++G+LS E+ + + FGEYG++ S+ L P+G +V + ++ A AL L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 215 KNTKLQGKTITL 226
T L G+ + L
Sbjct: 61 GGTDLLGRPVRL 72
>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 = 43.8 bits (103), Expect = 5e-05
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + +EE+ F G++ S L+ + G FV R +DA KA+
Sbjct: 4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63
Query: 213 KLKNTKLQGKTITLAWA 229
L +LQ KTI +++A
Sbjct: 64 SLNGLRLQNKTIKVSYA 80
Score = 33.0 bits (75), Expect = 0.15
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
+++ +LS E L FG +G V ++ +I +G FV M +AA A+ L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 215 KNTKLQGKTITLAWAPGK 232
L + + +++ K
Sbjct: 332 NGYTLGNRVLQVSFKTNK 349
Score = 31.1 bits (70), Expect = 0.57
Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMN 202
AR +++ L++ L K + + EL F +G +++ ++ +G F+ +
Sbjct: 80 ARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFD 139
Query: 203 RRQDAAKALYKLKNTKLQGKT--ITLAWAPGKGMKDK 237
+R +A +A+ L T G T IT+ +A +
Sbjct: 140 KRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNS 176
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 40.2 bits (95), Expect = 6e-05
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYK 213
++++G+L ++EEEL F + GDV ++ ++ R G +V + A AL K
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59
Query: 214 LKNTKLQGKTI 224
L KL+G+ I
Sbjct: 60 LNGIKLKGRKI 70
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 40.2 bits (95), Expect = 6e-05
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI------NLIPPRGCAFVCMNRRQDAAKALYKL 214
L++G+LS EE++ + F GD+ I P G FV R+DA A+ L
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 215 KNTKLQGKTITLAWAPG 231
TKL + I + W G
Sbjct: 61 NGTKLDDRIIRVDWDAG 77
>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 = 40.4 bits (94), Expect = 7e-05
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
T+L++ +++ + E+L FG YG +V + +P PRG A++ +DA AL
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDV-YVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59
Query: 212 YKLKNTKLQGKTITLAWAPG 231
Y L + G+ I + +A G
Sbjct: 60 YNLNRKWVCGRQIEIQFAQG 79
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 40.3 bits (94), Expect = 7e-05
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 6/64 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKL 214
L++G + + + E+E+ F E+G+V+ + +I + GC FV + R +A +A+ L
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61
Query: 215 KNTK 218
N +
Sbjct: 62 HNQR 65
>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 = 39.9 bits (93), Expect = 8e-05
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
++IG LS V+E+++ FG YG ++ I+L G FV +DA A+Y+L L
Sbjct: 2 VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--KNGYGFVEFEDSRDADDAVYELNGKDLC 59
Query: 221 GKTITLAWAPG 231
G+ + + A G
Sbjct: 60 GERVIVEHARG 70
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 39.9 bits (94), Expect = 8e-05
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 170 VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL----QGKTIT 225
V EEL F +YG V + + P + FV + +DAA A L +L Q K +
Sbjct: 15 VSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLY 74
Query: 226 LA 227
L+
Sbjct: 75 LS 76
>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 = 40.0 bits (94), Expect = 8e-05
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
L++ +L EEEL + F +G++ ++L +G AFV + A KA +L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 215 KNTKLQGKTI 224
+ QG+ +
Sbjct: 62 DGSIFQGRLL 71
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 40.1 bits (93), Expect = 9e-05
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + +EEL FG G++ S L+ + G FV +DA KA+
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64
Query: 213 KLKNTKLQGKTITLAWA 229
L +LQ KTI +++A
Sbjct: 65 TLNGLRLQTKTIKVSYA 81
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 39.9 bits (93), Expect = 1e-04
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 173 EELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA 227
+L FG YG V + R G AFV M +R++A AL ++ G+ + +
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75
Query: 228 WAPGK 232
WA K
Sbjct: 76 WAVQK 80
>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 = 40.1 bits (93), Expect = 1e-04
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + +EE FG G++ S L+ + G FV DA KA+
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63
Query: 213 KLKNTKLQGKTITLAWA 229
L KLQ KTI +++A
Sbjct: 64 TLNGLKLQTKTIKVSYA 80
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 39.6 bits (93), Expect = 1e-04
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSIN-LIPPRGCAFVCMNRRQDAAKALYKLKN 216
S TL++ +++ V++EEL F ++GD+ ++ RG V + A +A L+
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60
Query: 217 TKLQGKTI 224
T+L G+ +
Sbjct: 61 TELGGRKL 68
>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 = 39.4 bits (92), Expect = 1e-04
Identities = 21/55 (38%), Positives = 35/55 (63%), Gaps = 3/55 (5%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL-IPPR--GCAFVCMNRRQDAAKAL 211
T+++G+L ++E E+ D F +YG +V I+L +PPR G AF+ +DA A+
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAI 55
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 39.7 bits (92), Expect = 1e-04
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKALYKL 214
LW+ LS + +L + FG+YG V+S ++ P C V M+ + A+ + L
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 215 KNTKLQGKTITL 226
T+L G+ I++
Sbjct: 62 HRTELHGQQISV 73
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI----NLIPPRGCAFVCMNRRQDAAKALYKLKN 216
+++G+L + EL D F +YG + S+ N PP G AFV +DA A+ L
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN--PP-GFAFVEFEDPRDAEDAVRALDG 58
Query: 217 TKLQGKTIT 225
++ G +
Sbjct: 59 RRICGNRVR 67
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 40.4 bits (94), Expect = 2e-04
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
ST L+IG LS + L D F +GDVV +I RG FV N A A+
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93
Query: 212 YKLKNTKLQGKTI 224
++ +L G+ I
Sbjct: 94 SEMDGKELNGRHI 106
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 38.6 bits (90), Expect = 2e-04
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PP--RGCAFVCMNRRQDAAKALY 212
+++G + + E++L + F +YG V IN++ PP +GC FV R+ A +A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63
Query: 213 KLKNTK 218
L N K
Sbjct: 64 ALHNMK 69
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 38.3 bits (89), Expect = 3e-04
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
+++G++ + +EEL F YG V+S ++ R AFV + A +A+ +L +L
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--RQFAFVHLRGEAAADRAIEELNGRELH 60
Query: 221 GKTI 224
G+ +
Sbjct: 61 GRKL 64
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 38.1 bits (89), Expect = 3e-04
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
L++G+L E+L F G S+ L+ +GCAFV + + KAL K
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-K 60
Query: 214 LKNTKLQGKTI 224
L +T L+G+ I
Sbjct: 61 LHHTLLKGRKI 71
>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM4 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 38.1 bits (89), Expect = 3e-04
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 173 EELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP 230
EL + F ++G + + L+PP G A V +A A KL +K + + L WAP
Sbjct: 15 AELRELFSKFGSLGRV-LLPPAGITAIVEFLEPSEAKLAFRKLAYSKFKHVPLYLEWAP 72
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 38.2 bits (88), Expect = 4e-04
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + +EE FG G++ S L+ + G FV +DA KA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 213 KLKNTKLQGKTITLAWA 229
L +LQ KTI +++A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 38.0 bits (89), Expect = 4e-04
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 170 VQEEELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
V EE+L + FG G+V + + R G A V +R+DA +A+ + L G+ +
Sbjct: 12 VTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPM 71
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
TL++ +L +E+L + F E G + ++ RG +V +DA +AL +
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 214 LKNTKLQGKTITLAWA 229
K TK G+ I + +A
Sbjct: 61 KKKTKFGGRKIHVEFA 76
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 38.0 bits (89), Expect = 4e-04
Identities = 21/69 (30%), Positives = 37/69 (53%)
Query: 156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK 215
M + +W+ L + V E+ L+ F YG VV + + RG A V ++ + A A+ ++K
Sbjct: 5 MPTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMK 64
Query: 216 NTKLQGKTI 224
KL G+ +
Sbjct: 65 GRKLGGRKL 73
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 37.6 bits (88), Expect = 5e-04
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLKNTKLQGKTITLA 227
E EL +G V +P R AF+ M +DA + YK + GK+I +A
Sbjct: 15 EAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQALVSFYKTYPLTIGGKSIKVA 72
>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 = 37.8 bits (87), Expect = 6e-04
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + ++EL F G+V S LI + G FV +DA +A+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 213 KLKNTKLQGKTITLAWA 229
L +LQ KTI +++A
Sbjct: 62 TLNGLRLQSKTIKVSYA 78
>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 = 37.6 bits (87), Expect = 6e-04
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
++L++ +++ + E+L FG YG +V + +P PRG A+V +DA AL
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDV-YVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59
Query: 212 YKLKNTKLQGKTITLAWAPG 231
+ L + G+ I + +A G
Sbjct: 60 HNLDRKWICGRQIEIQFAQG 79
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 37.3 bits (86), Expect = 7e-04
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++ +L+ V EE L FG++G + + + + AF+ + R A KA+ ++ +L+
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKELE 61
Query: 221 GKTITLAWA 229
G+ I + +A
Sbjct: 62 GENIEIVFA 70
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 36.9 bits (86), Expect = 8e-04
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
++IG L +E ++ F YG + INL G FV +DA A+Y+L +L
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREINL--KNGFGFVEFEDPRDADDAVYELNGKELC 59
Query: 221 GKTITLAWAPG 231
G+ + + A G
Sbjct: 60 GERVIVEHARG 70
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 37.2 bits (87), Expect = 9e-04
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDV--VSINLIP----PRGCAFVCMNRRQDAAKAL 211
T++I +L EEEL + F ++G+V I +G AFV ++ A K L
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 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 = 36.9 bits (86), Expect = 0.001
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKAL 211
+++ +L E L F +G V ++ +I +G FV M ++A A+
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60
Query: 212 YKLKNTKLQGKTI 224
L +L G+ +
Sbjct: 61 ASLNGYRLGGRVL 73
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family
proteins. This subfamily corresponds to the RRM of the
GW182 family which includes three paralogs of TNRC6
(GW182-related) proteins comprising GW182/TNGW1, TNRC6B
(containing three isoforms) and TNRC6C in mammal, a
single Drosophila ortholog (dGW182, also called Gawky)
and two Caenorhabditis elegans orthologs AIN-1 and
AIN-2, which contain multiple miRNA-binding sites and
have important functions in miRNA-mediated translational
repression, as well as mRNA degradation in Metazoa. The
GW182 family proteins directly interact with Argonaute
(Ago) proteins, and thus function as downstream
effectors in the miRNA pathway, responsible for
inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 36.6 bits (85), Expect = 0.001
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 181 EYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
++G +++ +L G A + + +++AAKA L N L T+
Sbjct: 24 QHGPLLTFHLNLRHGNALIRYSSKEEAAKAQSALNNCVLGNTTL 67
>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 = 36.5 bits (85), Expect = 0.001
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC---AFVCMNRRQDAAKALYKLKNT 217
L++G+L + V E+ L++ F + G + S LI G AFV + AA AL +
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 218 KLQGKTITLAWA 229
+ G+ I + WA
Sbjct: 61 LILGQEIKVNWA 72
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 36.0 bits (83), Expect = 0.002
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L E+E+ F +YG V+ ++I G FV M+ + A +A+ L + KL
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYG--FVHMDDKTAADEAIRNLHHYKLH 60
Query: 221 GKTITL 226
G I +
Sbjct: 61 GVAINV 66
>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 = 36.2 bits (84), Expect = 0.002
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L + +L + + +EEL F G + S ++ R G FV DA KA+
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 213 KLKNTKLQGKTITLAWA 229
L +++ K + +++A
Sbjct: 61 TLNGFEIRNKRLKVSYA 77
>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 = 36.4 bits (85), Expect = 0.002
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
L++ +L + +E L + F +G + S ++ +G FVC + ++A KA+ ++
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63
Query: 216 NTKLQGKTITLAWA 229
+ GK + +A A
Sbjct: 64 GRIIGGKPLYVALA 77
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 36.3 bits (84), Expect = 0.002
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG-----CAFVCMNRRQDAAKA 210
LW+G+L + V+EE +S+ F YG V S+ ++P RG AFV + A KA
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56
>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 = 36.1 bits (84), Expect = 0.002
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 162 WIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLK 215
++G++ EE+L + F E G VVS L+ P+G F + AA A+ L
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 216 NTKLQGKTITLAWA 229
+ G+ + + +A
Sbjct: 62 GYEFNGRALRVDFA 75
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 35.8 bits (83), Expect = 0.002
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 171 QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP 230
++ L FG++G V + P + A V AA A K K LQ K I + W
Sbjct: 14 DKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASAALA--KKKGKLLQHKPIQIFWGS 71
Query: 231 GK 232
K
Sbjct: 72 KK 73
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 36.5 bits (85), Expect = 0.002
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
TL++ L+ E +L F EYG + I L+ PRG AF+ +D KA YK
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD-MKAAYK 61
>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 = 36.1 bits (84), Expect = 0.002
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
+T+++ +L + +L F +YG VV + ++ +G AF+ R+DA K +
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60
Query: 212 YKLKNTKLQGKTIT 225
L N +L G+T+
Sbjct: 61 KALNNKELFGRTLK 74
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 35.7 bits (83), Expect = 0.002
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
T L + +L V E+++ + F G + L+ P G A V R+ DA A+ K N +
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP-GVAEVVYVRKDDALTAIDKYNNRE 59
Query: 219 LQGKTI 224
L G+ +
Sbjct: 60 LDGQPM 65
>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 = 35.7 bits (83), Expect = 0.002
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYK 213
L + +L+ ++L F +YG+V + IP RG AFV ++DA A+
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDV-YIPRDRYTRESRGFAFVRFYDKRDAEDAMDA 59
Query: 214 LKNTKLQGKTITLA 227
+ +L G+ + +
Sbjct: 60 MDGKELDGRELRVQ 73
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 36.2 bits (84), Expect = 0.002
Identities = 12/48 (25%), Positives = 20/48 (41%)
Query: 172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
E ++ D F ++G S+ + C FV R+ A K + L
Sbjct: 16 EYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISENGL 63
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 35.8 bits (83), Expect = 0.002
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
T L I +L + + +EE F G V + ++ + G FV +DA +A+
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60
Query: 213 KLKNTKLQGKTITLAWA-PG 231
L +LQ K I +A+A PG
Sbjct: 61 TLNGLQLQNKRIKVAYARPG 80
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 35.9 bits (83), Expect = 0.002
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
S ++IG+L + EEEL + ++G + I ++ + AFV +A K + L
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 35.8 bits (83), Expect = 0.002
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
TL++G+L V EE L + F + G + + IP P+ AFV A+
Sbjct: 3 TLFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61
Query: 214 LKNTKLQGKTITL 226
L +L G+ + +
Sbjct: 62 LNGIRLFGRELRI 74
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 35.6 bits (83), Expect = 0.003
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDA-AKALYK 213
L++G LS V E +L + F +G V + +I P RG A++ + + K
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Query: 214 LKNTKLQGKTITLAWA 229
L TK +G + + A
Sbjct: 62 LNGTKWKGSVLKIEEA 77
>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 = 35.6 bits (82), Expect = 0.003
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
T + + +L ++++ F YG + S+ +P RG AFV + ++A A+
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59
Query: 213 KLKNTKLQGKTITLAWA 229
LK+T L G+ + L +A
Sbjct: 60 ALKDTHLLGRRLVLQYA 76
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 35.5 bits (82), Expect = 0.003
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKA 210
S L+I +L+ EE+L F +YG + ++L P P+G AFV + A KA
Sbjct: 2 SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHL-PIDKLTKKPKGFAFVTYMIPEHAVKA 60
Query: 211 LYKLKNTKLQGK 222
+L T QG+
Sbjct: 61 FAELDGTVFQGR 72
>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 = 35.5 bits (81), Expect = 0.003
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC----AFVCMNRRQDAAKALYKLK 215
TL++G+LS+ V E + F + G S +I FV +DAA AL +
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60
Query: 216 NTKLQGKTITLAWA 229
K+ GK + + WA
Sbjct: 61 GRKILGKEVKVNWA 74
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 35.3 bits (82), Expect = 0.003
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAAKALYK 213
L+IG+L V E+ L DTF +G ++ I +G AF+ + + + A+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 214 LKNTKLQGKTITLAWA 229
+ L + IT+++A
Sbjct: 64 MNGQYLCNRPITVSYA 79
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 35.2 bits (81), Expect = 0.004
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL- 219
++ G+ ++ E+ FG+YG V +++ G AFV M +DA A+ L N +
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDM--KSGFAFVYMEDERDAEDAIRGLDNFEFG 60
Query: 220 -QGKTITLAWA 229
Q + + + WA
Sbjct: 61 RQRRRLRVEWA 71
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 35.3 bits (82), Expect = 0.004
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG----CAFVCMNRRQDAAKALYKLK 215
TL + HL + E++ D +G S+ ++ RG AF + Q A++AL +L
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLH 59
Query: 216 NTKLQGKTITLAWA 229
K+ GK + + +A
Sbjct: 60 QLKILGKRLVVEYA 73
>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 = 35.0 bits (81), Expect = 0.004
Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
+++G LS + E L F +G++ ++ +G FV +++DA A+ +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 215 KNTKLQGKTITLAW 228
L G+ I W
Sbjct: 62 NGQWLGGRAIRTNW 75
>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 = 35.3 bits (82), Expect = 0.004
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
TL++G LS EE L + F YGD+ + L+ +G AFV +DA +A
Sbjct: 5 TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64
Query: 214 LKNTKLQGKTIT 225
+ G I
Sbjct: 65 AHKLVIDGSEIF 76
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 34.9 bits (80), Expect = 0.005
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L + EEE+ F +YG I + +G F+ + R A A +L N L+
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPLR 63
Query: 221 GKTI 224
GK +
Sbjct: 64 GKQL 67
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 34.5 bits (80), Expect = 0.006
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFV 199
L++G L + V EE+L + F +YG+V S+ ++ RG AFV
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFV 46
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 34.7 bits (79), Expect = 0.007
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
L++ L K + ++EL F +YG +++ ++ RG F+ ++R +A +A+ L
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 215 KNTKLQGKT--ITLAWA 229
K G IT+ +A
Sbjct: 65 NGQKPSGAAEPITVKFA 81
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 34.2 bits (78), Expect = 0.007
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG----CAFVCMNRRQDAAKALYKLK 215
TL++G+LS+ V E + F + G S +I FV + AA +L +
Sbjct: 1 TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60
Query: 216 NTKLQGKTITLAWA 229
K+ GK + + WA
Sbjct: 61 GRKIMGKEVKVNWA 74
>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 = 34.5 bits (80), Expect = 0.007
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 166 LSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKL 219
LS E +L + F YG + + ++ RG FV +DA +A +L ++
Sbjct: 7 LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66
Query: 220 QGKTI 224
G+ I
Sbjct: 67 DGRRI 71
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 34.1 bits (79), Expect = 0.007
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L+IG LS EE L + F +YG+VV ++ RG FV K L
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL-AA 59
Query: 215 KNTKLQGKTI 224
K L G+ I
Sbjct: 60 KPHVLDGREI 69
>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 = 34.2 bits (79), Expect = 0.008
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 168 KLVQEEELSDTFGEYGDVVSIN-LIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL 226
++V + L FG YGDVV + L + A + M Q A AL L +L GK + +
Sbjct: 10 EMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIRLHGKKLRV 69
Query: 227 A 227
Sbjct: 70 T 70
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 34.1 bits (78), Expect = 0.008
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
S L + +LS E+ L + F + SI IP P+G AFV +DA +AL
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFEK---ATSIR-IPQNNGRPKGYAFVEFESAEDAKEALN 56
Query: 213 KLKNTKLQGKTITL 226
NT+++G++I L
Sbjct: 57 SCNNTEIEGRSIRL 70
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 34.1 bits (78), Expect = 0.009
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKLK 215
L++G+L V E+ L F G V ++ +IP + FV ++ DA AL L
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 216 NTKLQGKTITLAWA 229
+++ I + WA
Sbjct: 61 GRQIENNEIRVNWA 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 = 34.1 bits (78), Expect = 0.009
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L+IG LS E+ L F +YG + + ++ RG FV DA A+ +
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 215 KNTKLQGKTI 224
+ G+ I
Sbjct: 63 NGKSVDGRQI 72
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 34.2 bits (78), Expect = 0.011
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 166 LSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKL 219
LS E +L + F YG + +N++ RG AFV R D+ +A+ +L
Sbjct: 7 LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66
Query: 220 QGKTITLAWAPGK 232
G+ I + ++ K
Sbjct: 67 DGRRIRVDYSITK 79
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 34.0 bits (78), Expect = 0.011
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKAL 211
L++G LSK E ++ F +G + ++ RGCAFV RQ A A+
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAI 59
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 33.5 bits (76), Expect = 0.014
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 161 LWIGHLSKLVQEEELSDTFGEY--GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
L++ +L E+ + TFG++ G V + I R AFV R+DA A+ L T+
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKI--RDYAFVHFTSREDAVHAMNNLNGTE 61
Query: 219 LQGKTITLAWA 229
L+G I + A
Sbjct: 62 LEGSCIEVTLA 72
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 33.4 bits (77), Expect = 0.015
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L++G+L + E++L F +G++ + L +G F+ +DA KAL +L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 215 KNTKLQGKTI 224
+L G+ I
Sbjct: 61 NGFELAGRPI 70
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 34.0 bits (77), Expect = 0.016
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L++ L K + ++EL F +YG +++ ++ RG F+ ++R +A +A+ L
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 215 KNTKLQGKT--ITLAWAPGKGMK 235
K G T IT+ +A K
Sbjct: 68 NGQKPPGATEPITVKFANNPSQK 90
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 33.5 bits (77), Expect = 0.016
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRG 195
TL++G+L + EEEL F YG V +++ PPRG
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRG 40
>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 = 33.4 bits (76), Expect = 0.016
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
++IG L+ +E+++ F YG + I+L RG FV + +DA A+Y+L +L
Sbjct: 2 VFIGRLNPAAREKDVERFFKGYGRIRDIDL--KRGFGFVEFDDPRDADDAVYELDGKELC 59
Query: 221 GKTITLAWA 229
+ +T+ A
Sbjct: 60 NERVTIEHA 68
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 33.7 bits (78), Expect = 0.016
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----------PRGCAFVCMNRRQDA 207
S L++ +LSK V EE+L FG + D S +G AFV + A
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60
Query: 208 AKALYKLKNTKLQGK 222
KAL + L+GK
Sbjct: 61 TKALNLVNGYVLKGK 75
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 33.2 bits (76), Expect = 0.018
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAA-KALYK 213
+++G++ EE+L D F E G VVS L+ P+G F C + Q+ A A+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGF-CEYKDQETALSAMRN 59
Query: 214 LKNTKLQGKTI 224
L +L G+ +
Sbjct: 60 LNGYELNGRQL 70
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 33.5 bits (77), Expect = 0.018
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKAL 211
+ L++G + + ++E++L F ++G + + ++ + GCAF+ R+ A KA
Sbjct: 5 AIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQ 64
Query: 212 YKLKNTK 218
L K
Sbjct: 65 SALHEQK 71
>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 = 33.0 bits (76), Expect = 0.019
Identities = 17/65 (26%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 161 LWIGHL-SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
+++G+L + V +E+L + F +YG ++ I+L +G FV + +DA A+ ++
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISLH--KGYGFVQFDNEEDARAAVAGENGREI 60
Query: 220 QGKTI 224
G+ +
Sbjct: 61 AGQKL 65
>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 = 33.3 bits (77), Expect = 0.020
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPR----GCAFVCMNRRQDA 207
TTL++ +L+ EE L F + G V S+ + P + G FV ++ A
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 208 AKALYKLKNTKLQGKTITL 226
KAL +L+ T L G + L
Sbjct: 61 QKALKRLQGTVLDGHALEL 79
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 33.1 bits (76), Expect = 0.020
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 165 HLSKL---VQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYKLKNT 217
H+S + ++ +L FG++G ++ + +I +G FV DA +A KL T
Sbjct: 4 HVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGT 63
Query: 218 KLQGKTI 224
++G+ I
Sbjct: 64 VVEGRKI 70
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 32.8 bits (75), Expect = 0.020
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC---AFVCMNRRQDAAKALY 212
+++G+L V+E++L D F +YG + I L RG AFV +DA A++
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVF 56
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 33.0 bits (76), Expect = 0.022
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKALYKLKNTK 218
TL + +L + ++EL F ++G+V I P R FV + A AL L
Sbjct: 3 TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62
Query: 219 LQGKTITLA 227
G + +
Sbjct: 63 FLGGRLKVK 71
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 32.8 bits (75), Expect = 0.023
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
+ TL+IG+L K +L + F +G+++ I++
Sbjct: 1 ATRTLFIGNLEKTTTYSDLREAFERFGEIIDIDI 34
>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 = 32.7 bits (75), Expect = 0.024
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC---AFVCMNRRQDAAKALY 212
+++G+L ++E ++ D F +YG + +I+L R AFV +DA A+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVR 56
>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 = 33.0 bits (75), Expect = 0.025
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
++IG LS +E ++ F YG ++ ++L G FV + +DA A+Y+L L
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEVDL--KNGYGFVEFDDLRDADDAVYELNGKDLC 59
Query: 221 GKTITLAWAPG 231
G+ + + A G
Sbjct: 60 GERVIVEHARG 70
>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 = 33.1 bits (76), Expect = 0.025
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 167 SKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
K V E++L + F +G++ I ++ +G A+V + AA+A+ ++ L
Sbjct: 11 GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLG 70
Query: 221 GKTITL 226
G T L
Sbjct: 71 GDTKPL 76
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
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 RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 32.8 bits (75), Expect = 0.025
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 155 NMCSTTLWIGHLSKL---VQEEELSDTFGEYGDVVSINLIPPRG--CAFVCMNRRQDAAK 209
C T I H+S L V EE++ + E+G +V++ + G A V + A +
Sbjct: 2 YCCPPTKMI-HVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATE 60
Query: 210 ALYKLKNTKLQGKTITLAW 228
AL + L G TI LA+
Sbjct: 61 ALACKHASSLNGSTIRLAF 79
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 33.1 bits (75), Expect = 0.027
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 160 TLWIGHLSKLVQEEELSDT-------FGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
T++I +L+ +++EEL + FG D+V++ + RG AFV A AL
Sbjct: 3 TIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNALR 62
Query: 213 KLKNTKLQGKTITLAWA 229
+L+ GK + + +A
Sbjct: 63 QLQGFPFYGKPMRIQYA 79
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 32.9 bits (75), Expect = 0.027
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLK 215
L++G L+K E+E+ + F YG V I ++ RGCAFV + ++ A A+ L
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
Query: 216 NT 217
Sbjct: 62 GV 63
>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 = 32.6 bits (75), Expect = 0.028
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
LW+G L EL F +G + I+ P R A++ +AA+A L+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYI-EYESIEAAQA----AKEALR 55
Query: 221 GKTITLAWAPGKGMK 235
G + PG+ ++
Sbjct: 56 GFPL---GGPGRRLR 67
>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 = 32.6 bits (75), Expect = 0.029
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINL-IPP--RGCAFVCMNRRQDAAKALYKLKNT 217
L++ +L + EEL D FG+YG + I + RG AFV DA A L
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64
Query: 218 KLQGK 222
+ +
Sbjct: 65 NVANR 69
>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 = 32.6 bits (75), Expect = 0.030
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI------NLIPPRGCAFVCMNRRQDAAKALYKL 214
L+I HL +++L F +G+V+S N + FV + + A A+ +
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 215 KNTKLQGK 222
++ GK
Sbjct: 61 NGFQVGGK 68
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes. Since
the Hu proteins share high homology with the Drosophila
embryonic lethal abnormal vision (ELAV) protein, the Hu
family is sometimes referred to as the ELAV family.
Drosophila ELAV is exclusively expressed in neurons and
is required for the correct differentiation and survival
of neurons in flies. The neuronal members of the Hu
family include Hu-antigen B (HuB or ELAV-2 or Hel-N1),
Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D
(HuD or ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 79
Score = 32.7 bits (75), Expect = 0.031
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
L++ L K + ++EL F YG +++ ++ RG F+ ++R +A +A+ L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 215 KNTKLQGKT--ITLAWA 229
T G T IT+ +A
Sbjct: 63 NGTIPPGATEPITVKFA 79
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 32.5 bits (74), Expect = 0.032
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTK 218
TL + +L V ++L FG YG++ I P R F+ + A AL L ++
Sbjct: 3 TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62
Query: 219 LQGKTITL 226
+ GK I L
Sbjct: 63 IAGKRIKL 70
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 32.3 bits (73), Expect = 0.041
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRR---QDAAKALY 212
L+IG +SK E ++ F +G + ++ RGCAFV R Q A KA++
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63
Query: 213 K 213
+
Sbjct: 64 Q 64
>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 = 32.2 bits (74), Expect = 0.044
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYK 213
+++G+L + V EE L + F + G VV+++ IP +G FV +DA A+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVH-IPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59
Query: 214 LKNTKLQGKTI 224
+ KL GK I
Sbjct: 60 MNMIKLYGKPI 70
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 31.9 bits (72), Expect = 0.046
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++ +L+ V EE L +F E+G + + + + AFV R A +A+ ++ +++
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEERDAAVRAMDEMNGKEIE 61
Query: 221 GKTITLAWA 229
G+ I + A
Sbjct: 62 GEEIEIVLA 70
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 32.1 bits (74), Expect = 0.047
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 160 TLWIGHLSKLVQEEELSDT----FGEYGDVVSINL---IPPRGCAFVCMNRRQDAAKALY 212
TL+I +L++ ++++EL + F ++G V+ I + RG AFV + A AL
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60
Query: 213 KLKNTKLQGKTITLAWA 229
L+ K + + +A
Sbjct: 61 ALQGFPFYDKPMRIQYA 77
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 31.9 bits (73), Expect = 0.051
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC----AFVCMNRRQDAAKALYKLK 215
T+ +G + + E++L + F G+V + L R AFV + A AL L
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLS 60
Query: 216 NTKLQGKTI 224
T L G +
Sbjct: 61 GTLLGGHPL 69
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein (SXL).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 78
Score = 32.2 bits (73), Expect = 0.053
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 160 TLWIGHLSKLVQEEELSDT-------FGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
T++I +L++ V++EEL + FG+ D+V++ + RG AFV A AL
Sbjct: 1 TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60
Query: 213 KLKNTKLQGKTITLAWA 229
++ K + +A++
Sbjct: 61 SMQGFPFYDKPMRIAYS 77
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 32.3 bits (73), Expect = 0.059
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 166 LSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKL 219
LS E +L + F +YG + ++++ RG AFV DA +A + +L
Sbjct: 17 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 76
Query: 220 QGKTITLAWAPGK 232
G+ I + ++ K
Sbjct: 77 DGRRIRVDFSITK 89
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 31.5 bits (72), Expect = 0.062
Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINL-IPPRGCAFV 199
+++G L++ + EE+L F ++G+V + + P R AFV
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFV 42
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 32.1 bits (74), Expect = 0.064
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 11/69 (15%)
Query: 167 SKLVQEEEL--SDTFGEYGDV--VSIN-------LIPPRGCAFVCMNRRQDAAKALYKLK 215
+L EE L + FG+YG + + IN P A+V +R++DA + + +
Sbjct: 15 PRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVD 74
Query: 216 NTKLQGKTI 224
L G+ +
Sbjct: 75 GFYLDGRLL 83
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 31.7 bits (72), Expect = 0.066
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
+++G LS V + L F + ++ RG FV +QDA A+ ++
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 215 KNTKLQGKTITLAW 228
L + I W
Sbjct: 62 NGKWLGSRPIRCNW 75
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 31.9 bits (72), Expect = 0.070
Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L+I L + + ++++ D F +G +++ ++ RG AF+ ++R +A +A+
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 215 KNTKLQGKT--ITLAWA 229
K G + IT+ +A
Sbjct: 63 NGHKPPGSSEPITVKFA 79
>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 = 31.6 bits (72), Expect = 0.075
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
L++ +L +E++L F ++G++ +++ +G A+V +DA KA +L
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 215 KNTKLQGKTI 224
QG+ I
Sbjct: 65 DGKVFQGRLI 74
>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 = 31.3 bits (71), Expect = 0.086
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
++IGHL E+EL F ++G V ++ +
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRV 31
>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 = 31.6 bits (71), Expect = 0.093
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKNTKL 219
+++G+L + EL FG YG + S+ + P G AFV +DAA A+ +L L
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 66
Query: 220 QGKTITLAWAPGK 232
G + + + G+
Sbjct: 67 CGCRVRVELSNGE 79
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 31.2 bits (71), Expect = 0.095
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 168 KLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
K EE+L + F E+GD+ ++++ +G +V ++ AA AL
Sbjct: 10 KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
>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 = 31.1 bits (70), Expect = 0.098
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYK 213
TL++ LS+ EE L ++F ++ ++ R G FV + +DA A
Sbjct: 2 TLFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58
Query: 214 LKNTKLQGKTITLAWAPGKG 233
+++ ++ G +TL +A KG
Sbjct: 59 MEDGEIDGNKVTLDFAKPKG 78
>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 = 33.8 bits (77), Expect = 0.100
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEY--GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
L++ +L EE + +F E+ G V + I R AFV R+DA KA+ +L +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDELNGKE 293
Query: 219 LQGKTI--TLAWAPGK 232
L+G I TLA K
Sbjct: 294 LEGSEIEVTLAKPVDK 309
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 31.5 bits (72), Expect = 0.11
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 24/88 (27%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL--IPPRGC--------------------- 196
T+++G+L ++++L F ++G + S+ +P +
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61
Query: 197 AFVCMNRRQDAAKALYKLKNTKLQGKTI 224
A+V + A KAL KL T+ +G I
Sbjct: 62 AYVVFKEEESAEKAL-KLNGTEFEGHHI 88
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 31.3 bits (71), Expect = 0.11
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKL 214
L++G LSK E+++ F +G + ++ +GCAFV + +A A+ L
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINAL 62
>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 = 31.0 bits (71), Expect = 0.11
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
T +++G L ++ L F ++G++ +I RG FV ++ A +A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC- 59
Query: 213 KLKNTKLQGKTITLAWA 229
K N + G+ + A
Sbjct: 60 KDPNPIIDGRKANVNLA 76
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 31.1 bits (71), Expect = 0.11
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP---PRGCAFVCMNRRQDAAKALYKLK 215
+++ +L V ++L D F E G+V+ + +G V +DA +A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 216 NTKLQGKTI 224
L+G+ +
Sbjct: 61 GYDLEGREL 69
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 31.0 bits (71), Expect = 0.12
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 158 STTLWIGHL-SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL 211
+TTL + ++ +L +L++ F ++G +V+I + A V + ++A KA
Sbjct: 1 NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAY 55
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 30.7 bits (70), Expect = 0.13
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKL 214
+++G + EEEL D F +G V + +I R G FV ++DA K L +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL-AM 62
Query: 215 KNTKLQGKTITLAWA 229
N +GK + + A
Sbjct: 63 GNLNFRGKKLNIGPA 77
>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 = 30.3 bits (69), Expect = 0.16
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 6/69 (8%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
T ++I L +E+L +G ++S I +G FV + + A KA+
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 213 KLKNTKLQG 221
L +Q
Sbjct: 61 GLNGRGVQA 69
>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 = 31.0 bits (71), Expect = 0.16
Identities = 23/82 (28%), Positives = 31/82 (37%), Gaps = 22/82 (26%)
Query: 165 HLSKLVQEEELSD-------------TFGEYGDVVSINLIPPR---------GCAFVCMN 202
L +V EEL D G+YG V+S+ + P G FV
Sbjct: 5 CLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFA 64
Query: 203 RRQDAAKALYKLKNTKLQGKTI 224
+DA KA L K G+T+
Sbjct: 65 DVEDAQKAQLALAGRKFDGRTV 86
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 30.3 bits (69), Expect = 0.16
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
T+ + ++S V EE++ F + G V I L P A V DA KA L +
Sbjct: 1 RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNGS 60
Query: 218 KLQGKTITL 226
+ GKTI +
Sbjct: 61 QFGGKTIKI 69
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.8 bits (70), Expect = 0.16
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 171 QEEELSDTFGEYGDVVSINLIPP---------RGCAFVCMNRRQDAAKALYKLK-NTKLQ 220
+EL + F +G++ ++ L P RG FV +QDA +A L +T L
Sbjct: 13 TVKELRELFSTFGELKTVRL--PKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLY 70
Query: 221 GKTITLAWA 229
G+ + L WA
Sbjct: 71 GRRLVLEWA 79
>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 = 30.7 bits (70), Expect = 0.16
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
L +G+L +E+ + +G V L+ +G FV + A KA +
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60
Query: 214 LKNTKLQGKTITLAWAP 230
L ++ G+ + + WA
Sbjct: 61 LDGKQIGGRKLQVDWAD 77
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 30.7 bits (70), Expect = 0.17
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
S ++IG L + E ++ F +YG++V INL+ +G AF+ ++ A+
Sbjct: 9 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68
Query: 212 YKLKNTKLQGKTI 224
L KL G+TI
Sbjct: 69 DNLNGIKLLGRTI 81
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 30.6 bits (69), Expect = 0.17
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTK 218
TL I +L V E L F YGDV + P R FV +DAAKAL + +
Sbjct: 3 TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKE 62
Query: 219 LQGKTITL 226
+ GK + +
Sbjct: 63 ISGKPVVI 70
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 30.5 bits (69), Expect = 0.18
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 161 LWIGHL-SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
L+IG+L +K V +E+L F YG++ I L G FV + + A A+ + +
Sbjct: 2 LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYG--FVQFDSPESCANAINCEQGKMI 59
Query: 220 QGKTITL 226
+G+ + L
Sbjct: 60 RGRKLHL 66
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 30.8 bits (69), Expect = 0.18
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
++I +L + E L FG +G V ++ +I +G FV M ++AA A+ L
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 215 KNTKLQGKTITLAWAPGKGMK 235
+L K + +++ K K
Sbjct: 64 NGYRLGDKILQVSFKTSKSHK 84
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 30.4 bits (69), Expect = 0.19
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
+++G L V EEE + F ++G VV L+ RG FV + + A + ++
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFD-SESAVERVFSA 60
Query: 215 KNTKLQGKTI 224
+L GK +
Sbjct: 61 GMLELGGKQV 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 = 30.5 bits (69), Expect = 0.19
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 158 STTLWIGHLSKLVQEEEL----SDTFGEYGDVVSINLIPP---RGCAFVCMNRRQDAAKA 210
S +++ L ++EL ++ F +YG +V + ++ R AFV DA A
Sbjct: 2 SACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNA 61
Query: 211 LYKLKNTKLQGKTI 224
L K + T L G+ I
Sbjct: 62 LAKGQGTILDGRHI 75
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 30.1 bits (68), Expect = 0.19
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG--CAFVCMNRRQDAAKALY 212
+++G+L ++ +++ D F +YG + I+L RG AFV +DA A+Y
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVY 55
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 30.3 bits (68), Expect = 0.21
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKL 214
TL++G+L V+EE L + F + G + + + P+ FVC + A+ L
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALL 62
Query: 215 KNTKLQGKTI 224
+L G+ I
Sbjct: 63 NGIRLYGRPI 72
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 30.3 bits (68), Expect = 0.21
Identities = 16/64 (25%), Positives = 34/64 (53%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L + E+E F +YG+ + + +G F+ + R A A +L +T ++
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMR 63
Query: 221 GKTI 224
G+ +
Sbjct: 64 GRQL 67
>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 = 30.3 bits (68), Expect = 0.22
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLK 215
+++G + + V E+EL F G + + L+ RG AFV ++ +A +A+ +L
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
Query: 216 NTKLQ 220
N +++
Sbjct: 64 NYEIR 68
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 30.2 bits (68), Expect = 0.22
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 174 ELSDTFGEYGDVVSINLIPPRGC-----AFVCMNRRQDAAKALYKLKNTKLQ--GKTITL 226
+L+ F YG +V ++ PPR AFV +DA A ++ + G T+ +
Sbjct: 15 DLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDTLHV 74
Query: 227 AWA 229
WA
Sbjct: 75 QWA 77
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 29.9 bits (68), Expect = 0.27
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 8/71 (11%)
Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG--CAFVCMNRRQDAAKALYKL 214
C+T L++ +L EEEL F + + G FV +D + A L
Sbjct: 2 CNT-LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFV---EFEDVSFATQAL 57
Query: 215 KNTKLQGKTIT 225
+ LQG ++
Sbjct: 58 NS--LQGAVLS 66
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 30.0 bits (68), Expect = 0.27
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKL 214
TL++G+LS ++++L + F E G+VV + + +G V + A KAL +
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59
Query: 215 KNTKLQGKTI 224
+L G+ I
Sbjct: 60 SGEELLGREI 69
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 30.8 bits (69), Expect = 0.27
Identities = 27/104 (25%), Positives = 47/104 (45%), Gaps = 10/104 (9%)
Query: 149 ARNGVENMCSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQD 206
GV +T L + +L+ ++V + L FG YGDV + ++ + A + M
Sbjct: 4 GMPGVSAGGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQ 63
Query: 207 AAKALYKLKNTKLQGKTITLAWA-------PGKGMKDKDW-KDF 242
+ A+ L K+ GK I + + P +G+ D+ KDF
Sbjct: 64 SQLAMSHLNGQKMYGKIIRVTLSKHQTVQLPREGLDDQGLTKDF 107
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 32.2 bits (73), Expect = 0.28
Identities = 24/72 (33%), Positives = 31/72 (43%), Gaps = 12/72 (16%)
Query: 43 VVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQD-------KDVFGPRFARNLKATF 95
++ SV+KFI K P+ LYV D L Q+R D DV GP N T
Sbjct: 189 ILSSVKKFIKKNPPDI---VLYV-DRLDMQTR-DSNDLPLLRTITDVLGPSIWFNAIVTL 243
Query: 96 QHLYQCPPEDKS 107
H PP+ +
Sbjct: 244 THAASAPPDGPN 255
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 30.1 bits (68), Expect = 0.28
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG 195
L++G+L + E+EL + F E+G+V+ + + G
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGG 40
>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 = 30.3 bits (69), Expect = 0.28
Identities = 24/82 (29%), Positives = 33/82 (40%), Gaps = 7/82 (8%)
Query: 158 STTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKAL 211
S L++ L K L F + G L PRG AFV +DA +A
Sbjct: 2 SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61
Query: 212 YKLKNTKLQGKTITLAW-APGK 232
L LQG I +++ PG+
Sbjct: 62 QALNGHSLQGSPIRVSFGNPGR 83
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 30.0 bits (68), Expect = 0.29
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 163 IGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLKNTKLQ 220
I + V E++ F ++G+V ++ ++ + A KA + K L
Sbjct: 6 ITSIGPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKAREAFVEKGEGLL 65
Query: 221 GKTITLA 227
GK I L+
Sbjct: 66 GKEIKLS 72
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 29.6 bits (67), Expect = 0.30
Identities = 11/50 (22%), Positives = 24/50 (48%)
Query: 175 LSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
L D F +G ++ + L+P + + R+ A +A+ L ++ G +
Sbjct: 16 LEDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEVNGVKL 65
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 29.9 bits (68), Expect = 0.31
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYK 213
T L + +L V ++++ + F E+G + + R G A V RR DA KA+ +
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
Query: 214 LKNTKLQGK 222
L G+
Sbjct: 61 YNGVPLDGR 69
>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 = 29.9 bits (67), Expect = 0.31
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALYKLK 215
++IG L + + E+EL + G + + ++ RG AFV + +Q+A A+ +L
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63
Query: 216 NTKLQ 220
N +++
Sbjct: 64 NYEIR 68
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 29.6 bits (66), Expect = 0.34
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP----PRGCAFVCMNRRQDAAKALYKL 214
++IG LS +++L D F ++G+VV ++ L P RG FV + K + +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 59
Query: 215 KNTKLQGKTI 224
K KL GK I
Sbjct: 60 KEHKLNGKVI 69
>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 = 29.7 bits (67), Expect = 0.37
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------------PRGCAFVCMNRRQD 206
++I +LS EE+L + ++ VS+ LIP P G A+ + +
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFE-PVSV-LIPSQTVRGFRSRRVRPLGIAYAEFSSPEQ 58
Query: 207 AAKALYKLKNTKLQGKTITL 226
A K + L + + + +
Sbjct: 59 AEKVVKDLNGKVFKNRKLFV 78
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 29.4 bits (66), Expect = 0.40
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKN 216
S +L++ ++ + V E L F YGDV + G V +DA +A+ +L
Sbjct: 1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60
Query: 217 TKLQGKTI 224
+Q + +
Sbjct: 61 RHMQQQAL 68
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 29.5 bits (66), Expect = 0.41
Identities = 17/66 (25%), Positives = 33/66 (50%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L++G+L + EE+ F +YG+ + + RG F+ + R A A +L T L+
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 63
Query: 221 GKTITL 226
+ + +
Sbjct: 64 NRPLRI 69
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 29.5 bits (67), Expect = 0.44
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 188 INLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT 225
I L+ + AFV ++ KAL L K +G+ ++
Sbjct: 36 IKLLKRQDFAFVTFRSEEERQKALEILDGFKWKGRVLS 73
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 29.1 bits (66), Expect = 0.45
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG 231
+E L F ++ + L+P RG AFV + A AL LQG IT PG
Sbjct: 16 KEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVAL-----QALQGFKIT----PG 66
Query: 232 KGMK 235
MK
Sbjct: 67 HAMK 70
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 29.3 bits (65), Expect = 0.56
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
+++ +LS E L FG +G V ++ +I +G FV M +AA A+ L
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 215 KNTKLQGKTITLAWAPGKGMK 235
+L + + +++ K K
Sbjct: 64 NGYRLGDRVLQVSFKTSKQHK 84
>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to the
RRM2 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D member
3, known previously as PMP-70) and/or PXF (peroxisomal
farnesylated protein, known previously as PEX19). It
associates with LIM kinase 2 (LIMK2) and may serve as a
relatively common target of human autoantibodies
reactive to cytoplasmic vesicle-like structures. LKAP
contains two RNA recognition motifs (RRMs), also known
as RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). However, whether those RRMs are bona fide RNA
binding sites remains unclear. Moreover, there is no
evidence of LAKP localization in the nucleus. Therefore,
if the RRMs are functional, their interaction with RNA
species would be restricted to the cytoplasm and
peroxisomes.
Length = 89
Score = 29.2 bits (66), Expect = 0.59
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 175 LSDTFGEYGDVVSINLIP-PRG--CAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG 231
L++ F +G V+S++L P G A V + QDA A+ +L K+ K I +++A G
Sbjct: 25 LTNQFKRHGKVLSVSLRPQTDGSLVASVRVPNLQDAQYAISQLHRRKIGSKRILVSYAQG 84
Query: 232 KGMK 235
K
Sbjct: 85 SSNK 88
>gnl|CDD|241303 cd01273, PTB_CED-6, Cell death protein 6 homolog (CED-6/GULP1)
Phosphotyrosine-binding (PTB) domain. CED6 (also known
as GULP1: engulfment adaptor PTB domain containing 1)
is an adaptor protein involved in the specific
recognition and engulfment of apoptotic cells. CED6
has been shown to interact with the cytoplasmic tail of
another protein involved in the engulfment of apoptotic
cells, CED1. CED6 has a C-terminal PTB domain, which
can bind to NPXY motifs. PTB domains have a common
PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 144
Score = 30.3 bits (69), Expect = 0.62
Identities = 13/59 (22%), Positives = 29/59 (49%)
Query: 20 PISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQ 78
+ + K T + + AIR +KF + + +S + K + + + + + D ++ HQF
Sbjct: 23 EVDQPKGTEVVKEAIRKLKFARQIKKSEGAKLPKVELQISIDGVKIQDPKTKEIMHQFP 81
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 29.1 bits (65), Expect = 0.66
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLK 215
+++G + + + E+EL F G + L+ RG AFV +++A A+ L
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILN 63
Query: 216 NTKL-QGKTI 224
N ++ GK I
Sbjct: 64 NYEIRPGKFI 73
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 28.8 bits (64), Expect = 0.67
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK-NTKL 219
L+IG+LS V E+L FG+ ++ ++ G AFV + A +A+ L +L
Sbjct: 4 LYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL 63
Query: 220 QGKTITLAWAPGK 232
GK + + ++ K
Sbjct: 64 HGKVMEVDYSVPK 76
>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast
sporulation-specific protein 2 (Ssp2) and similar
protein. This subfamily corresponds to the RRM of the
lineage specific yeast sporulation-specific protein 2
(Ssp2) and similar proteins. Ssp2 is encoded by a
sporulation-specific gene necessary for outer spore wall
assembly in the yeast Saccharomyces cerevisiae. It
localizes to the spore wall and may play an important
role after meiosis II and during spore wall formation.
Ssp2 contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.9 bits (65), Expect = 0.70
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 165 HLSKLVQEEELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKAL--YKLKNTKLQG 221
L EEL D F +G++V I+ I R C + + A +A + K + L
Sbjct: 1 VLPSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLEDKGSSLNN 60
Query: 222 KTITLAWA--PGKGMKDK 237
K I W+ GK + DK
Sbjct: 61 KYIK-QWSIWYGKDITDK 77
>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 = 28.7 bits (65), Expect = 0.77
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKAL 211
+TLW+ + + ++ D F +YG+++SI P R +V + AA A+
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSIRF--PSLRFNKTRRFCYVQFTSPESAAAAV 58
Query: 212 YKLKNTKLQGKTIT 225
L +G +
Sbjct: 59 ALLNGKLGEGYKLV 72
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in a family that represents a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), at
their N-terminus, and an RS domain at their C-terminus.
Length = 70
Score = 28.7 bits (64), Expect = 0.78
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 171 QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
+ +L F YG +V++ + R AFV ++DA KAL +K+ + I++ +A
Sbjct: 13 RTRDLERHFEPYGKLVNVRI--RRNFAFVQYETQEDATKALESTNMSKVLDRVISVEYA 69
>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 = 28.7 bits (65), Expect = 0.82
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINL-IPP----RGCAFVCMNRRQDAAKALYK 213
+++G + + + E+EL F + G + + L + RG AFV ++ A +A+ +
Sbjct: 2 CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61
Query: 214 LKNTKLQ-GKTIT 225
L N +++ GK +
Sbjct: 62 LHNYEIRPGKRLG 74
>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 = 28.4 bits (64), Expect = 0.82
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
L++G+L V +EL + F ++G V S N+ +G FV + R AL K
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 214 LKNTKLQGKTITLA 227
K+ L+G + +
Sbjct: 61 QKH-ILEGNKLQVQ 73
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 28.7 bits (64), Expect = 0.83
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP----PRGCAFVCMNRRQDAAKALYKL 214
+++G LS +++L + F ++G+VV +I + P RG FV K L
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL-DQ 59
Query: 215 KNTKLQGKTI 224
K KL G+ I
Sbjct: 60 KEHKLDGRVI 69
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 28.7 bits (64), Expect = 0.93
Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDV--VSINLIPPRGCAFVCMNRRQDAAKALYKLK 215
+ TL++ +L + +EL + F + D+ S +G A++ +A KAL + +
Sbjct: 3 ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62
Query: 216 NTKLQGKTITL 226
++ G++I +
Sbjct: 63 GAEVDGRSIVV 73
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 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 = 76
Score = 28.4 bits (64), Expect = 1.00
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 165 HLSKL---VQEEELSDTFGE-YGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLKNTKL 219
HLS + V EE+L + F + G V + P R A + M ++A +AL L N +L
Sbjct: 3 HLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQL 62
>gnl|CDD|241155 cd12711, RRM_TNRC6A, RNA recognition motif in vertebrate GW182
autoantigen. This subgroup corresponds to the RRM of
the GW182 autoantigen, also termed trinucleotide
repeat-containing gene 6A protein (TNRC6A), or CAG
repeat protein 26, or EMSY interactor protein, or
protein GW1, or glycine-tryptophan protein of 182 kDa, a
phosphorylated cytoplasmic autoantigen involved in
stabilizing and/or regulating translation and/or storing
several different mRNAs. GW182 is characterized by
multiple glycine/tryptophan (G/W) repeats and is a
critical component of GW bodies (GWBs, also called
mammalian processing bodies, or P bodies). The mRNAs
associated with GW182 are presumed to reside within
GWBs. GW182 has been shown to bind multiple Ago-miRNA
complexes, and thus plays a key role in miRNA-mediated
translational repression and mRNA degradation. In the
absence of Ago2, GW182 may induce translational
silencing effect. GW182 is composed of an N-terminal
G/W-rich region containing an Ago hook responsible for
Ago protein-binding; a ubiquitin-associated (UBA) domain
and a glutamine (Q)-rich region in the middle region; a
middle G/W-rich region, a RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal G/W-rich
region, at the C-terminus. A bipartite C-terminal region
including the middle and C-terminal G/W-rich regions is
referred to as silencing domain that triggers silencing
of bound transcripts by inhibiting protein expression
and promoting mRNA decay via deadenylation. .
Length = 83
Score = 28.5 bits (63), Expect = 1.0
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 181 EYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
++G +++ +L P G A V + +++ KA L L TI +A
Sbjct: 24 QHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFA 72
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a ubiquitously expressed pre-mRNA splicing
factor that enhances messenger RNA (mRNA) splicing in a
cell-specific manner or in a certain developmental
process, such as spermatogenesis. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It may play a more
specific role in meiosis entry and progression. Together
with additional testis-specific RNA-binding proteins,
RBM7 may regulate the splicing of specific pre-mRNA
species that are important in the meiotic cell cycle.
RBM7 contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. .
Length = 75
Score = 28.3 bits (63), Expect = 1.1
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
TL++G+L V EE + + F + G V+ + IP P+ AFV A+
Sbjct: 3 TLFVGNLDPKVTEELIFELFLQAGPVIKVK-IPKDKDGKPKQFAFVNFKHEVSVPYAMNL 61
Query: 214 LKNTKLQGKTITL 226
L KL G+ + +
Sbjct: 62 LNGIKLYGRPLNI 74
>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 = 30.6 bits (69), Expect = 1.1
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
L++G+L + E+EL F +GD+ + L +G F+ + ++A +AL +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
Query: 215 KNTKLQGKTI 224
+L G+ I
Sbjct: 249 NGFELAGRPI 258
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 28.5 bits (63), Expect = 1.1
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
+++G LS + E++ F +G + ++ +G FV + DA A+ +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 215 KNTKLQGKTITLAWA 229
L G+ I WA
Sbjct: 64 GGQWLGGRQIRTNWA 78
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 77
Score = 28.1 bits (62), Expect = 1.2
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK-NTKL 219
L+IG+L++ V +L F ++ S + G AFV Q A KA+ +L
Sbjct: 4 LYIGNLNESVTPADLEKVFEDHKISYSGQFLVKSGYAFVDCPDEQWAMKAIETFSGKVEL 63
Query: 220 QGKTITL 226
GK + +
Sbjct: 64 HGKRLEI 70
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 27.9 bits (63), Expect = 1.2
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFV 199
++IGHL E EL F ++G V + L +G AFV
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFV 46
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 28.5 bits (63), Expect = 1.2
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
+++ +LS E L FG +G V ++ +I +G FV M +AA A+ L
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 215 KNTKLQGKTITLAWAPGKGMK 235
+L + + +++ K K
Sbjct: 66 NGYRLGDRVLQVSFKTNKTHK 86
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 28.0 bits (63), Expect = 1.3
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 174 ELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQGKTITL 226
+L D + GDV ++ + G V ++D +AL KL T+ +G+ + +
Sbjct: 16 DLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 69
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 28.7 bits (64), Expect = 1.3
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 13/78 (16%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDV--------VSINLIPPRGCAFVCMNRRQDAAK 209
TL++ +L EE L+ F ++G V S +G FVC + Q
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGR--AKGTGFVCF-KDQYTYN 57
Query: 210 ALYKLKNTKLQGKTITLA 227
A LKN G T L+
Sbjct: 58 AC--LKNAPAAGSTSLLS 73
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 28.1 bits (63), Expect = 1.3
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI 191
+++G LS EE++ + FG++G++V I L
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELP 32
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 28.1 bits (62), Expect = 1.3
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
+++ +L+ E L FG +G V ++ +I +G FV M +AA A+ L
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 215 KNTKLQGKTITLAWAPGKGMK 235
+L + + +++ K K
Sbjct: 66 NGYRLGDRVLQVSFKTNKTHK 86
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 28.1 bits (62), Expect = 1.4
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
+++G LS EE++ + FG +G++ +I L
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIEL 31
>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 = 27.9 bits (63), Expect = 1.6
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 11/83 (13%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP------PRGCAFVCMNRRQDAAK 209
+ TL + L L EE++ V + LI RG AFV +DA +
Sbjct: 2 TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61
Query: 210 ALYKLKN---TKLQGKTITLAWA 229
+ L N + G+ + +++A
Sbjct: 62 WMDALNNLDPFVIDGRVVRVSYA 84
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 27.7 bits (62), Expect = 1.6
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 166 LSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALYKLKNTKLQ 220
L K ++E++L F +G + + L R FV ++A KAL N+ +
Sbjct: 8 LPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFID 67
Query: 221 GKTITL 226
IT+
Sbjct: 68 TSKITV 73
>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 = 27.5 bits (62), Expect = 1.6
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 170 VQEEELSDTFGEYG-DVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT 223
EE++ D F I+++ P G A+V +DA +AL K N K+ G+
Sbjct: 11 ATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNN-KMGGRY 69
Query: 224 ITL 226
I +
Sbjct: 70 IEV 72
>gnl|CDD|148894 pfam07536, HWE_HK, HWE histidine kinase. Two-component systems,
consisting of a histidine kinase and a cognate response
regulator protein, represent the best-known apparatus
for transducing external cues into a physiological
response in bacteria. The HWE domain is found in a
subset of two-component system kinases, belonging to
the same superfamily as pfam00512. The family was
defined by the presence of a highly conserved H residue
in the kinase domain and a WxE motif in a C-terminal
ATPase domain that is related to pfam02518. These
proteins are found in a variety of alpha- and
gamma-proteobacteria, with significant enrichment in
the rhizobia.
Length = 83
Score = 28.0 bits (63), Expect = 1.8
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 63 LYVIDSLVRQSRHQFQDKDVFGPRFARNLKA 93
L V+ S+ RQ+ D F F+ L+A
Sbjct: 10 LAVVQSIARQTLRSAASLDEFVEAFSGRLQA 40
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 27.5 bits (62), Expect = 2.0
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR--------GCAFVCMNRRQDAAKAL 211
T+++ K +++ + F ++G V +I + R G FV +DA K L
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRM---RRDLDKKFKGSVFVEFKTEEDAKKFL 57
Query: 212 YKLKNTKLQGKTITL 226
+ + K + K +T+
Sbjct: 58 -EKEKLKYKEKELTV 71
>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 = 27.7 bits (61), Expect = 2.0
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
+++G LS + +++ F +G + ++ +G FV + DA A+ ++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 215 KNTKLQGKTITLAWA 229
L G+ I WA
Sbjct: 64 GGQWLGGRQIRTNWA 78
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 27.6 bits (62), Expect = 2.4
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 173 EELSDTFGEYGDVVSINLIPP 193
E + + F G + I ++ P
Sbjct: 16 ESVLELFSTCGVIALIRILRP 36
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 27.6 bits (61), Expect = 2.5
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
L+IG+L V E EL F +YG + + + P R Q A A K +N
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRP--------ARGQGGAYAFLKFQN 58
>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 = 29.1 bits (65), Expect = 2.6
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 9/76 (11%)
Query: 173 EELSDTFGEYGDVVSI---------NLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKT 223
E++ F +YG +++I N P G F+ + A KA+ + K +
Sbjct: 434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRV 493
Query: 224 ITLAWAPGKGMKDKDW 239
+ A+ K D+
Sbjct: 494 VVAAFYGEDCYKAGDY 509
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 26.8 bits (59), Expect = 3.4
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
S L++G+L V + EL + F +YG+VV + +
Sbjct: 3 SHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI 35
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 26.9 bits (59), Expect = 3.9
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP----PRGCAFVCMNRRQDAAKALYKL 214
++IG LS +++L++ +G+V+ +I P RG FV K L +L
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL-EL 60
Query: 215 KNTKLQGKTI 224
K KL GK I
Sbjct: 61 KEHKLDGKLI 70
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 26.8 bits (59), Expect = 4.4
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRG 195
TL++G+L V E +L F +G + +++ P RG
Sbjct: 9 TLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRG 45
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 26.6 bits (59), Expect = 4.4
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 194 RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA 227
V D +A+ KL T+L G+ I L
Sbjct: 37 PNEGVVEFATYSDMKRAIEKLDGTELNGRKIKLI 70
>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 = 26.6 bits (59), Expect = 5.0
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALY 212
T+++ L K E L F +YG VV ++ +P +G AF+ ++A KA
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVS-LPRYKHTGDIKGFAFIEFETPEEAQKACK 59
Query: 213 KLKN 216
L N
Sbjct: 60 HLNN 63
>gnl|CDD|183252 PRK11640, PRK11640, putative transcriptional regulator;
Provisional.
Length = 191
Score = 27.7 bits (62), Expect = 5.2
Identities = 10/17 (58%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 135 DPNHPIHRELAEIQARN 151
DP+HPIH +LAE Q +
Sbjct: 109 DPDHPIH-QLAEQQKQA 124
>gnl|CDD|173872 cd08507, PBP2_SgrR_like, The C-terminal solute-binding domain of
DNA-binding transcriptional regulator SgrR is related to
the ABC-type oligopeptide-binding proteins and contains
the type 2 periplasmic-binding fold. A novel family of
SgrR transcriptional regulator contains a two-domain
structure with an N terminal DNA-binding domain of the
winged helix family and a C-terminal solute-binding
domain. The C-terminal domain shows strong homology with
the ABC-type oligopeptide-binding protein family, a
member of the type 2 periplasmic-binding fold protein
(PBP2) superfamily that also includes the C-terminal
substrate-binding domain of LysR-type transcriptional
regulators. SgrR (SugaR transport-related Regulator) is
negatively autoregulated and activates transcription of
divergent operon SgrS, which encodes a small RNA
required for recovery from glucose-phosphate stress.
Hence, the small RNA SgrS and SgrR, the transcription
factor that controls sgrS expression, are both required
for recovery from glucose-phosphate stress. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 448
Score = 28.0 bits (63), Expect = 5.5
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 193 PRGCAFVCMNRR----QDAA--KALYKLKNTK--LQ--GKTITLAWAPGKGMKDKDW 239
GC F+ N+R QD A +AL +L + + +Q G W P G+ +
Sbjct: 226 EEGCYFLLFNQRKPGAQDPAFRRALSELLDPEALIQHLGGERQRGWFPAYGLLPEWP 282
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 26.1 bits (57), Expect = 5.6
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
+++G LS EE++ + FG +G+V SI L
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIEL 31
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 26.5 bits (58), Expect = 5.9
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
S L++G+L + E EL + F +G+VV + +
Sbjct: 5 SHQLFVGNLPHDIDESELKEFFMSFGNVVELRI 37
>gnl|CDD|143604 cd07580, nitrilase_2, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 268
Score = 27.7 bits (62), Expect = 5.9
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 19/67 (28%)
Query: 111 RVLNLW-QKNEVFTP-DIIHPLFDMADPNHPIHR------------ELAEIQARNGVENM 156
R +LW ++ +F P D+ P+FD P R E + A G + +
Sbjct: 110 RKAHLWNEEKLLFEPGDLGLPVFDT-----PFGRIGVAICYDGWFPETFRLLALQGADIV 164
Query: 157 CSTTLWI 163
C T W+
Sbjct: 165 CVPTNWV 171
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 26.1 bits (58), Expect = 6.3
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
L++ L+ + +E+L F +G + S +I + AF+ ++D +A +
Sbjct: 4 NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63
Query: 213 KLKN 216
K+ N
Sbjct: 64 KMDN 67
>gnl|CDD|221522 pfam12309, KBP_C, KIF-1 binding protein C terminal. This family of
proteins is found in bacteria and eukaryotes. Proteins
in this family are typically between 365 and 621 amino
acids in length. There is a conserved LLP sequence
motif. KBP is a binding partner for KIF1Balpha that is a
regulator of its transport function and thus represents
a type of kinesin interacting protein.
Length = 365
Score = 27.7 bits (62), Expect = 7.2
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 9 QELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVE-----KFIIKCKPEYKVPAL 63
+L D KPP A I I +AIK+Y+ + S++ K + P L
Sbjct: 236 AQLDLPQDEKPPSPHA-IKKINSLCRKAIKYYEKFLDSLKDPSTGKLPETLDEDELRPIL 294
Query: 64 Y 64
Sbjct: 295 V 295
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 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 = 93
Score = 26.4 bits (59), Expect = 7.3
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 12/83 (14%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIPPRGC----------AFVCMNRRQD 206
T++ G L K V +E+L + F +Y ++ + A V ++ +
Sbjct: 3 DTVYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEET 62
Query: 207 AAKALYKLKNTKLQGKTITLAWA 229
+ + LK+ KL GK I+L A
Sbjct: 63 LDEIIESLKSKKLNGKKISLKPA 85
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 28.1 bits (63), Expect = 7.3
Identities = 40/190 (21%), Positives = 62/190 (32%), Gaps = 30/190 (15%)
Query: 86 RFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHR--- 142
R L++ + ED +L+L ++ PD IHP DPN +
Sbjct: 139 RIESTLRSAGFGCRRVDAED------LLSLVREMLNPDPDSIHPWPISYDPNQLLRDQIV 192
Query: 143 ------ELAE--IQARNGVENMCSTTLWIG-HLSKLVQEEELSDTFGEYGDV--VSINLI 191
E+ E ++ + T + + +E L T GD+ S+ +
Sbjct: 193 DPDTDLEVHEGGLEVDHEDNQGEVKTRIRVFSIKRFPEEFTLWQTGNLIGDLLNPSLQIT 252
Query: 192 PPRGCAFVCMNRR---QDAAKALYKLKNTKL--QGKTITLAWAPGKGMKDKDWKDFWEVQ 246
P + R Q KA K L Q K+ W P K K+ K E
Sbjct: 253 CP---FLLSFTVRVEDQVKKKAKATAKAKDLNKQAKSSMAKWVPSLEKKLKEIKYLREAI 309
Query: 247 D--GVSYIPY 254
G S +
Sbjct: 310 ASGGDSLVSM 319
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 25.8 bits (57), Expect = 7.4
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
L+IG LS ++ L + F ++G++ ++ RG FV + A+
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-NA 60
Query: 215 KNTKLQGKTI 224
+ K+ G+ +
Sbjct: 61 RPHKVDGREV 70
>gnl|CDD|211356 cd08346, PcpA_N_like, N-terminal domain of Sphingobium
chlorophenolicum 2,6-dichloro-p-hydroquinone
1,2-dioxygenase (PcpA), and similar proteins. The
N-terminal domain of Sphingobium chlorophenolicum
(formerly Sphingomonas chlorophenolica)
2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and
similar proteins. PcpA is a key enzyme in the
pentachlorophenol (PCP) degradation pathway, catalyzing
the conversion of 2,6-dichloro-p-hydroquinone to
2-chloromaleylacetate. This domain belongs to a
conserved domain superfamily that is found in a variety
of structurally related metalloproteins, including the
bleomycin resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases.
Length = 126
Score = 26.8 bits (60), Expect = 7.8
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 26 ITAITRSAIRAIKFYKHV 43
+T +TR A + FY V
Sbjct: 5 VTLVTRDAQETVDFYTDV 22
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding protein
that is abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation; it directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 26.3 bits (58), Expect = 8.2
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVV--------SINLIPPRGCAFV 199
+++G L + E+E++ +F +G +V S + PP+G AF+
Sbjct: 3 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFL 49
>gnl|CDD|226505 COG4018, COG4018, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 505
Score = 27.5 bits (61), Expect = 8.3
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 3 VIKTFNQELSSLYDTKPPISKAKITAITRSA 33
V+ +EL S Y+TK PI K ++ AI R+A
Sbjct: 334 VMAIMREELGSGYNTKVPIGKEELEAIARAA 364
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 25.8 bits (57), Expect = 8.5
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 170 VQEEELSDTFGEYGDVVSINLIPPRGC-AFVCMNRRQDAAKALYKLKNTKLQGKTITL 226
EE+L D F +G V+++ + +G A V + ++ K L + ++T L G + +
Sbjct: 14 TSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSEPQHT-LNGHRLRV 70
>gnl|CDD|226993 COG4646, COG4646, DNA methylase [Transcription / DNA replication,
recombination, and repair].
Length = 637
Score = 27.6 bits (61), Expect = 8.5
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 8 NQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCK 55
+L + Y P +TR RA K Y++V+ K + + +
Sbjct: 561 PLDLRAEYVPVPARDTGARQIVTRKPGRAFKRYQYVLSPRIKAMEERE 608
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 0.424
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,678,707
Number of extensions: 1381324
Number of successful extensions: 1626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1513
Number of HSP's successfully gapped: 277
Length of query: 282
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 186
Effective length of database: 6,679,618
Effective search space: 1242408948
Effective search space used: 1242408948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)