RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11527
(206 letters)
>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 = 142 bits (360), Expect = 2e-44
Identities = 48/79 (60%), Positives = 64/79 (81%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
PC+TLFVANLG +E+E++ +F PGF R++MHNKGG PV F+E+ DV+FA QA+++L
Sbjct: 1 PCNTLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFVEFEDVSFATQALNSL 60
Query: 164 NGSYLASSDRGAIRIEYAK 182
G+ L+SSDRG IRIEYAK
Sbjct: 61 QGAVLSSSDRGGIRIEYAK 79
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 65.0 bits (159), Expect = 3e-14
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGG-----SPVAFIEYTDVNFAIQAM 160
TLFV+ L V E+E+ +F FPG+ R+ K PV F++++ A AM
Sbjct: 1 RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60
Query: 161 SNLNGSYLASSDRGAIRIE 179
L G +R+E
Sbjct: 61 DALQGYRFDPDTSSVLRLE 79
>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 = 60.7 bits (148), Expect = 8e-13
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P LF+ NL + +++ ++ +F FPGF VR+ + G +AF+E+ A A+ L
Sbjct: 1 PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRG--IAFVEFETEEQATVALQAL 58
Query: 164 NG 165
G
Sbjct: 59 QG 60
>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 = 60.3 bits (147), Expect = 1e-12
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS---PVAFIEYTDVNFAIQAMSNLN 164
LFV NL +E+++KD+F F +R+ AF+E+ D A +A+ LN
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 165 GSYL 168
G L
Sbjct: 61 GKEL 64
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 55.7 bits (135), Expect = 7e-11
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS----PVAFIEYTDVNFAIQAMSN 162
TLFV NL +E+E++++F F VR+ + AF+E+ A +A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 163 LNGSYL 168
LNG L
Sbjct: 61 LNGKEL 66
>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 = 54.6 bits (132), Expect = 2e-10
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSP--VAFIEYTDVNFAIQAMSNLN 164
LFV NL +E++++++F F VR+ +K G AF+E+ A +A+ LN
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 165 GSYL 168
G L
Sbjct: 61 GKEL 64
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 55.3 bits (132), Expect = 3e-09
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 10/116 (8%)
Query: 71 MHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFP 130
G S SP S+ + TLFV NL V+E++++++F F
Sbjct: 84 NDGERGYTKEFEEELFRS--SESPKSRQKSKEENN-TLFVGNLPYDVTEEDLRELFKKFG 140
Query: 131 GFSRVRMHNKGGSPV----AFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAK 182
RVR+ + AF+E+ A +A+ LNG L +R++ A+
Sbjct: 141 PVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP---LRVQKAQ 193
>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 = 47.4 bits (113), Expect = 9e-08
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRV---RMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
TLFV NL ++E+E++ F + V R G+ AF+++ +++ A +A +
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63
Query: 164 NGSYLASSDRGAIRIEYAK 182
+G Y+ R I+I Y K
Sbjct: 64 SGQYIG---RNQIKIGYGK 79
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 46.1 bits (110), Expect = 3e-07
Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVA---FIEYTDVNFAIQAMSNL 163
+FV +LG V+++ + F +P F + + + +K F+ ++D N ++AM +
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68
Query: 164 NGSYLAS 170
NG Y+ +
Sbjct: 69 NGKYVGN 75
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed in
all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. The family also
includes yeast ortholog mRNA 3'-end-processing protein
RNA15 and similar proteins. RNA15 is a core subunit of
cleavage factor IA (CFIA), an essential transcriptional
3'-end processing factor from Saccharomyces cerevisiae.
RNA recognition by CFIA is mediated by an N-terminal
RRM, which is contained in the RNA15 subunit of the
complex. The RRM of RNA15 has a strong preference for
GU-rich RNAs, mediated by a binding pocket that is
entirely conserved in both yeast and vertebrate RNA15
orthologs.
Length = 75
Score = 45.7 bits (109), Expect = 4e-07
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 109 FVANLGQFVSEQEIKDIF---GSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLN 164
FV N+ +E+++ +IF G F V + G F E+ D+ A A+ NLN
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 165 GSYLASSDRGAIRIEYA 181
G + R A+R+++A
Sbjct: 62 GYEF--NGR-ALRVDFA 75
>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 = 45.1 bits (107), Expect = 7e-07
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGG-SPVAFIEYTDVNFAIQAMSNLNG 165
TLF+ NL + + ++++ F F + + +GG AFI+Y D+ ++AM ++G
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63
Query: 166 SYLASS 171
YL ++
Sbjct: 64 EYLGNN 69
>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 = 43.7 bits (104), Expect = 2e-06
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 13/72 (18%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPG------FSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
TL V NL +S+QE++ +F F G + +R K F+E+ D+ A A
Sbjct: 2 GTLLVFNLDSPISDQELRSLFSQF-GEVKDIRETPLRPSQK------FVEFYDIRAAEAA 54
Query: 160 MSNLNGSYLASS 171
+ LNG
Sbjct: 55 LDALNGRPFLGG 66
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 42.9 bits (102), Expect = 4e-06
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLNG 165
L+V NL V+E+++++ F + VR+ P AF+E+ A A+ LNG
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
>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 = 42.9 bits (102), Expect = 4e-06
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV----AFIEY--TDVNFAIQAMS 161
LFV L V+E ++++ F F S V + K + A+I+ ++ + S
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLK-KCKS 60
Query: 162 NLNGS-YLASSDRG-AIRIEYAK 182
LNG+ + +G ++IE AK
Sbjct: 61 TLNGTKW-----KGSVLKIEEAK 78
>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 = 42.6 bits (101), Expect = 6e-06
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQA 159
L+V NL V+E+++KD+FG F + R+ ++G F+E A A
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRG---FGFVEMETAEEANAA 57
Query: 160 MSNLNGS 166
+ LNG+
Sbjct: 58 IEKLNGT 64
>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 = 45.6 bits (108), Expect = 6e-06
Identities = 36/139 (25%), Positives = 51/139 (36%), Gaps = 9/139 (6%)
Query: 33 AADLPGTASLHQHTLVHPALHPQVPSLNIPHPTAALTAMHHANGMPHFLPSPALPS-PVG 91
P H + H S P A P PA + P+
Sbjct: 206 RQRQPALLGQHPSSYGHDGYS----SHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLA 261
Query: 92 SSPPSQGMNGMSPCSTLFVANLGQF-VSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIE 149
+ S G G P S L V+ L Q V+ + ++F + RV+ M NK + A IE
Sbjct: 262 PAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKET--ALIE 319
Query: 150 YTDVNFAIQAMSNLNGSYL 168
D A A+++LNG L
Sbjct: 320 MADPYQAQLALTHLNGVKL 338
Score = 29.4 bits (66), Expect = 1.4
Identities = 19/86 (22%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGS--FPGFSRVRMHNK--GGSPVAFIEYTDVNFAIQA 159
P +TL ++N+ VSE+++K++F + + K S + +E+ V A++A
Sbjct: 393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEA 452
Query: 160 MSNLNGSYLASSDRGA---IRIEYAK 182
+ LN L + A +++ ++
Sbjct: 453 LIALNHHQLNEPNGSAPYHLKVSFST 478
Score = 27.5 bits (61), Expect = 5.4
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 99 MNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQ 158
G + + V N ++ + IF + R+ K A +E+ VN A
Sbjct: 90 SAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQH 149
Query: 159 AMSNLNGSYLASSDRGAIRIEYAK 182
A + LNG+ + + ++IEYAK
Sbjct: 150 AKAALNGADIYNG-CCTLKIEYAK 172
>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 = 42.3 bits (99), Expect = 7e-06
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
LFV NL V+E+ ++ FG F RV K AFI + + + A++AM +NG
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERV----KKLKDYAFIHFDERDGAVKAMEEMNGKE 59
Query: 168 LASSDRGAIRIEYAK 182
L + I I +AK
Sbjct: 60 LEGEN---IEIVFAK 71
>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 = 42.0 bits (99), Expect = 9e-06
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 107 TLFVANLG-QFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
TLFV E++I+ +F F R + AF+E+ D A +A+ L+G
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRK----TFAFVEFEDSEDATKALEALHG 56
Query: 166 SYLASSDRGAIRIEYAK 182
S + D + +E+ K
Sbjct: 57 SRI---DGSVLTVEFVK 70
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL--- 163
TL+V LG+ V+E++++D F F + + + AF+ +T A +A L
Sbjct: 3 TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC--AFVTFTTREAAEKAAERLFNK 60
Query: 164 ---NGSYL 168
NG L
Sbjct: 61 LIINGRRL 68
>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 = 41.6 bits (97), Expect = 1e-05
Identities = 28/66 (42%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-PG-FSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L+V NL SE IK FG F PG RV K AF+ +T A+ AM+NLNG
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERV----KKIRDYAFVHFTSREDAVHAMNNLNG 59
Query: 166 SYLASS 171
+ L S
Sbjct: 60 TELEGS 65
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 105 CSTLFVANLGQFVSEQEIKDIFGSFPGFS-------RVRMHNKG---GSPVAFIEYTDVN 154
L+V NL + V+E+++ IFG F S +R+ +G G AF+ +
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQ--AFVTFPSEE 58
Query: 155 FAIQAMSNLNG 165
A +A++ +NG
Sbjct: 59 IATKALNLVNG 69
>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 = 41.2 bits (97), Expect = 2e-05
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-KGGSPVAFIEYTDVNFAIQAMSNLNG 165
++V NL + E++I+D+F + + + N + G P AF+E+ D A A+ +G
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 166 SYLASSDRGAIRIEY 180
D +R+E+
Sbjct: 61 YDF---DGYRLRVEF 72
>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 = 41.1 bits (97), Expect = 2e-05
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-KGGSPVAFIEYTDVNFAIQAMSNLNGS 166
L+V NL +S +E+ D+FG + ++R+ N K AF+ Y D+ A A +L+G
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64
Query: 167 YLA 169
+A
Sbjct: 65 NVA 67
>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 = 2e-05
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L+V NL +E++++++F + RV K AF+ + + + A++AM +NG
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERV----KKIKDYAFVHFEERDDAVKAMEEMNGKE 59
Query: 168 L 168
L
Sbjct: 60 L 60
>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 = 40.9 bits (96), Expect = 3e-05
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSP--VAFIEYTDVNFAIQAMSNL 163
LFV+ L V+++E++ +F VR+ N+ G P +A++EY + + A QA+ +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 164 NG 165
+G
Sbjct: 64 DG 65
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 40.7 bits (96), Expect = 3e-05
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 108 LFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
+F+ L ++SE ++K++ FG F+ V+ G S AF EY D + QA++ L
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 164 NG 165
NG
Sbjct: 63 NG 64
>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 = 40.4 bits (95), Expect = 3e-05
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L+V NL + V+E + ++F ++ G P AF+EY D A A+ +NG
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNG 59
>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 = 40.2 bits (95), Expect = 4e-05
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRV-------RMHNKGGSPVAFIEYTDVNFAIQA 159
T+ V NL + E +++++F F SRV ++G AF+ + A +A
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRG---FAFVTFHTREDAERA 57
Query: 160 MSNLNG 165
+ LNG
Sbjct: 58 IEKLNG 63
>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 = 39.8 bits (94), Expect = 5e-05
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSPV--AFIEYTDVNFAIQAMSNL 163
L+V NL + +E++I ++F R+ M +P F+EY A A+ L
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 164 NGSYLASSDRGAIRIE 179
NG+ L D IR++
Sbjct: 61 NGTKL---DDRIIRVD 73
>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 = 39.8 bits (93), Expect = 5e-05
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-PGFS-RVRMHNKGGSP--VAFIEYTDVNFAIQAMSNL 163
+FV N+ +E+++KDIF P S R+ + G P F EY D A+ AM NL
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 164 NG 165
NG
Sbjct: 61 NG 62
>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 = 39.8 bits (93), Expect = 6e-05
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS-PVAFIEYTDVNFAIQAMSNLNGS 166
++V NL V E++++D+F + + + N+ G P AF+ + D A A+ NG
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG- 60
Query: 167 YLASSDRGAIRIEY 180
Y R +R+E+
Sbjct: 61 YDFGQCR--LRVEF 72
>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 = 39.6 bits (93), Expect = 6e-05
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLN 164
T+ V + +SE ++K+ F + +RVR+ AF+E+ D A+ A+ NL+
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLS 60
Query: 165 GSYLASSDRGAIRIEYAKT 183
G+ L +R+ +KT
Sbjct: 61 GTLLGGHP---LRVSPSKT 76
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 39.7 bits (93), Expect = 6e-05
Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
T++ ++K +F + +V M ++ P AFI + ++ A A+ LNG+
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60
Query: 167 YLASSDRGAIRIEY 180
+ + I+++
Sbjct: 61 SVDGN---CIKVQR 71
>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 = 39.5 bits (93), Expect = 6e-05
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSP--VAFIEYTDVNFAIQAMSN 162
+ L V+NL V+E++++++FG +V+++ ++ G A + + A +A+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 163 LNGSYLASS 171
NG L
Sbjct: 61 FNGVLLDGQ 69
>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 = 39.5 bits (93), Expect = 7e-05
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L+V LG + S E++ F F R+ ++ G A+IEY + A A L G
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRID-YDPGR-NYAYIEYESIEAAQAAKEALRGFP 58
Query: 168 LASSDRGAIRIEYAK 182
L R +R+++A
Sbjct: 59 LGGPGR-RLRVDFAD 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 = 39.1 bits (92), Expect = 1e-04
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNK--GGSP-VAFIEYTDVNFAIQAMS 161
+ LFV+ L +E+E++ +F F V M + G S F+ + V A A+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 162 NLNGSYLASSDRGAIRIEYAKT 183
+LNG L I++E AK
Sbjct: 62 DLNGKELEGR---VIKVEKAKR 80
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-------NKGGSPVAFIEYTDVNFAIQAM 160
L+V NL ++E +++ IF F V++ +KG FI++ D A +A+
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKG---YGFIQFADAEDAKKAL 57
Query: 161 SNLNGSYLA 169
LNG LA
Sbjct: 58 EQLNGFELA 66
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 16/58 (27%), Positives = 31/58 (53%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
++V NL + ++I+D+F + + + N+ G P AF+E+ D A A+ +G
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDG 59
>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 = 38.5 bits (89), Expect = 1e-04
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
LFV NL V+E+ ++ F F RV K AF+ + + + A++AM +NG
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERV----KKLKDYAFVHFEERDAAVRAMDEMNGKE 59
Query: 168 LASSDRGAIRIEYAK 182
+ + I I AK
Sbjct: 60 IEGEE---IEIVLAK 71
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 38.6 bits (90), Expect = 1e-04
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L+V SE I++IF + V+M + AF+E+ + AI+A +++G
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN----FAFVEFESLESAIRAKDSVHGKV 57
Query: 168 LA 169
L
Sbjct: 58 LN 59
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 28/87 (32%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF------------PGFSRVRMHNKGGSPVAFIEYTDVNF 155
++V NLG +++E++D F + PGF AF+E+ D
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGF-------------AFVEFEDPRD 48
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAK 182
A A+ L+G + + +R+E ++
Sbjct: 49 AEDAVRALDGRRICGN---RVRVELSR 72
>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 = 38.9 bits (91), Expect = 2e-04
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 104 PCSTLFVANLGQFVSEQE----IKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQ 158
P + +FVA+L S+ E + + F + V+ + + P AF+++T+ + A
Sbjct: 1 PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKN 60
Query: 159 AMSNLNGSYLASSDRGAIRIEYAK 182
A++ G+ L D IR E AK
Sbjct: 61 ALAKGQGTIL---DGRHIRCERAK 81
>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 = 41.0 bits (96), Expect = 2e-04
Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 17/106 (16%)
Query: 76 GMPH-FLPSPALPSPVGSSP-PSQGMNGMSPCST----------LFVANLGQFVSEQEIK 123
PH ++P P + +P S P + +++ NL ++ E +IK
Sbjct: 255 RRPHDYIPVPQI-TPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIK 313
Query: 124 DI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLNG 165
++ FG F+ ++ G S AF EY D + A++ LNG
Sbjct: 314 ELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNG 359
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 37.7 bits (88), Expect = 4e-04
Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 10/83 (12%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF------PGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMS 161
LF+ NL V E+ + D F +F P R AFI Y + A+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPD-TGNSKGFAFISYDSFEASDAAIE 62
Query: 162 NLNGSYLASSDRGAIRIEYAKTK 184
+NG YL + I + YA K
Sbjct: 63 AMNGQYLCNR---PITVSYAFKK 82
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B"), a unique protein that comprises the U2 snRNP.
It was initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent of U2 snRNA binding. U2B"
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). It also contains a nuclear localization signal
(NLS) in the central domain. However, nuclear import of
U2B'' does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 80
Score = 37.3 bits (86), Expect = 4e-04
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P LF+ NL + +E + +F FPGF VR+ G +AF+E+ + A A L
Sbjct: 4 PNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFENEAQAGAARDAL 62
Query: 164 NGSYLASSDRGAIRIEYAK 182
G + S A++I YAK
Sbjct: 63 QGFKITPSH--AMKITYAK 79
>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 = 37.1 bits (86), Expect = 5e-04
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 108 LFVANLGQFVSEQEIKDIF---GSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
L+V NL V+E +K IF G + N G F+EY + A A+ LN
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 165 GSYLASSDRGAIRIEYA 181
G + +++ IR+ +A
Sbjct: 61 GRQIENNE---IRVNWA 74
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 37.2 bits (87), Expect = 5e-04
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-------NKGGSPVAFIEYTDVNFAIQAM 160
L+V L + V E+ + F F +++ ++G AF+E+ + A A+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRG---FAFVEFEEPEDAAAAI 57
Query: 161 SNLNGSYL 168
N+N S L
Sbjct: 58 DNMNESEL 65
>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 = 37.3 bits (87), Expect = 5e-04
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQA 159
P S LF+ G+ V+E ++++ F F + + K VA++++ + A +A
Sbjct: 2 PNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60
Query: 160 MSNLNGSYLASSDR 173
M +NG L +
Sbjct: 61 MEEMNGKCLGGDTK 74
>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 = 37.2 bits (87), Expect = 5e-04
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 108 LFVAN--LGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L VAN LG VS +E+ +F + + M G P F+ Y+ + A A LNG
Sbjct: 4 LVVANGGLGNGVSREELLRVFEKYGTVEDLVM--PPGKPYCFVSYSSIEDAAAAYDALNG 61
Query: 166 SYLASSDRGA 175
L +
Sbjct: 62 KELELPQQNK 71
>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 = 37.2 bits (87), Expect = 6e-04
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKG-GSP--VAFIEY 150
TLFVA L +E +++ F + R+R+ +K G P AFIE+
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEF 50
>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 = 36.9 bits (86), Expect = 6e-04
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
+T+FV L V+E E++ +FG F V++ G F+++ A A+ L G
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP--GKGCGFVQFVHRAAAEAAIQQLQG 59
Query: 166 SYLASSDRGAIRI 178
+ + S IR+
Sbjct: 60 TIIGGS---RIRL 69
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 20/87 (22%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-PGFS-----------RVRMHNKGGSPVAFIEYTDVNF 155
L+V NL V+E+ + FG F P S R R N G VAF+ D
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGF--VAFMNRAD--- 58
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAK 182
A +A+ L+G + + +++ + K
Sbjct: 59 AERALDELDGKDVMGYE---LKLGWGK 82
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
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 = 77
Score = 36.9 bits (86), Expect = 8e-04
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPG-FSRVRM-HNKGGSP--VAFIEYTDVNFAIQAMS 161
S L V NL ++E E+K+ F G + V++ + G +AFI Y A +A
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60
Query: 162 NLNGSYLASSDRGAIRIEYA 181
N +Y+ +S I +E+A
Sbjct: 61 YFNNTYINTS---KISVEFA 77
>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 = 36.7 bits (85), Expect = 8e-04
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVR-----MHNKGGSPVAFIEYTDVNFAIQAMS 161
TL V NL VS ++ IFG++ +R H+K FIE+ DV A A+
Sbjct: 3 TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHK------FIEFYDVRSAEAALK 56
Query: 162 NLNGSYLASSDRGAIRIE 179
LN S +A I++E
Sbjct: 57 ALNRSEIAGK---RIKLE 71
>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 = 36.8 bits (85), Expect = 8e-04
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKG---GSPVAFIEYTDVNFAIQAMSNL 163
TLF+ NL V+E +++ F F + V + G S F+++ +++ A +A +
Sbjct: 9 TLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAM 68
Query: 164 NGSYLASSDRGAIRIEYAK 182
+G L R I+I Y K
Sbjct: 69 SGKVLR---RNPIKIGYGK 84
>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 = 36.7 bits (86), Expect = 8e-04
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 107 TLFVANLGQFVSEQEIKD----IFGSFPGFSRVRMHNKGGSPV----AFIEYTDVNFAIQ 158
TL++ NL + + + E+K +F F + + AF+ + DV A
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATN 57
Query: 159 AMSNLNGSYLASSDRGAIRIEYAK 182
A+ L G D+ +RI+YAK
Sbjct: 58 ALRALQGFPFY--DK-PMRIQYAK 78
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 36.3 bits (84), Expect = 0.001
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 20/83 (24%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDVNFAIQAM 160
LFV NL +E E++ FG RVRM KG AF+++ ++ FA A+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKG---FAFVDFEEIEFATNAL 57
Query: 161 SN--LNGSYLASSDRGAIRIEYA 181
LNG A+R+EY
Sbjct: 58 KGKHLNGR--------ALRVEYG 72
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 36.4 bits (85), Expect = 0.001
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 119 EQEIKDIFGSFPGFSRVRMHNKGGSP-----VAFIEYTDVNFAIQAMSNLNGSYLA 169
+ EI++ + V +H S F+E++D + AI+A+ LNG +
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFG 75
>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 = 36.1 bits (83), Expect = 0.001
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 6/60 (10%)
Query: 108 LFVANLGQFVSEQEIKDIFG--SFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L++ NL V+ ++++ +FG P +V + S AF++Y D N+AI+A+ L+G
Sbjct: 4 LYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLK----SGYAFVDYPDQNWAIRAIETLSG 59
>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 = 38.8 bits (90), Expect = 0.001
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSF-PG-FSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
M+ L+V NL +E+ I+ F F PG RV K AF+ + D A++A
Sbjct: 230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERV----KKIRDYAFVHFEDREDAVKA 285
Query: 160 MSNLNGSYLASSDRGAIRIEYAK 182
M LNG L S+ I + AK
Sbjct: 286 MDELNGKELEGSE---IEVTLAK 305
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or
U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins,
including polypyrimidine tract binding protein (PTB),
polypyrimidine-tract binding protein-associated factor
(PSF), and non-POU-domain-containing, octamer-binding
(NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5).
U1A also binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and it
may be free for binding other proteins. U1A also
contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 36.2 bits (83), Expect = 0.001
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P LF+ NL + +E + +F FPGF VR+ G +AF+E+ + A A L
Sbjct: 4 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAAREAL 62
Query: 164 NGSYLASSDRGAIRIEYAK 182
G + S+ A++I +AK
Sbjct: 63 QGFKITQSN--AMKISFAK 79
>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 = 35.8 bits (83), Expect = 0.002
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS 143
LFV NL ++E E+K+ F F VR+++KGG
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGG 41
>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 = 35.3 bits (82), Expect = 0.002
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLN 164
TLFV N+ V ++E++ +F F +R + Y D+ A +A L
Sbjct: 3 TLFVRNINSNVEDEELRALFEQ---FGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQ 59
Query: 165 GSYL 168
G+ L
Sbjct: 60 GTEL 63
>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 = 35.3 bits (82), Expect = 0.002
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
L V+NL V+E +I ++F + R R+ G + V ++ D A+ A+ N
Sbjct: 2 RLVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGVAEVVYVRKDD---ALTAIDKYNNR 58
Query: 167 YL 168
L
Sbjct: 59 EL 60
>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 = 37.9 bits (88), Expect = 0.002
Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 14/105 (13%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFS--RVRMHNKGGSPV-AFIEYTDVNFAIQAMSNLN 164
L+V NL V+E +++++F F + V G S AF+ + A +A+ +N
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240
Query: 165 GSYLASSDRGAI-----------RIEYAKTKMAEFTTEHRTRHQG 198
G + + G R + K E E + + QG
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQG 285
Score = 29.8 bits (67), Expect = 1.1
Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 7/89 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLN 164
+FV NL + V + + D F F +V G S F+ + A A+ +N
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150
Query: 165 GSYLASSD----RGAIRIEYAKTKMAEFT 189
G L + R + E + +FT
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFT 179
>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 = 35.4 bits (82), Expect = 0.003
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 105 CS-TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSPVAFIEYTDVNFAIQAMSN 162
CS TL++ +L + V+E+++K++F + + M +G + V D + A+Q + N
Sbjct: 1 CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRN 60
Query: 163 LNGS 166
+ +
Sbjct: 61 VKLA 64
>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 = 35.8 bits (82), Expect = 0.003
Identities = 32/104 (30%), Positives = 50/104 (48%), Gaps = 12/104 (11%)
Query: 90 VGSSPPSQGMNGMSPCSTLFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAF 147
VG S G N + L V+NL + V+ Q + +FG + RV+ ++NK S A
Sbjct: 3 VGMPGVSAGGNTV-----LLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDS--AL 55
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTE 191
I+ D N + AMS+LNG + IR+ +K + + E
Sbjct: 56 IQMADGNQSQLAMSHLNGQKMYGK---IIRVTLSKHQTVQLPRE 96
>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 = 35.1 bits (81), Expect = 0.003
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAIQAMS 161
+ L V L Q +++ EI+ +F S +R G S F+ Y D A +A++
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 162 NLNGSYLASSDRGAIRIEYA 181
LNG L + I++ YA
Sbjct: 62 TLNGLRLQNK---TIKVSYA 78
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is 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 = 34.9 bits (81), Expect = 0.003
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSR-VRM-------HNKGGSPVAFIEYTDVNFAIQ 158
T+FV L V E+++ + F S G R VR+ +KG VA++E+ D
Sbjct: 1 TVFVMQLSLKVRERDLYEFF-SKAGKVRDVRIIRDRNSRRSKG---VAYVEFYDEESVPL 56
Query: 159 AMSNLNG 165
A+ L G
Sbjct: 57 ALG-LTG 62
>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 = 34.9 bits (81), Expect = 0.004
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VAFIEYTDVNFAIQAMSN 162
S + V NL ++V+E +++ F S + V+ M + G F+ + A QA+
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 163 LNGSYLASSDRGAIRIEYA 181
N +++ +S I +E A
Sbjct: 61 FNKTFIDTS---KISVELA 76
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 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. It 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 = 74
Score = 34.7 bits (80), Expect = 0.004
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRV--RMHNKGGSP-VAFIEYTDVNFAIQAMSNLN 164
+FVANL V +++K++F R + +G S + +++ A+QA+S N
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60
Query: 165 GSYL 168
G L
Sbjct: 61 GQML 64
>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 = 34.5 bits (80), Expect = 0.004
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS--PVAFIEYTDVNFAIQAMSNLN 164
TL V +L +SE + +D+ F G S VR+ ++ G AF + + A QA+S L+
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHF-GASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLH 59
>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM2 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 = 80
Score = 34.7 bits (79), Expect = 0.004
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P LF+ NL + +E + +F FPGF VR+ G +AF+E+ + + A L
Sbjct: 4 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFENEVQSAAAKEAL 62
Query: 164 NGSYLASSDRGAIRIEYAK 182
G + + A++I +AK
Sbjct: 63 QGFKITPTH--AMKITFAK 79
>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 = 34.4 bits (79), Expect = 0.005
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFS--RVRMHNKGGSP--VAFIEYTDVNFAIQAMSNL 163
+FV +L V++ + F +FP S RV K G F+ + A A++ +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 164 NGSYLASSDRGAIRIEY 180
NG +L S IR +
Sbjct: 62 NGKWLGSR---PIRCNW 75
>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 = 34.3 bits (79), Expect = 0.005
Identities = 11/59 (18%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 105 CSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
+++ NL + SE+E+++ F ++++ + +AF+ + + AI+ ++ L
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKN--IAFVHFLSIANAIKVVTTL 59
>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 = 33.7 bits (78), Expect = 0.008
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPV-----AFIEYTDVNFA 156
+TLFV NL +E+ +K F G V + KG + F+E+ A
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 157 IQAMSNLNGSYL 168
+A+ L G+ L
Sbjct: 61 QKALKRLQGTVL 72
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 33.7 bits (78), Expect = 0.009
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPG------FSRVRMHN--KGGSPVAFIEYTDVNFAIQA 159
L V L + V++ +K+IF ++ G R N +G A++E+ A +A
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNY-GTVKDVDLPIDREVNLPRG---YAYVEFESPEDAEKA 56
Query: 160 MSNLNGSYL 168
+ +++G +
Sbjct: 57 IKHMDGGQI 65
>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 = 33.4 bits (77), Expect = 0.009
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAM 160
LFV NL +E+E++++F +F S V + +KG AF+ + A++A
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKG---FAFVSFMFPEHAVKAY 58
Query: 161 SNLNGS 166
S L+GS
Sbjct: 59 SELDGS 64
>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 = 33.4 bits (77), Expect = 0.009
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
LFV NL ++E+E K++F + S V ++ + G FI A +A + L+G
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKG--FGFIRLDTRTNAEKAKAELDG 59
Query: 166 S 166
Sbjct: 60 I 60
>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 = 33.9 bits (77), Expect = 0.010
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAIQAMS 161
+ L V L Q ++++E K +FGS VR G S F+ Y D N A +A++
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63
Query: 162 NLNGSYLASSDRGAIRIEYAK 182
LNG L + I++ YA+
Sbjct: 64 TLNGLKLQTK---TIKVSYAR 81
>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 = 33.7 bits (77), Expect = 0.011
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPVAFIEYTDVNFAIQAMSNLN 164
LFV L + +E+E++++F + + M K AF++Y+ A A+ LN
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
Query: 165 GSY 167
G Y
Sbjct: 62 GVY 64
>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 = 33.8 bits (78), Expect = 0.011
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFA 156
P TLFV L +E+ ++++F + R+R+ +KG AF+EY A
Sbjct: 2 PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKG---YAFVEYEHERDA 58
Query: 157 IQAMSNLNGSYLASS 171
++A + + + S
Sbjct: 59 LRAYRDAHKLVIDGS 73
>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 = 33.7 bits (77), Expect = 0.011
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 118 SEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIR 177
E+E++ + +R+ + AFI + ++ AI A+ LNG + +R
Sbjct: 20 PEKELRKECEKYGEIESIRILREKA--CAFINFMNIPNAIAALQTLNGKKPYDTI---VR 74
Query: 178 IEYAK 182
I Y K
Sbjct: 75 INYGK 79
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 33.3 bits (77), Expect = 0.011
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFA--- 156
T+F+ NL +E+E+K++F F R+ H+KG AF+++ A
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKG---TAFVKFKTKESAQKC 58
Query: 157 IQAMSNLNGSYLASSDR 173
++A N S L+ R
Sbjct: 59 LEAADNAEDSGLSLDGR 75
>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 = 33.4 bits (77), Expect = 0.011
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSP-VAFIEYTDVNFAIQAMSNL 163
L V L + +E++++++F + +V++ G S F+ + V A +A L
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61
Query: 164 NGSYLASSDRGAIRIEYAKT 183
NG + D IR++Y+ T
Sbjct: 62 NGMEI---DGRRIRVDYSIT 78
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 33.4 bits (77), Expect = 0.011
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 108 LFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L V+NL + V+ + +FG + RV+ + NK + A I+ D A A+++LNG
Sbjct: 2 LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDT--ALIQMADPQQAQTALTHLNG 59
Query: 166 SYLASSDRGAIRIEYAK 182
L +R+ +K
Sbjct: 60 IRLHGK---KLRVTLSK 73
>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 = 33.5 bits (77), Expect = 0.012
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMSNL 163
LF+ NL +E++++ +F + S V + K AF+ Y A++A + L
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 164 NGS 166
+G+
Sbjct: 65 DGT 67
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.4 bits (77), Expect = 0.012
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 107 TLFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKG-GSPVAFIEYTDVNFAIQAMSN 162
T+FV N+ + VS+ I+ + G + RV+ + G F E+ D A++A+
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61
Query: 163 LNG 165
LNG
Sbjct: 62 LNG 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 = 33.2 bits (76), Expect = 0.013
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGS---PVAFIEYTDVNFAIQAMSNLN 164
L+V NL + V E+ I + F + V++ K GS AF+++ D+ A +A + +N
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61
>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 = 33.0 bits (76), Expect = 0.014
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 9/66 (13%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH------NKGGSPVAFIEYTDVNFAIQA 159
+ L V+NL VS+ +IK++F F + +H + G + V F D A++A
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRAD---ALKA 57
Query: 160 MSNLNG 165
M NG
Sbjct: 58 MKQYNG 63
>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 = 33.8 bits (78), Expect = 0.014
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP 144
TLFV N+ + +E+ +K +F V + K G
Sbjct: 2 TLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPA 39
>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 = 35.3 bits (81), Expect = 0.016
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMH---NKGGSP-VAFIEYTDVNFAIQAMSNL 163
L+V NL ++EQE++ IF F V++H G S FI++ D A +A+ +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
Query: 164 NGSYLA 169
NG LA
Sbjct: 249 NGFELA 254
>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 = 33.0 bits (75), Expect = 0.017
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLN 164
L V NL SE ++++F + +R+ G P AF+E+ A +A+++ N
Sbjct: 3 VLVVNNLSYSASEDSLQEVFEKA---TSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCN 59
Query: 165 GSYLASSDRGAIRIEY 180
+ + +IR+E+
Sbjct: 60 NTEIEGR---SIRLEF 72
>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 = 33.1 bits (76), Expect = 0.019
Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 13/70 (18%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSF-----------PGFSRVRMHNKGGSPVAFIEYTDVNF 155
++++NL SE+++++ F R R G +A+ E++
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLG--IAYAEFSSPEQ 58
Query: 156 AIQAMSNLNG 165
A + + +LNG
Sbjct: 59 AEKVVKDLNG 68
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 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 = 80
Score = 32.8 bits (75), Expect = 0.019
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV--AFIEYTDVNFAIQAMSNLN 164
T++V+++ Q V+E+++ +F + R+ S + AFIE+TD A A+S L+
Sbjct: 4 TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS-LS 62
Query: 165 GSYLASSDRGAIRIEYAKT 183
G+ L +R+ +KT
Sbjct: 63 GTMLGFY---PVRVLPSKT 78
>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 = 32.8 bits (74), Expect = 0.020
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAIQAMS 161
+ L V L Q ++++E+K +FGS VR G S F+ Y D A +A++
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64
Query: 162 NLNGSYLASSDRGAIRIEYAK 182
LNG L + I++ YA+
Sbjct: 65 TLNGLRLQTK---TIKVSYAR 82
>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 = 32.6 bits (74), Expect = 0.023
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSP--VAFIEYTDVNFAIQAMS 161
+ L+V NL + ++E E++ IF ++ + + G P VAF+ Y A A+S
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 162 NLNGSYLASSDRGAIRIEYA 181
+LNG+ S + + YA
Sbjct: 61 SLNGTIPPGSTMP-LSVRYA 79
>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 = 32.5 bits (74), Expect = 0.025
Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPVAFIEYTDVNFAIQAMSNLN 164
+ V NL ++++++ +F S+ VR+ ++ AF+E++ A+ AM+ L
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62
Query: 165 GSYL 168
++L
Sbjct: 63 DTHL 66
>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 = 32.3 bits (74), Expect = 0.027
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGS--PVAFIEYTDVNFAIQAMSN 162
S L V NL + + E +++ +F +F + V+ + K G F+ Y A +A+ +
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60
Query: 163 LNGSYLASSDRGAIRIE 179
N S++ +S I +E
Sbjct: 61 FNNSFIDTS---KITVE 74
>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 = 32.3 bits (73), Expect = 0.029
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSF-PGFS-RVRMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
TL+V NL + V+E I +F P S ++ M G P F+E+ + A +++ +N
Sbjct: 1 TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60
Query: 165 G 165
G
Sbjct: 61 G 61
>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 = 32.0 bits (73), Expect = 0.034
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVR--MHNKGGSPVAF--IEYTDVNFAIQAMSNL 163
LFV NL E I + FG + S VR G P F +E++ A A+ L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 164 NGSYLA 169
G+ L
Sbjct: 61 GGTDLL 66
>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 = 32.0 bits (73), Expect = 0.036
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAM 160
LFV NL E +++ +F F S V + +KG A++ + D A++A
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKG---FAYVLFLDPEDAVKAY 61
Query: 161 SNLNGS 166
L+G
Sbjct: 62 KELDGK 67
>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 = 32.2 bits (73), Expect = 0.037
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKG---GSPVAFIEYTDVNFAIQAMSNLN 164
LF+ NL VSE E++ F + V + G AF+++ +++ A +A ++
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMS 70
Query: 165 GSYLASSDRGAIRIEYAK 182
G + R I+I Y K
Sbjct: 71 GRVI---GRNPIKIGYGK 85
>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 = 31.6 bits (72), Expect = 0.043
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L++ NL V+E +++ +F + KGG AF++ D ++A +A+ LNG
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGG--YAFVDCPDQSWADKAIEKLNGKI 58
Query: 168 L 168
L
Sbjct: 59 L 59
>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 = 31.9 bits (73), Expect = 0.046
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPG--------FSRVRMHNKGGSPVAFIEYTDVNFAIQ 158
L V NL ++++ +++ F G +S +KG F+EY A++
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPF-GAVERCFLVYSESTGESKG---YGFVEYASKASALK 56
Query: 159 AMSNLNG 165
A + L+G
Sbjct: 57 AKNQLDG 63
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 31.4 bits (72), Expect = 0.049
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYT---DVNFAIQAMSN- 162
T++V NL ++E+E++ F F VR+ G AF+ + AI A++
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG--YAFVRFDTHEAAATAIVAVNGT 59
Query: 163 -LNGS 166
+NG
Sbjct: 60 SINGQ 64
>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 = 31.6 bits (72), Expect = 0.055
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 13/78 (16%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVR----MH---NKGGSPVAFIEYTDVNFAIQAM 160
+FV +L + + ++ F F S R M +KG V+F++ D AIQ+M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 161 SNLNGSYLASSDRGAIRI 178
NG +L AIR
Sbjct: 62 ---NGQWLGGR---AIRT 73
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 31.4 bits (72), Expect = 0.060
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-NKGGSP-VAFIEYTDVNFAIQAMSNLN 164
++V NLG+ + ++++K++FG + S M ++G S F+ + + A +A+ LN
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63
Query: 165 GS 166
G
Sbjct: 64 GK 65
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.5 bits (71), Expect = 0.062
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 9/69 (13%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM------HNKGGSPVAFIEYTDVNFAIQA 159
ST+FVANL V +++K++F R + ++G V F + + A+QA
Sbjct: 1 STIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIE---AVQA 57
Query: 160 MSNLNGSYL 168
+S NG +L
Sbjct: 58 ISMFNGQFL 66
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show 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. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 31.5 bits (71), Expect = 0.062
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P L + NL +E+E+ ++ F + + AF+E+ D+N AI +S
Sbjct: 1 PSKVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAIAMVS-- 58
Query: 164 NGSYLASSDRGAIR 177
Y +SS+ +R
Sbjct: 59 --YYASSSEPAQVR 70
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 31.2 bits (70), Expect = 0.065
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-PG-FSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L+V NL +E+ IK F F PG RV K AF+ + + A+ AMS +NG
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERV----KKLRDYAFVHFFNREDAVAAMSVMNG 59
Query: 166 SYLASSDRGAIRIEYAK 182
+ D +I + AK
Sbjct: 60 KCI---DGASIEVTLAK 73
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 31.2 bits (71), Expect = 0.068
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 4/80 (5%)
Query: 105 CSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
C T+FV L + +E+ I+++F +RM K + F E V+ AI +S
Sbjct: 6 CKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKNFCHIRFAEEFAVDKAI-YLSGYR 64
Query: 165 ---GSYLASSDRGAIRIEYA 181
GS + G + +++A
Sbjct: 65 VRIGSSTDPKNSGRLHVDFA 84
>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 = 31.4 bits (71), Expect = 0.068
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP--VAFIEYTDVNFAIQAMS 161
+ L+V+ L + ++++E++ +F + SR+ G V FI + A +A+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 162 NLNG 165
LNG
Sbjct: 61 GLNG 64
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 31.2 bits (71), Expect = 0.071
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 110 VANLGQFVSEQEIKDIFGS-FPGFSRVRM-HNKGGSP--VAFIEYTDVNFAIQAMSNLNG 165
V+NL + V+E +I++ F S RV + +N+GG +A I + A +A NG
Sbjct: 4 VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNG 63
Query: 166 SYLASSDRGAIRIE 179
+++E
Sbjct: 64 RID--DGNRKMKVE 75
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM3 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 83
Score = 31.2 bits (70), Expect = 0.072
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSF-PG-FSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
MS L+V NL +E+ I+ F S PG RV K AF+ +++ A+ A
Sbjct: 5 MSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERV----KKIRDYAFVHFSNREDAVDA 60
Query: 160 MSNLNGSYLASSDRGAIRIEYAK 182
M+ LNG + D I + AK
Sbjct: 61 MNALNGKVI---DGSPIEVTLAK 80
>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 = 30.9 bits (70), Expect = 0.072
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIE-YTDVNFAIQAMSNLNGS 166
+F N + EI+ +FG + RV M K G ++E D AI+ + N
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDM--KSGFAFVYMEDERDAEDAIRGLDNFEFG 60
Query: 167 YLASSDRGAIRIEYAK 182
R +R+E+AK
Sbjct: 61 R----QRRRLRVEWAK 72
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 31.4 bits (72), Expect = 0.072
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGF--SRVR-MHNKGGSP---VAFIEYTDVNFAI 157
P +TL + L +E++I + VR + +K AF+E+ + A
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60
Query: 158 QAMSNLNGSYLASSDRGAIRIEYA 181
Q M LN D +R+ YA
Sbjct: 61 QWMDALNNLDPFVIDGRVVRVSYA 84
>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 = 31.1 bits (70), Expect = 0.089
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKG 141
LFV NL + E E+K+ F SF +R++ KG
Sbjct: 8 LFVGNLPHDIDESELKEFFMSFGNVVELRINTKG 41
>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 = 30.7 bits (70), Expect = 0.098
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 11/84 (13%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGSP---VAFIEYTDVNFAIQAM 160
TLFV NL +++++++ F R V+ +KG ++ + A +A+
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVK--DKGSKKCRGFGYVTFALEEDAKRAL 58
Query: 161 SNLNGSYLASSDRGAIRIEYAKTK 184
+ I +E+AK K
Sbjct: 59 EEKKKTKFGGR---KIHVEFAKKK 79
>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM3 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. Rod1 contains
four repeats of RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain) and does have RNA binding activities. .
Length = 76
Score = 30.7 bits (69), Expect = 0.099
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 106 STLFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNL 163
S L V+NL ++ + +FG + RV+ M NK + A ++ D A AMS+L
Sbjct: 1 SVLLVSNLNPDAITPHGLFILFGVYGDVHRVKIMFNKKEN--ALVQMADATQAQLAMSHL 58
Query: 164 NGSYL 168
NG L
Sbjct: 59 NGQRL 63
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 30.7 bits (70), Expect = 0.10
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSPV-AFIEYTDVNFAIQAMS 161
T+FV+NL V E E++ +F + VR+ + KG S A++E+ + +A+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK 58
>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 = 30.7 bits (70), Expect = 0.11
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 7/81 (8%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSPVAF--IEYTDVNFAIQAMSNL 163
TLFV NL + ++++ F VR+ + G F +E+ A +A+
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59
Query: 164 NGSYLASSDRGAIRIEYAKTK 184
+G L + IR++ A +
Sbjct: 60 SGEELLGRE---IRVDLATER 77
>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 = 30.8 bits (70), Expect = 0.11
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSPVAFIEYTDVNFAIQAMSNLN 164
++FV L V+++E+ + F V + + AFI++ A +A+ + N
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64
Query: 165 GSYLASSDRGAIRIEY 180
S L + + ++Y
Sbjct: 65 HSMLKNK---TMHVQY 77
>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 = 30.6 bits (69), Expect = 0.11
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLNG 165
TLFV NL ++ E+K++F R+ G S +A+IE+ A +A+ G
Sbjct: 5 TLFVKNLPYNITVDELKEVFEDAVDI-RLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQG 63
Query: 166 S 166
+
Sbjct: 64 A 64
>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 = 29.8 bits (68), Expect = 0.12
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 122 IKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA 181
+ +F F ++++ K AF+E++ A +A+ LNG +R++Y+
Sbjct: 1 LYKLFSPFGNVEKIKL-LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGG---RPLRVDYS 56
>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 = 30.3 bits (69), Expect = 0.15
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMSNL 163
L V NL +E ++K +F F V + K AF+++T A +A+ +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKG-FAFVQFTSKADAEKAIKGV 60
Query: 164 NGS 166
NG
Sbjct: 61 NGK 63
>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 = 30.3 bits (69), Expect = 0.16
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGF---SRVRMHNKGGSP--VAFIEYTDVNFAIQAMSN 162
L+V+ L + +++QE++ +F + G SR+ N G V FI + A +A+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPY-GRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61
Query: 163 LNGS 166
LNG+
Sbjct: 62 LNGT 65
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 30.0 bits (67), Expect = 0.17
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM------HNKGGSPVAFIEYTDVNFAIQA 159
ST+FVANL V +++K++F R + ++G V F + + A+QA
Sbjct: 1 STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIE---AVQA 57
Query: 160 MSNLNGSYL 168
+S NG L
Sbjct: 58 ISMFNGQLL 66
>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative
RNA-binding protein 15B (RBM15B) from vertebrate. This
subgroup corresponds to the RRM3 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 = 76
Score = 30.0 bits (67), Expect = 0.17
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P + L+V LG S + F F G R + KG S A+I+Y ++ A A + +
Sbjct: 1 PTTRLWVGGLGPNTSLAALAREFDRF-GSIRTIDYVKGDS-FAYIQYESLDAAQAACAQM 58
Query: 164 NGSYLASSDRGAIRIEYAK 182
G L DR +R+++AK
Sbjct: 59 RGFPLGGPDR-RLRVDFAK 76
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 29.9 bits (68), Expect = 0.18
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRV-RMHNKGGSPV------AFIEYTDVNFAIQA 159
L++ NL ++E + +F + + + +K G F+ + A +A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 160 MSNLNG 165
+ +LNG
Sbjct: 61 LKSLNG 66
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 30.3 bits (69), Expect = 0.20
Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSF-----PGF--SRVRMHNKGGSPVAFIEYTDVNFAIQ 158
L + NL + + ++K++ GF +++ H ++ Y+ V A+
Sbjct: 2 RALHIDNLVRPFTLNQLKELLSETGTGVIEGFWMDKIKSH-------CYVTYSTVEEAVA 54
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEH 192
L+G SS+ +++++ + E E
Sbjct: 55 TREALHGLQWPSSNPKRLKVDFVPQEELEEAIEE 88
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both nuclear and
cytoplasmic roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 86
Score = 30.0 bits (68), Expect = 0.20
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 146 AFIEYTDVNFAIQAMSNLNGSYLASSDRG--AIRIEYAKT 183
A +E+ V+ A +A + LNG A G ++IEYAK
Sbjct: 43 AMVEFDSVDSAQRAKAALNG---ADIYAGCCTLKIEYAKP 79
>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 = 30.0 bits (68), Expect = 0.21
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMS 161
ST++V+NL ++ ++ IF + +V + + VAFI + D A + +
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
Query: 162 NLNGSYL 168
LN L
Sbjct: 62 ALNNKEL 68
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 31.6 bits (72), Expect = 0.22
Identities = 19/82 (23%), Positives = 25/82 (30%), Gaps = 7/82 (8%)
Query: 23 LWHHPLAYATAADLPGTASLHQHTLVHPALHPQVPSLNIPHPTAALTAMHHANGMPHFLP 82
LW L+ + A+ P S V P P PT AL A+ + H P
Sbjct: 34 LWEKKLSQSGVAEFPWDPSPQAPPPVAQLPQPLPQ----PPPTQALQALPAGDQQQHNTP 89
Query: 83 ---SPALPSPVGSSPPSQGMNG 101
A P + P
Sbjct: 90 TGSPAANPPATFALPAGPAGPT 111
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 29.8 bits (68), Expect = 0.22
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 5/75 (6%)
Query: 117 VSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS--YLASSDRG 174
V+ + +F + ++ + K A +++ V A A LNG Y
Sbjct: 13 VTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNIY---DGCC 69
Query: 175 AIRIEYAKTKMAEFT 189
+ I++++ K
Sbjct: 70 TLDIQFSRLKELTVK 84
>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 = 29.9 bits (68), Expect = 0.23
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 22/74 (29%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF-------------PGFSRVRMHNKGGSPVAFIEYTDVN 154
+FV + + E+++ D F F GF KG A IEY
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFV------KG---YALIEYETKK 59
Query: 155 FAIQAMSNLNGSYL 168
A A+ LNG L
Sbjct: 60 EAQAAIEGLNGKEL 73
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 29.7 bits (67), Expect = 0.24
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-----VAFIEYTDVNFAIQAMS 161
T ++ NL V+E++IK+ F S VR+ + G P + E+ D + +QA+S
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGLN-VSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61
Query: 162 NLNGSYLASSDRGAIRIEYA 181
LN L + IR++ A
Sbjct: 62 -LNDESLKNR---RIRVDIA 77
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 29.6 bits (67), Expect = 0.24
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 105 CSTLFVANLGQFVSEQEIKDIF-GSFPGFS--RVRMHNKGGSP--VAFIEYTDVNFAIQA 159
++FV +L V++ +++ F +P +V M G F+ + D + +A
Sbjct: 1 DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60
Query: 160 MSNLNGSYLASSDRGAIRIEYA 181
++ +NG Y +S +R+ A
Sbjct: 61 LTEMNGVYCSSR---PMRVSPA 79
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 29.4 bits (67), Expect = 0.24
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 10/67 (14%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVR-------MHNKGGSPVAFIEYTDVNFAIQAM 160
LFV L + +E++++ +F + V +KG AF++++ A +A+
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKG---CAFVKFSSREEAQKAI 58
Query: 161 SNLNGSY 167
L+G
Sbjct: 59 EALHGKV 65
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 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 = 82
Score = 29.8 bits (67), Expect = 0.25
Identities = 26/86 (30%), Positives = 47/86 (54%), Gaps = 14/86 (16%)
Query: 105 CS-TLFVANLGQFVSEQEIKDIFGSFPG-FSRVRM-----HNKGGSPVAFIEYTDVNFAI 157
C+ T++ N+ + V++ ++K F S G SR+R+ H+ + +AF+E+ AI
Sbjct: 3 CARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHS---TRIAFVEFAMAESAI 59
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAKT 183
A+ N +G+ L S IR+ +KT
Sbjct: 60 AAL-NCSGAVLGSL---PIRVSPSKT 81
>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 = 29.8 bits (68), Expect = 0.29
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 146 AFIEYTDVNFAIQAMSNLNG 165
F+E+ DV A +A L G
Sbjct: 59 VFVEFADVEDAQKAQLALAG 78
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, 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-1 contains 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
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 29.5 bits (66), Expect = 0.30
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 10/70 (14%)
Query: 108 LFVANLGQFVSEQEIKDI---FGS----FPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
L +ANL ++Q+ +++ FG+ F +S H+KG F+EY + A +A
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKG---YGFVEYMKKDSAARAK 58
Query: 161 SNLNGSYLAS 170
S+L G L S
Sbjct: 59 SDLLGKQLGS 68
>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 = 29.5 bits (67), Expect = 0.30
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP-VAFIEYTDVNFAIQAMSN 162
L+V NL + ++ +++ F F ++V KG S F+ ++ A +A++
Sbjct: 2 VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTE 61
Query: 163 LNGSYLAS 170
+NG +
Sbjct: 62 MNGRIIGG 69
>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 = 29.7 bits (66), Expect = 0.30
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMSNL 163
+F+ NLGQ E + +FG F + V++ + F+ T+ A A+++L
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 164 NGSYLA 169
NG L
Sbjct: 64 NGYRLG 69
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding protein
with multiple splicing (RBP-MS). The biological function
of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 76
Score = 29.2 bits (65), Expect = 0.32
Identities = 19/74 (25%), Positives = 33/74 (44%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
TLFV+ L + +E+ +F F G+ + PV F+ + A A + LNG
Sbjct: 3 TLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVTFDSRAGAEAAKNALNGI 62
Query: 167 YLASSDRGAIRIEY 180
+ +R+E+
Sbjct: 63 RFDPENPQTLRLEF 76
>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato
(cpo) coding RNA-binding protein and similar proteins.
This subfamily corresponds to the RRM of Cpo, an
RNA-binding protein encoded by Drosophila couch potato
(cpo) gene. Cpo contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It may
control the processing of RNA molecules required for the
proper functioning of the peripheral nervous system
(PNS). .
Length = 83
Score = 29.7 bits (66), Expect = 0.33
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGG---SPVAFIEYTDVNFAIQAMS 161
TLFV+ L +E+ +F ++ G+ S +++ +K G SPV F+ + A A
Sbjct: 3 TLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFETRAGAEAAKQ 62
Query: 162 NLNGSYLASSDRGAIRIEYAK 182
+L G IR+E+AK
Sbjct: 63 DLQGVRFDPDIPQTIRLEFAK 83
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 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 = 29.1 bits (66), Expect = 0.35
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 107 TLFVANLGQFVSEQEIKDIF---GSFPGFSRVRMHNKGGSPVAFIEYTD 152
T+ V NL + +E +I+ F G V++ G VA IE+
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEIR---EVKIVESEGGLVAVIEFET 47
>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 = 29.1 bits (66), Expect = 0.39
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNK--GGSP-VAFIEYTDVNFAIQAMSN 162
+ L V N+ +++E++++F F VR+ K G AF+E+ A AM
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
Query: 163 LNGSYL 168
L ++L
Sbjct: 61 LKSTHL 66
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 30.9 bits (70), Expect = 0.42
Identities = 27/177 (15%), Positives = 52/177 (29%), Gaps = 11/177 (6%)
Query: 4 SNAKVLDIGAPFFHAGGP-ELWHHPLAYATA-------ADLPGTASLHQHTLVHPALHPQ 55
+L + A + P A T+ +PG +S + +
Sbjct: 96 RQLGLLGVKAKDSQFTVVSQAKKSPPASKTSTPMNTSEPLVPGHSSFSDSPSRSASPSRK 155
Query: 56 VPSLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGS--SPPSQGMNGMSPCSTLFVANL 113
+ + LT + SP+ S +G S ++ SP + +
Sbjct: 156 FSPSSTIQQSPQLTPSNKPASPSSSYQSPSYSSSLGPVNSSGNRSNLRSSPWALRSSGDK 215
Query: 114 GQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLAS 170
++++ + F + M A T +F + S N S AS
Sbjct: 216 KDITTDEKYLETFLA-EVDEEQHMITSSAGKNATPPETINSFGSSSPSFWNYSRNAS 271
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 30.8 bits (70), Expect = 0.44
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPG-FSRVRMHNKGG-SPVAFIEYTD 152
+ T+ V+N+ +E++IK+ F SF G V M ++ S +A++ + D
Sbjct: 1 VMQVRTVKVSNVSLKATERDIKEFF-SFSGDIEYVEMQSENERSQIAYVTFKD 52
>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 = 28.8 bits (65), Expect = 0.45
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 14/72 (19%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM----------HNKGGSPVAFIEYTDVNFAI 157
++V NL + E +++ IF F +R+ N G AF+ + D + A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNG---FAFVTFKDASSAE 59
Query: 158 QAMSNLNGSYLA 169
A+ LNG+ L
Sbjct: 60 NALQ-LNGTELG 70
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 28.8 bits (65), Expect = 0.47
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRV---RMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
LFV + + V+++++ +F PG R G S A++ Y++ AI A L
Sbjct: 3 LFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKL 61
Query: 164 NG 165
NG
Sbjct: 62 NG 63
>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 = 29.2 bits (66), Expect = 0.48
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 106 STLFVANL-GQFVSEQEIKDIFGSF--PGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMS 161
LFV L F ++ +F P F ++ + G AF+EY A +A
Sbjct: 3 RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQ 62
Query: 162 NLNG 165
LNG
Sbjct: 63 ALNG 66
>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 = 28.7 bits (64), Expect = 0.49
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
LFV NL ++E++ K +F + S V ++ G FI A A + L+G+
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRG--FGFIRLESRTLAEIAKAELDGTI 61
Query: 168 LASSDRGAIRIEY 180
L + +RI +
Sbjct: 62 LKNR---PLRIRF 71
>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 = 28.7 bits (64), Expect = 0.49
Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSF-----------PGFSRVRMHNKGGSPVAFIEYTDVN 154
S LFV NL ++E+E++ +F + GF +R+ + + +A E ++
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMP 61
Query: 155 F 155
Sbjct: 62 L 62
>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 = 28.9 bits (64), Expect = 0.51
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
++V NLG ++ E++ FG + V + N G AF+E+ D A A+ L+G
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAADAVRELDGR 64
Query: 167 YLASSDRGAIRIEYA 181
L +R+E +
Sbjct: 65 TLCGC---RVRVELS 76
>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 = 28.9 bits (65), Expect = 0.52
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQA 159
TLFV NL V ++ +K F F R+ ++G V F D AI+A
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 160 MS 161
M
Sbjct: 61 MD 62
>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 = 28.7 bits (64), Expect = 0.54
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSN 162
LFV NL V + E+K+ F + +R+++ G P F+ + D + +SN
Sbjct: 6 LFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDDSEPVQKILSN 61
>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 = 28.5 bits (64), Expect = 0.57
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF 129
+FV L +E++I++ FG F
Sbjct: 2 IFVGGLSPETTEEKIREYFGKF 23
>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 = 28.6 bits (64), Expect = 0.59
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLNG 165
T++V NL + E+E++D+F + + + P AFIE+ D A A+ +G
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 28.5 bits (63), Expect = 0.61
Identities = 19/74 (25%), Positives = 33/74 (44%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
TLFV+ L + +E+ +F F G+ + PV F+ + + A A + LNG
Sbjct: 3 TLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGI 62
Query: 167 YLASSDRGAIRIEY 180
+R+E+
Sbjct: 63 RFDPEIPQTLRLEF 76
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence show that the
RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 28.8 bits (64), Expect = 0.62
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 108 LFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
L V+NL + V+ Q + +FG + RV+ + NK + A ++ D N A AMS+LNG
Sbjct: 2 LLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHLNG 59
Query: 166 SYLASSDRGAIRIEYAKTKMAEFTTE 191
L +RI +K + + E
Sbjct: 60 QKLHGK---PLRITLSKHQTVQLPRE 82
>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 = 28.5 bits (64), Expect = 0.63
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSPV--AFIEYTDVNFAIQAMS 161
+ L V L Q ++++E++ +F + ++ G + F++Y D N A +A++
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 162 NLNG 165
LNG
Sbjct: 61 TLNG 64
>gnl|CDD|117486 pfam08919, F_actin_bind, F-actin binding. The F-actin binding
domain forms a compact bundle of four antiparallel
alpha-helices, which are arranged in a left-handed
topology. Binding of F-actin to the F-actin binding
domain may result in cytoplasmic retention and
subcellular distribution of the protein, as well as
possible inhibition of protein function.
Length = 179
Score = 29.7 bits (66), Expect = 0.68
Identities = 14/48 (29%), Positives = 21/48 (43%)
Query: 76 GMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIK 123
P P +P P S PS+ NG P S F+ + VS ++ +
Sbjct: 18 AKPVGTPPSPVPLPSTSPSPSKMANGTQPSSAAFIPLISTRVSLRKTR 65
>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 = 28.6 bits (64), Expect = 0.72
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRV---RMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
LFV L + +E +++ +F F R + AF++++ A A++ L+
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
Query: 165 GS 166
GS
Sbjct: 64 GS 65
>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 = 28.5 bits (64), Expect = 0.73
Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMS 161
++L+V N+ +++ +FG + V + + + A++++ DV A A+
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 162 NLNGSYLASSDRGAIRIEYA----KTK 184
L+ + + I I++A KT
Sbjct: 61 YLDRTRFLGRE---IEIQFAQGDRKTP 84
>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 = 28.3 bits (64), Expect = 0.76
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 21/73 (28%)
Query: 105 CSTLFVANLGQFVSEQEIKDIFGSFPGFSRV------RM------HNKGGSPVAFIEYTD 152
+FV + + + E E+ P F + R+ N+G AF+ YT+
Sbjct: 1 GCEVFVGKIPRDLFEDEL------VPLFEKAGPIYELRLMMDFSGLNRG---YAFVTYTN 51
Query: 153 VNFAIQAMSNLNG 165
A +A+ L+
Sbjct: 52 KEAAQRAVKQLHN 64
>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 = 28.4 bits (64), Expect = 0.81
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN------KGGSPVAFIEYTDVNFAIQA 159
+ +FV + +E+E++D F F V++ KG V F D I A
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAE-KILA 61
Query: 160 MSNLN 164
M NLN
Sbjct: 62 MGNLN 66
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 28.3 bits (63), Expect = 0.84
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNK 140
+TLFV NL + Q + D F GF R+ K
Sbjct: 1 ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTK 35
>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 = 28.0 bits (63), Expect = 0.84
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-NKGGSPVAFIEYTDVNFAIQAMSNL 163
T+ + N+ V+E++IK F P ++ + + G A +E+ + A +A +L
Sbjct: 1 RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG---ALVEFESPSDAGKASLSL 57
Query: 164 NGS 166
NGS
Sbjct: 58 NGS 60
>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 = 28.1 bits (63), Expect = 0.87
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 5/66 (7%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSP--VAFIEYTDVNFAIQAMSN 162
LFV NL + +++ F + VR+ K G AF+E+ A+
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAE-AMTKALK 60
Query: 163 LNGSYL 168
L+ + L
Sbjct: 61 LHHTLL 66
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show 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. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 28.7 bits (64), Expect = 0.89
Identities = 16/73 (21%), Positives = 32/73 (43%)
Query: 110 VANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLA 169
+ N+ V+ + +F +F ++ + K G A I+Y DV A+ A L G +
Sbjct: 8 IENMQYAVTVDVLHTVFSAFGFVQKIAIFEKNGGFQALIQYPDVPTAVNAKEALEGHCIY 67
Query: 170 SSDRGAIRIEYAK 182
+ + Y++
Sbjct: 68 DGGYCKLHLSYSR 80
>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 = 27.9 bits (62), Expect = 1.1
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVR-----MHNKGGSPVAFIEYTDVNFAIQAMS 161
TL + NL VS + ++ IF + +R + F+E+ DV A +A+
Sbjct: 3 TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQR------FVEFFDVRDAAKALR 56
Query: 162 NLNG 165
+NG
Sbjct: 57 AMNG 60
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 28.0 bits (63), Expect = 1.1
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSR--------VRMH-NKGGSPV--AFIEYTDVNFA 156
++++ L V+E + ++FG R ++++ +K P A + Y D + A
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60
Query: 157 IQAMSNLNG 165
A+ NG
Sbjct: 61 QAAIEWFNG 69
>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 = 29.5 bits (66), Expect = 1.1
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAIQA 159
+ L V L Q ++++EI+ +F S VR G S F+ Y A +A
Sbjct: 2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61
Query: 160 MSNLNGSYLASSDRGAIRIEYAK 182
+++LNG L + I++ YA+
Sbjct: 62 VNSLNGLRLQNK---TIKVSYAR 81
Score = 28.4 bits (63), Expect = 3.0
Identities = 32/171 (18%), Positives = 51/171 (29%), Gaps = 30/171 (17%)
Query: 6 AKVLDIGAPFFHAGGPELWHHPLAYATAADLPGTASLHQHTLVHPALHPQVPSLNIPHPT 65
+ A G P+ +A A P +A L H V +
Sbjct: 190 QTTRVPLSTILTAAG----IGPMHHAAARFRP-SAGDFTAVLAHQQQQHAVAQQHAAQRA 244
Query: 66 AALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDI 125
+ G+ + +G C +FV NL E + +
Sbjct: 245 SPPATDGQTAGL-------------AAGAQIAASDGAGYC--IFVYNLSPDTDETVLWQL 289
Query: 126 FGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLA 169
FG F V++ KG F+ T+ + A A+ +LNG L
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKG---YGFVSMTNYDEAAMAILSLNGYTLG 337
>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 = 28.1 bits (63), Expect = 1.2
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 107 TLFVANLGQFVSEQEIKD-IFGSFPGFSRV-----RMHNKGGSPVAFIEYTDVNFAIQAM 160
L V+NL +S +E++ + F +V R G S VA + ++ A A+
Sbjct: 6 DLQVSNLDYRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDG-SLVASVRVPNLQDAQYAI 64
Query: 161 SNL 163
S L
Sbjct: 65 SQL 67
>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 = 27.6 bits (62), Expect = 1.3
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNK--GGSP-VAFIEYTDVNFAIQAMSN 162
TL++ +L ++ E I F + V++ NK G S F+E+ A QA+ +
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
Query: 163 LNGSYLASSDR 173
LNG + ++ +
Sbjct: 61 LNGKPIPNTQQ 71
>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 = 27.6 bits (62), Expect = 1.3
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGF-SRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
TL ++N+ V+E+++K++F G + K +A I+ V AI+A+ L+
Sbjct: 1 TLHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPK-DRKMALIQMGSVEEAIEALIALHN 59
Query: 166 SYLASSDRGAIRIEYAKT 183
L+ S +R+ ++K+
Sbjct: 60 YQLSESSH--LRVSFSKS 75
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 27.3 bits (61), Expect = 1.3
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 108 LFVANLGQFVSEQEIKDIF---GSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
L V + + VS +K+IF G G ++ +KG V+F D+ AI+A +L
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFH---DLRQAIKAYKDLQ 60
Query: 165 GSYLASSDR 173
S A D
Sbjct: 61 -SKRAFGDA 68
>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 = 27.7 bits (61), Expect = 1.5
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGG--SPVAFIEYTDVNFAIQAMS 161
+ L+++ L + +++++++D+F F SRV + G VAFI + + A +A++
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60
Query: 162 NLNG 165
+ NG
Sbjct: 61 SFNG 64
>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 = 27.7 bits (61), Expect = 1.5
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQAMS 161
++LFV N+ ++++ FG + V + + + A+I++ DV A A+
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60
Query: 162 NLNGSYLASSDRGAIRIEYAK 182
NLN ++ I I++A+
Sbjct: 61 NLNRKWVCGRQ---IEIQFAQ 78
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 27.5 bits (62), Expect = 1.5
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 122 IKDIFGSFPGFSRVRMH-----NKGGSPVAFIEYTDVNFAIQAMSNLNGSYL 168
++ IF F V ++ AF+E+ A +A+ LNG L
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75
>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 = 27.6 bits (62), Expect = 1.5
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 105 CSTLFVANLGQFVSEQEIKDIF---GSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAM 160
+ +++ L ++E +I +F G + VR G S AF+ Y D I A+
Sbjct: 9 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68
Query: 161 SNLNGSYLASSDRGAIRIEYAK 182
NLNG L R IR+++ +
Sbjct: 69 DNLNGIKLL--GR-TIRVDHVR 87
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 27.6 bits (61), Expect = 1.8
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTD 152
+T+FV LG+ V+ + + D F ++ + K G P+ + YTD
Sbjct: 3 NTIFVQGLGEDVTIESVADYFKQ---IGIIKTNKKTGQPMINL-YTD 45
>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 = 27.2 bits (61), Expect = 1.8
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP---VAFIEYTDVNFAIQAMSNL 163
+ V NL +E+E++++F F R+ + P +A +E+ + + A +A +L
Sbjct: 2 VILVKNLPFGTTEEELRELFEKFGSLGRLLL-----PPSRTIALVEFLEPSDARKAFKSL 56
Query: 164 N 164
Sbjct: 57 A 57
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 26.8 bits (60), Expect = 2.4
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 15/73 (20%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEY---TDVNFAI 157
++VA++ +SE +IK +F +F + +KG FIEY AI
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKG---YGFIEYENPQSAQDAI 59
Query: 158 QAMSN--LNGSYL 168
+M+ L G L
Sbjct: 60 ASMNLFDLGGQQL 72
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 27.2 bits (61), Expect = 2.7
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 12/56 (21%)
Query: 124 DIFGSFPGFSRVRM---------HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLAS 170
D+ F F V H +G +++Y A+ A NG + A
Sbjct: 44 DVLPEFEKFGEVVQFKVCCNYEPHLRGN---VYVQYQSEEEALAAFKMFNGRWYAG 96
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 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 = 80
Score = 26.9 bits (59), Expect = 2.8
Identities = 21/86 (24%), Positives = 47/86 (54%), Gaps = 11/86 (12%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIF----GSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
P +TL ++N+ Q V+E++++ +F G+ F + H +A ++ + V AIQA
Sbjct: 2 PSATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHK-----MALLQMSTVEEAIQA 56
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTKM 185
+ +L+ L + +R+ ++K+ +
Sbjct: 57 LIDLHNYNLG--ENHHLRVSFSKSTI 80
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It 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. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 27.0 bits (60), Expect = 3.0
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPG-FSRVRMHNKGGSPVAF 147
TLF+ NL +E+ ++ +FGS G V +
Sbjct: 1 RTLFLVNLPVDTTERHLRKLFGSGGGIIESVVFVEELLEEDEE 43
>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 = 26.5 bits (59), Expect = 3.6
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
TL+V G ++E+ +K F F + M + F+ + + A +A++ LNG+
Sbjct: 6 TLYVHGYG--LTEEILKKAFSPFGNIINISMEKEKNC--GFVTFEKMESADRAIAELNGT 61
>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 = 26.2 bits (58), Expect = 3.7
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
T+ V N + +E++D+F +RV M G +A +E+ + A A L
Sbjct: 2 TILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAG--TIAIVEFANPQQARLAFKAL 56
>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 = 26.0 bits (57), Expect = 3.9
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLN 164
LFV NL +EQEI+ +F + + G F+ D A +A+ NL+
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYG----FVHMDDKTAADEAIRNLH 55
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 26.2 bits (58), Expect = 4.2
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 108 LFVANLGQFVSEQEIKDIFGS 128
+FV+NL +EQ++ + FGS
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGS 21
>gnl|CDD|217453 pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd protein. Tymoviruses
are single stranded RNA viruses. This family includes a
protein of unknown function that has been named based on
its molecular weight. Tymoviruses such as the ononis
yellow mosaic tymovirus encode only three proteins. Of
these two are overlapping this protein overlaps a larger
ORF that is thought to be the polymerase.
Length = 458
Score = 27.8 bits (62), Expect = 4.7
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 46 TLVHPALHPQV---PSLNIPHPTAALTA-MHHANGMPHFLPSPALPSPVGSSPPSQG 98
L AL P V PS+ +PHP +AL + + ++ H LP LP P SSP
Sbjct: 379 ALPLTALAPLVRHSPSIPLPHPPSALPSHVGASSSKHHRLPPSVLPGPRLSSPSPSP 435
>gnl|CDD|241228 cd12784, RRM2_ROD1, RNA recognition motif 2 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM2 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein and negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It might
play a role controlling differentiation in mammals. Rod1
contains four repeats of RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and does have RNA binding
activities. .
Length = 103
Score = 26.5 bits (58), Expect = 4.7
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
G SP + V NL V+ + + IF F ++ K A ++Y D A A
Sbjct: 1 GQSPVLRIIVENLFYPVTLEVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPMNAHHAK 60
Query: 161 SNLNGSYLASSDRGAIRIEYAK 182
L+G + ++ +RI+++K
Sbjct: 61 MALDGQNIYNA-CCTLRIDFSK 81
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM1 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 = 75
Score = 26.1 bits (57), Expect = 5.1
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
L V N+G +SE ++ + F +++ M A ++ DV+ AI A+
Sbjct: 3 LHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQ--ALLQMQDVSSAISAL 53
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 26.0 bits (58), Expect = 5.3
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 14/69 (20%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV-----------AFIEYTDVNFA 156
L+V NL ++E+E+ D F ++ G+PV AF+E+ V A
Sbjct: 4 LYVGNLPPGITEEELVDFFNQ--AMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEA 61
Query: 157 IQAMSNLNG 165
A+ L+G
Sbjct: 62 TAAL-ALDG 69
>gnl|CDD|211788 TIGR03098, ligase_PEP_1, acyl-CoA ligase (AMP-forming),
exosortase A-associated. This group of proteins
contains an AMP-binding domain (pfam00501) associated
with acyl CoA-ligases. These proteins are generally
found in genomes containing the exosortase/PEP-CTERM
protein expoert system , specifically the type 1
variant of this system described by the Genome Property
GenProp0652. When found in this context they are
invariably present next to a decarboxylase enzyme. A
number of sequences from Burkholderia species also hit
this model, but the genomic context is obviously
different. The hypothesis of a constant substrate for
this family is only strong where the exosortase context
is present.
Length = 517
Score = 27.4 bits (61), Expect = 5.3
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 26 HPLAYATAADLPGTASL--HQHTLVHPALHPQVPSL 59
H L AA LP +L H TL + AL +V +L
Sbjct: 3 HHLLEDAAARLPDATALVHHDRTLTYAALSERVLAL 38
>gnl|CDD|221247 pfam11825, Nuc_recep-AF1, Nuclear/hormone receptor activator site
AF-1. Nuclear receptors (NRs) are a family of
ligand-inducible transcription factors, and, like other
transcription factors, they contain a distinct DNA
binding domain that allows for target gene recognition
and several activation domains that possess the ability
to activate transcription. One of these activation
domains is at the N-terminal, although there are two
distinct motifs within this domain, between residues
20-36 and between 74 and the end of this domain, which
are the binding regions. One of the co-activators is
TIF1beta, which appears to bind at the first motif.
Length = 106
Score = 26.3 bits (58), Expect = 6.4
Identities = 22/106 (20%), Positives = 45/106 (42%), Gaps = 6/106 (5%)
Query: 39 TASLHQHTLVHPALHPQVPSLNIPHPTAALTAMHHANGM--PHFLPSPALPSPVGSSPPS 96
+ S + ++ P LHP + + + + + NG+ P+ + S ++ SP S P +
Sbjct: 4 SPSTGRGSMSAPDLHPSLLGSPMGPMSTLSSPI---NGLGSPYSVISSSMGSPSMSLPST 60
Query: 97 QGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGG 142
G+ + S +++ S ++IK G G H+ G
Sbjct: 61 PGLGYGTGSSPQINSSMNSVSSSEDIKPPPG-LNGLMNYPSHSPGS 105
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 27.4 bits (60), Expect = 6.4
Identities = 20/98 (20%), Positives = 26/98 (26%), Gaps = 4/98 (4%)
Query: 11 IGAPFFHAGGPELWHHP-LAYATAADLPG-TASLHQHTLVHPALHPQVPSLNIPHPTAAL 68
G F GGP +P + A + Q HP+ +
Sbjct: 521 GGMMGFPMGGPSASPNPMMNGFAAGSMGMYMPFQPQPMFYHPSPQMMPVMGSNGAEEGGG 580
Query: 69 TAMHH--ANGMPHFLPSPALPSPVGSSPPSQGMNGMSP 104
H A M +P P QGM G P
Sbjct: 581 NISPHVPAGFMAAGPGAPMGAFGYPGGIPFQGMMGSGP 618
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 26.2 bits (58), Expect = 6.6
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 117 VSEQEIKDIFGSFPGFSRVR--MHNKGGSP--VAFIEYTD 152
SE IK+ F SF + +R P + I+Y
Sbjct: 14 TSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYG 53
>gnl|CDD|241145 cd12701, RRM4_PTBP1, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM4 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 76
Score = 25.4 bits (55), Expect = 7.5
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGS 166
TL ++N+ VSE+++K +F S G + + +A I+ V AIQ++ +L+
Sbjct: 1 TLHLSNIPPSVSEEDLKMLFSSNGGTVKGFKFFQKDRKMALIQMGSVEEAIQSLIDLHNH 60
Query: 167 YLASSDRGAIRIEYAKT 183
L + +R+ ++K+
Sbjct: 61 DLGENHH--LRVSFSKS 75
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
0.318 0.132 0.408
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,520,025
Number of extensions: 961933
Number of successful extensions: 1312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1223
Number of HSP's successfully gapped: 243
Length of query: 206
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 114
Effective length of database: 6,857,034
Effective search space: 781701876
Effective search space used: 781701876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.9 bits)