RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3854
(222 letters)
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 126 bits (318), Expect = 1e-37
Identities = 51/98 (52%), Positives = 68/98 (69%), Gaps = 6/98 (6%)
Query: 37 GIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMP------KKRKPGEKKPAKQFTEGWIE 90
GI+YLS++PP MN +L + +S++GEVGR+YL P K+RK K+FTEGW+E
Sbjct: 1 GIVYLSRIPPRMNPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVE 60
Query: 91 FLKKKVAKQVAAQYNNTQIDCRKRSKHYDFIWNFKYLP 128
F KKVAK+VA NNT I +KRS++ D +WN KYLP
Sbjct: 61 FEDKKVAKRVAESLNNTPIGGKKRSRYRDDLWNLKYLP 98
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 44.8 bits (107), Expect = 9e-07
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+Y+ +PP + L EF S +G+V V L+ K +P ++EF + A+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--------RGFAFVEFASPEDAE 52
Query: 99 QVAAQYNNTQIDCRK 113
+ N +D R
Sbjct: 53 AALKKLNGLVLDGRT 67
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 41.9 bits (99), Expect = 1e-05
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ +PP L E S+FGE+ V ++ K K F ++EF + A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKS-----KGF--AFVEFESPEDAE 53
Query: 99 QVAAQYNNTQIDCRK 113
+ N ++D RK
Sbjct: 54 KALEALNGKELDGRK 68
>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 = 39.5 bits (93), Expect = 8e-05
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
++Y+ +P +L ++ S+FG V R+ L + +K G+ K ++EF +VA
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRL-SRSKKTGKSK-----GYAFVEFESPEVA 54
Query: 98 KQVAAQYNN 106
K VA NN
Sbjct: 55 KIVAETMNN 63
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 39.1 bits (92), Expect = 9e-05
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ +PP +L E S+FG+V V L+ K E +K F ++EF ++ A+
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK----ETGKSKGF--AFVEFESEEDAE 55
Query: 99 QVAAQYNNTQID 110
+ N ++D
Sbjct: 56 KALEALNGKELD 67
>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 = 38.6 bits (90), Expect = 2e-04
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVA 97
+IY+ +P +L ++ S+FG V V R KK G+I+FL +VA
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNV------RVARSKKTGNSKHYGFIQFLNPEVA 54
Query: 98 KQVAAQYNNTQIDCRKRSKHY 118
A NN + + H
Sbjct: 55 AIAAKSMNNYLLMGKVLQVHV 75
>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 = 35.3 bits (82), Expect = 0.003
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+ + +P Q E +S FG V R +L+ + GE K G++E+ K A
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSE-STGESK-----GYGFVEYASKASAL 55
Query: 99 QVAAQYNNTQIDCRK 113
+ Q + QI RK
Sbjct: 56 KAKNQLDGKQIGGRK 70
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 33.5 bits (77), Expect = 0.012
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKR 73
++++ +P + L E +S FG + V +MPKKR
Sbjct: 4 VVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKR 39
>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM4 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 32.3 bits (74), Expect = 0.026
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMP 70
+I + +P +L E S+FG +GRV L P
Sbjct: 2 VILVKNLPAGTLTAELRELFSKFGSLGRVLLPP 34
>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 = 0.060
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 11/65 (16%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ ++ M L ++ S+FGEV VY +P KP + F ++ F +VA+
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVY-IP--------KPFRAF--AFVTFADPEVAQ 51
Query: 99 QVAAQ 103
+ +
Sbjct: 52 SLCGE 56
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 31.1 bits (71), Expect = 0.091
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
IY++ V P ++ + FG++ L P + + K G+IE+ + A+
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAP------DPETGKHKGYGFIEYENPQSAQ 56
Query: 99 QVAAQYNN 106
A N
Sbjct: 57 DAIASMNL 64
>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 = 30.5 bits (69), Expect = 0.11
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 44 VPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPG 76
+P ++ +++E R+G V V ++PK+ G
Sbjct: 7 LPENVREERISEHFKRYGRVESVKILPKRGSDG 39
>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 = 29.9 bits (68), Expect = 0.24
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
IY+ + ++ L S+FGEV + +PKK+ + + F ++ F K +
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIR-IPKKQDEKQGRLNNGF--AFVTF-KDASSA 58
Query: 99 QVAAQYNNTQIDCRK 113
+ A Q N T++ RK
Sbjct: 59 ENALQLNGTELGGRK 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 = 29.5 bits (67), Expect = 0.32
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLM-PKKRKPGEKKPAK 82
+Y+ + P + L + RFG + V +M P R E++ +
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWP--RTEEERRRNR 46
>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 = 29.2 bits (66), Expect = 0.34
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 36 KGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKK 95
K +Y+S +P + L + S++G+V +V ++ K K A +I FL ++
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVA------FILFLDRE 54
Query: 96 VAKQVAAQYNNTQIDCRK 113
A + NN ++ R
Sbjct: 55 DAHKCVKALNNKELFGRT 72
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 29.1 bits (66), Expect = 0.40
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+Y+ +P ++ L + +FGEV ++ + E ++ F G++E + A
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDR----ETGRSRGF--GFVEMETAEEAN 55
Query: 99 QVAAQYNNTQIDCRK 113
+ N T R
Sbjct: 56 AAIEKLNGTDFGGRT 70
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 29.3 bits (66), Expect = 0.44
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 12/85 (14%)
Query: 33 KYKKGIIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFL 92
+ KK I++ +PP++ T L ++ S+FG V V +M EKK + F G+I F
Sbjct: 1 RTKK--IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDH----EKKRPRGF--GFITFE 52
Query: 93 KKKVAKQVAAQY----NNTQIDCRK 113
+ QV ++ N +++ ++
Sbjct: 53 SEDSVDQVVNEHFHDINGKKVEVKR 77
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 28.7 bits (65), Expect = 0.62
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
I + +P ++ +L E GEV V +M + +++F G++ F ++ A+
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-----DGKSRRF--GFVGFKSEEDAQ 55
Query: 99 QVAAQYNNTQID 110
Q +N T ID
Sbjct: 56 QAVKYFNKTFID 67
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 30.6 bits (70), Expect = 0.80
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 4/86 (4%)
Query: 131 KWIHLNERLAYEKQAHRQKLRAEIAEAKREALYFSNNLDVADRIQKKNGKKKTNVPEQSS 190
K L E + ++ + I EAK+EA L + + K E
Sbjct: 556 KKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAH----ELIE 611
Query: 191 NKKNDGKGKQIVKKSNTKPVEDRKQF 216
+K K + +K K E +++
Sbjct: 612 ARKRLNKANEKKEKKKKKQKEKQEEL 637
>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 = 28.1 bits (63), Expect = 0.92
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
I + +P V +L E S FGE+ V L PK K + F G+++F+ K+ AK
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRL-PK--KMTGTGSHRGF--GFVDFITKQDAK 57
>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 = 28.0 bits (63), Expect = 0.95
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
I++ +P H L ++ S+FGE+ + R+ G+ + G++ F K K +
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVV-ITDRQTGKSR-----GYGFVTF-KDKESA 55
Query: 99 QVAAQYNNTQIDCRK 113
+ A + N ID RK
Sbjct: 56 ERACKDPNPIIDGRK 70
>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 = 28.0 bits (63), Expect = 0.97
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 40 YLSKVPPHMNVTQLTE-FMSRFGEVGRVYLMPKKRK 74
+LS +PP + L E F G V PK RK
Sbjct: 3 HLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRK 38
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 27.7 bits (62), Expect = 1.1
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEV 63
+ LS VPPH+ TQL + ++G V
Sbjct: 4 LLLSGVPPHIPETQLRRDLEQWGAV 28
>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 = 27.5 bits (62), Expect = 1.6
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEG--WIEFLKKKV 96
+Y+ + + Q+ E SR G++ R+ +M R K P G ++E+ ++
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRI-IMGLDRF--TKTPC-----GFCFVEYYTRED 52
Query: 97 AKQVAAQYNNTQIDCR 112
A+ N T++D R
Sbjct: 53 AENAVKYLNGTKLDDR 68
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 29.1 bits (66), Expect = 1.8
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 13/59 (22%)
Query: 142 EKQAHRQKLRAEIAEAKREALYFSNNLDVADRIQKKNGKKKTNVPEQSSNKKNDGKGKQ 200
E++ R+K R +A++E +K KK K DG+ K+
Sbjct: 410 ERKKLRKKQRKAEKKAEKEE-------------AEKAAAKKKAEAAAKKAKGPDGETKK 455
>gnl|CDD|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM1 of hnRNP-L, a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-L shows significant sequence homology
to polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 27.3 bits (60), Expect = 2.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 53 LTEFMSRFGEVGRVYLMPKKRK 74
L E + FG + V +MPKKR+
Sbjct: 19 LVEALQEFGTISYVVVMPKKRQ 40
>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 = 26.9 bits (60), Expect = 2.3
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRV 66
++L + + LT SR+G V V
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVVHV 37
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 29.0 bits (65), Expect = 2.3
Identities = 23/122 (18%), Positives = 44/122 (36%), Gaps = 6/122 (4%)
Query: 3 EDAGSSNESSPAEEPGKYVLKPKDNTENSKKYKKGIIYLSKVPPHMNVTQLTEFMSRFGE 62
D G ++ + KP +N+ + ++LS +P ++ L E + G
Sbjct: 361 LDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGV 420
Query: 63 VGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQIDCRKRSKHYDFIW 122
KK K K + G +E+ + A + N+ Q++ S Y
Sbjct: 421 -----HKVKKFKFFPKDNERS-KMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKV 474
Query: 123 NF 124
+F
Sbjct: 475 SF 476
>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 = 26.9 bits (60), Expect = 2.5
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+Y+ +P + L S++G V V L R K F +IEF + A+
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSL---PRYKHTGDI-KGF--AFIEFETPEEAQ 55
Query: 99 QVAAQYNN 106
+ NN
Sbjct: 56 KACKHLNN 63
>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 = 26.3 bits (59), Expect = 2.8
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 53 LTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQID 110
L + S FG V ++ L+ KK ++EF ++ A++ N
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPG-----------FAFVEFSTEEAAEKAVQYLNGVLFG 47
>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 = 26.4 bits (59), Expect = 2.9
Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ +PP L + S+FG + + ++ E +K F ++EF ++ A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-----ETGRSKGF--AFVEFEDEEDAE 53
Query: 99 QVAAQYNNTQID 110
+ N ++
Sbjct: 54 KALEALNGKELG 65
>gnl|CDD|240416 PTZ00432, PTZ00432, falcilysin; Provisional.
Length = 1119
Score = 28.6 bits (64), Expect = 3.2
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 133 IHLNERLAYEKQAHRQKLRAEIAEAKREALYFSNNLDVADRIQKKNG-KKKTNVPEQSSN 191
+ L + E RQK R +I E +E Y +AD ++K +K V ++
Sbjct: 1052 LALLRIIRNESDEDRQKFRKDILETTKEDFY-----RLADLMEKSKEWEKVIAVVNSKTS 1106
Query: 192 KKNDGKGKQI 201
KQ+
Sbjct: 1107 DTAPSDFKQL 1116
>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 = 26.4 bits (59), Expect = 3.4
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKKKVAK 98
+++ K+ ++N L E S +G V V +P R+ + + ++EF + A+
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVD-LPIDREVNLP---RGY--AYVEFESPEDAE 54
Query: 99 QVAAQYNNTQID 110
+ + QID
Sbjct: 55 KAIKHMDGGQID 66
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal Rrp7 domain. .
Length = 102
Score = 26.9 bits (60), Expect = 3.5
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 44 VPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEGWIEFLKK--KVA 97
VPP+ L SR G+V V L + KPG + ++ + K KVA
Sbjct: 8 VPPYCTEESLKRLFSRCGKVESVEL---QEKPGPAESEDLTSKFFPPKPIKGFKVA 60
>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 = 26.4 bits (59), Expect = 4.1
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEVGRVYLM 69
+++S + +L S+FG V V LM
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLM 34
>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 = 26.4 bits (59), Expect = 4.8
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 10/72 (13%)
Query: 38 IIYLSKVPPHMNVTQLTEFMSRFGEVGRVYLMPKKRKPGEKKPAKQFTEG--WIEFLKKK 95
+++ +P +L E S+FGEV ++ K ++G +++F K+
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIV--------KDKLTGHSKGTAFVKFKTKE 53
Query: 96 VAKQVAAQYNNT 107
A++ +N
Sbjct: 54 SAQKCLEAADNA 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 = 25.7 bits (57), Expect = 5.5
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 53 LTEFMSRFGEVGRVYLMPKKRKPGEKK 79
L ++GEVG VY +P+ R E +
Sbjct: 15 LRRVFEKYGEVGDVY-IPRDRYTRESR 40
>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 = 25.8 bits (57), Expect = 6.6
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 39 IYLSKVPPHMN-VTQLTEFMSRFGEVGRVYLMPKK 72
I +P +N L +FG+V RVY P+K
Sbjct: 3 IQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRK 37
>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 = 25.6 bits (57), Expect = 7.5
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 51 TQLTEFMSRFGEVGRVY--LMPKKRKPGEKKPAKQFTEGWIEFLKKKVAKQVAAQYNNTQ 108
T F + G V + KK+ P G++EF K+ A++ + T
Sbjct: 12 TTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTV 71
Query: 109 ID 110
+D
Sbjct: 72 LD 73
>gnl|CDD|224441 COG1524, COG1524, Uncharacterized proteins of the AP superfamily
[General function prediction only].
Length = 450
Score = 27.1 bits (60), Expect = 7.9
Identities = 8/59 (13%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 84 FTEGWIEFLKKKVAKQVAAQYNNTQIDCRKRSKHYDFIWNFKYLPRFKW-IHLNERLAY 141
E L K + + I + S H+ F+ + + L +
Sbjct: 331 SDSLISEILTKLSIPKRNSFGIGELIIWAEFSVHFLFVTEAADFGFARKSLELLGTHGF 389
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 25.4 bits (56), Expect = 8.0
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 39 IYLSKVPPHMNVTQLTEFMSRFGEV 63
+Y+S +P HM+ L + +G+V
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQV 27
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.1 bits (60), Expect = 9.7
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 139 LAYEKQAHRQKLRAEIAEAKREALY--FSNNLDVADRIQKKNGKKKTNVPEQSSNKKNDG 196
LA K K +++ KR+ L ++ L + + K +T+ E++ K +
Sbjct: 347 LALTKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEV-KDETDASEEAEAKAKEE 405
Query: 197 KGKQIVKKSNTKPVEDRKQ 215
K KQ + K D +
Sbjct: 406 KLKQEENEKKQKEQADEDK 424
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
0.312 0.129 0.370
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,973,283
Number of extensions: 1002933
Number of successful extensions: 1059
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1051
Number of HSP's successfully gapped: 80
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.8 bits)