RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy633
(300 letters)
>gnl|CDD|216174 pfam00887, ACBP, Acyl CoA binding protein.
Length = 87
Score = 98.8 bits (247), Expect = 3e-26
Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 2/87 (2%)
Query: 75 MEDRFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAW 132
+E+ F A ++ L K + + LK YALYKQAT G N +P +++ K+K++AW
Sbjct: 1 LEEEFEAAVKFVKKLPKDGRPSNEEKLKLYALYKQATEGDVNTPRPGMFDVIGKAKWDAW 60
Query: 133 NSLGQMAKSEAMSKYIALLNEVDAGWE 159
L M+K EAM KY+ L+ E+ +
Sbjct: 61 KKLKGMSKEEAMKKYVELVEELVEKYG 87
>gnl|CDD|238248 cd00435, ACBP, Acyl CoA binding protein (ACBP) binds thiol esters
of long fatty acids and coenzyme A in a one-to-one
binding mode with high specificity and affinity.
Acyl-CoAs are important intermediates in fatty lipid
synthesis and fatty acid degradation and play a role in
regulation of intermediary metabolism and gene
regulation. The suggested role of ACBP is to act as a
intracellular acyl-CoA transporter and pool former.
ACBPs are present in a large group of eukaryotic species
and several tissue-specific isoforms have been detected.
Length = 85
Score = 87.4 bits (217), Expect = 5e-22
Identities = 32/85 (37%), Positives = 55/85 (64%)
Query: 75 MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 134
+++ F A + + L K + L+ Y+LYKQATVG CN ++P ++++ ++K++AWNS
Sbjct: 1 LQEEFEAAAEKVKKLKTKPSNEEKLQLYSLYKQATVGDCNTERPGMFDLKGRAKWDAWNS 60
Query: 135 LGQMAKSEAMSKYIALLNEVDAGWE 159
L M+K +AM YIA + E+ A +
Sbjct: 61 LKGMSKEDAMKAYIAKVEELIAKYA 85
>gnl|CDD|226731 COG4281, ACB, Acyl-CoA-binding protein [Lipid metabolism].
Length = 87
Score = 70.3 bits (172), Expect = 1e-15
Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75 MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 134
+ RF QA + L +K + LLK YAL+KQ +VG + +KP ++++ + KY AW
Sbjct: 2 LSTRFEQAQTDVKELSEKPSNDELLKLYALFKQGSVGDNDGEKPGFFDIVGRYKYEAWAG 61
Query: 135 LGQMAKSEAMSKYIALLNEVDAG 157
L ++ +A +YIAL+ E+ A
Sbjct: 62 LKGKSQEDARQEYIALVEELKAK 84
>gnl|CDD|185637 PTZ00458, PTZ00458, acyl CoA binding protein; Provisional.
Length = 90
Score = 67.9 bits (166), Expect = 1e-14
Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 75 MEDRFNQACDYLPSLVKK--LDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAW 132
M D F + ++ SL K L L Y YKQ+TVG CNI +PS + + + KY AW
Sbjct: 1 MADLFEECVSFINSLPKTVNLSVEIKLDLYKYYKQSTVGNCNIKEPSMFKYQDRKKYEAW 60
Query: 133 NSLGQMAKSEAMSKYIALLNEVDAGWEDKE 162
S+ + + +A +Y+ ++ E+ WE E
Sbjct: 61 KSIENLNREDAKKRYVEIVTELFPNWEKGE 90
>gnl|CDD|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate
protein-protein interactions in very diverse families of
proteins. The number of ANK repeats in a protein can
range from 2 to over 20 (ankyrins, for example). ANK
repeats may occur in combinations with other types of
domains. The structural repeat unit contains two
antiparallel helices and a beta-hairpin, repeats are
stacked in a superhelical arrangement; this alignment
contains 4 consecutive repeats.
Length = 126
Score = 68.2 bits (167), Expect = 2e-14
Identities = 33/86 (38%), Positives = 49/86 (56%), Gaps = 3/86 (3%)
Query: 210 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 269
A G L++ VK L + ++N D +G LH A GHL++V+ L+EK GADVN D
Sbjct: 15 ASNGHLEV-VKLLLENGA-DVNAKDNDGRTPLHLAAKNGHLEIVKLLLEK-GADVNARDK 71
Query: 270 DGDYGLDYAKAIEHTDLIEYLVNSGA 295
DG+ L A + D+++ L+ GA
Sbjct: 72 DGNTPLHLAARNGNLDVVKLLLKHGA 97
Score = 65.1 bits (159), Expect = 2e-13
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 210 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 269
AK G L++ VK L + ++N D++G LH A G+L VV+ L++ GADVN D
Sbjct: 48 AKNGHLEI-VKLLLEKGA-DVNARDKDGNTPLHLAARNGNLDVVKLLLKH-GADVNARDK 104
Query: 270 DGDYGLDYAKAIEHTDLIEYLV 291
DG L A H ++++ L+
Sbjct: 105 DGRTPLHLAAKNGHLEVVKLLL 126
Score = 63.9 bits (156), Expect = 7e-13
Identities = 28/65 (43%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 231 NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 290
N DE+G LH A GHL+VV+ L+E GADVN D+DG L A H ++++ L
Sbjct: 1 NARDEDGRTPLHLAASNGHLEVVKLLLEN-GADVNAKDNDGRTPLHLAAKNGHLEIVKLL 59
Query: 291 VNSGA 295
+ GA
Sbjct: 60 LEKGA 64
Score = 27.3 bits (61), Expect = 4.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 265 NVTDSDGDYGLDYAKAIEHTDLIEYLVNSGAH 296
N D DG L A + H ++++ L+ +GA
Sbjct: 1 NARDEDGRTPLHLAASNGHLEVVKLLLENGAD 32
>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies).
Length = 91
Score = 63.0 bits (154), Expect = 7e-13
Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 210 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 269
AK G L++ VK L + K ++N D + LH A G+L++V+ L+E GADVN D
Sbjct: 5 AKNGNLEL-VKLLLE-KGADVNLGDTD--TALHLAARNGNLEIVKLLLEH-GADVNAKDK 59
Query: 270 DGDYGLDYAKAIEHTDLIEYLVNSGA 295
DG+ L A + ++++ L+ GA
Sbjct: 60 DGNTALHLAARNGNLEIVKLLLEHGA 85
Score = 51.1 bits (123), Expect = 1e-08
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 210 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 268
A+ G L++ VK L + ++N D++G LH A G+L++V+ L+E GAD+N+ D
Sbjct: 36 ARNGNLEI-VKLLLE-HGADVNAKDKDGNTALHLAARNGNLEIVKLLLEH-GADINLKD 91
Score = 44.2 bits (105), Expect = 4e-06
Identities = 21/55 (38%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 241 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGA 295
LH A G+L++V+ L+EK GADVN+ D+ D L A + ++++ L+ GA
Sbjct: 1 LHLAAKNGNLELVKLLLEK-GADVNLGDT--DTALHLAARNGNLEIVKLLLEHGA 52
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 57.7 bits (140), Expect = 4e-11
Identities = 20/46 (43%), Positives = 33/46 (71%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
+ +V FDK TGLSKG+GFV+F +++ ++ H+LEG++L +Q
Sbjct: 28 SCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGNKLQVQ 73
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway; it binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 75
Score = 55.8 bits (135), Expect = 2e-10
Identities = 20/46 (43%), Positives = 31/46 (67%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
A +M D +TG S+GFGFVTF ++ AV++VFS L G ++ ++
Sbjct: 29 AQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKR 74
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 54.9 bits (133), Expect = 3e-10
Identities = 20/37 (54%), Positives = 26/37 (70%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
+M D TG S+GFGFVTF + +VDKV + HVL+G
Sbjct: 30 IMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDG 66
>gnl|CDD|222277 pfam13637, Ank_4, Ankyrin repeats (many copies).
Length = 54
Score = 54.6 bits (132), Expect = 3e-10
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 237 GLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV 291
G LH A G L++V++L+EK G D+N TD DG+ L A + ++++ L+
Sbjct: 1 GRTALHKAAISGRLELVKYLLEK-GVDINRTDEDGNTALHIAAENGNLEVLKLLL 54
Score = 38.8 bits (91), Expect = 1e-04
Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 2/48 (4%)
Query: 210 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLI 257
A G+L+ LVK L + K +IN+ DE+G LH A + G+L+V++ L+
Sbjct: 9 AISGRLE-LVKYLLE-KGVDINRTDEDGNTALHIAAENGNLEVLKLLL 54
>gnl|CDD|206028 pfam13857, Ank_5, Ankyrin repeats (many copies).
Length = 56
Score = 50.4 bits (121), Expect = 1e-08
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 222 LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 278
L + ++N D NG LH A G L++VQ L++ G D+N+ DSDG LD A
Sbjct: 1 LLEHGPIDLNATDGNGNTPLHLAAKYGALELVQWLLKP-GVDLNLRDSDGLTALDLA 56
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has
been identified as a regulator of the hematopoietic
stem cell (HSC) compartment and of leukemic stem cells
after transplantation of cells with loss and gain of
function of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 47.4 bits (113), Expect = 2e-07
Identities = 18/42 (42%), Positives = 26/42 (61%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR 43
+A +MFDK T +GFGFVTF++++ VDKV H +
Sbjct: 28 DAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIHFHEINNKM 69
>gnl|CDD|200936 pfam00023, Ank, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities. Repeats 13-24 are especially active,
with known sites of interaction for the Na/K ATPase,
Cl/HCO(3) anion exchanger, voltage-gated sodium channel,
clathrin heavy chain and L1 family cell adhesion
molecules. The ANK repeats are found to form a
contiguous spiral stack such that ion transporters like
the anion exchanger associate in a large central cavity
formed by the ANK repeat spiral, while clathrin and cell
adhesion molecules associate with specific regions
outside this cavity.
Length = 33
Score = 46.0 bits (110), Expect = 2e-07
Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 236 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 268
+G LH A GHL+VV+ L+E GADVN D
Sbjct: 1 DGNTPLHLAARNGHLEVVKLLLEA-GADVNARD 32
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This
subgroup corresponds to the RRM3 of the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
proteins, a family of structurally related RNA-binding
proteins involved in the regulation of pre-mRNA
splicing in the nucleus and in the control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or
NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or
ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed
BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also
termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts. .
Length = 73
Score = 46.9 bits (112), Expect = 2e-07
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFSTDSHVLEGSRLSIQ 47
++A V DKNTG SK FGFV++ N E A + + + + G RL +Q
Sbjct: 26 ISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 46.8 bits (112), Expect = 3e-07
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI 46
+ ++ DK TG SKGF FV F+++E +K + L+G L +
Sbjct: 28 SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1)
is a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation,
and tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator
of the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 75
Score = 46.3 bits (110), Expect = 5e-07
Identities = 19/40 (47%), Positives = 26/40 (65%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
VM D T S+GFGFVTF + +VDKV + H L+G ++
Sbjct: 30 VMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKI 69
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 46.1 bits (110), Expect = 6e-07
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
++ DK TG +GF FVTF + + VDK+ H + G R+
Sbjct: 29 VEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQKYHTINGHRV 70
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 80
Score = 44.3 bits (105), Expect = 3e-06
Identities = 14/43 (32%), Positives = 29/43 (67%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
VM+D +GFGF+TF+++++VD+V + H + G ++ ++
Sbjct: 34 VMYDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVK 76
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to
the RRM1 of hnRNP A0 which is a low abundance hnRNP
protein that has been implicated in mRNA stability in
mammalian cells. It has been identified as the
substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 79
Score = 44.0 bits (104), Expect = 3e-06
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS 49
VM D NT S+GFGF+TF + + D+ H ++G+++ ++ +
Sbjct: 34 VMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSIDGNQIELKRA 78
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 43.7 bits (104), Expect = 3e-06
Identities = 13/40 (32%), Positives = 25/40 (62%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
D+ TG+ KGFG+V F+ K++V + L+G ++ ++
Sbjct: 34 DRKTGIGKGFGYVLFKTKDSVALALKLNGIKLKGRKIRVK 73
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 43.4 bits (103), Expect = 5e-06
Identities = 15/45 (33%), Positives = 31/45 (68%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
A V+ D+ TG S+G+GFVTF++KE+ ++ + +++G + ++
Sbjct: 30 AVVITDRQTGKSRGYGFVTFKDKESAERACKDPNPIIDGRKANVN 74
>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 = 43.4 bits (103), Expect = 6e-06
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR 43
A V+ D TG SKG+GFV F +++ D+ + + V SR
Sbjct: 31 GAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSR 72
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition, steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway. It binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 76
Score = 43.0 bits (101), Expect = 7e-06
Identities = 17/41 (41%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
+ +VM D TG S+GFGF+TF+ ++V++V + H+L+G
Sbjct: 26 TDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE-HILDG 65
>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction
only].
Length = 235
Score = 46.0 bits (108), Expect = 7e-06
Identities = 29/115 (25%), Positives = 46/115 (40%), Gaps = 10/115 (8%)
Query: 190 SSMINDESQL--DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDR 247
+I D D + + A D +VK L ++N D +G LH A
Sbjct: 58 LKLIVDRHLAARDLDGRLPLHSAASKGDDKIVKLLLAS-GADVNAKDADGDTPLHLAALN 116
Query: 248 GHLK-----VVQHLIEK--CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGA 295
G+ V + L+E N+ D DG+ L +A D++E L+ +GA
Sbjct: 117 GNPPEGNIEVAKLLLEAGADLDVNNLRDEDGNTPLHWAALNGDADIVELLLEAGA 171
Score = 44.4 bits (104), Expect = 2e-05
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 220 KQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA- 278
L + D ++ D +G LH A +G K+V+ L+ GADVN D+DGD L A
Sbjct: 56 LLLKLIVDRHLAARDLDGRLPLHSAASKGDDKIVKLLLAS-GADVNAKDADGDTPLHLAA 114
Query: 279 ----KAIEHTDLIEYLVNSGAHSSN 299
+ ++ + L+ +GA
Sbjct: 115 LNGNPPEGNIEVAKLLLEAGADLDV 139
Score = 29.4 bits (65), Expect = 1.9
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 198 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLI 257
D++ WA +V+ L + + N + G+ L A G +++V+ L+
Sbjct: 142 LRDEDGNTPLHWAALNGDADIVELLLEAGA-DPNSRNSYGVTALDPAAKNGRIELVKLLL 200
Query: 258 EK 259
+K
Sbjct: 201 DK 202
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 42.9 bits (101), Expect = 8e-06
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNSQV 56
+M DK T S+GFGFV F++ V V + H L+G + +P Q
Sbjct: 31 IMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGRTIDPKPCTPRGMQP 82
>gnl|CDD|222984 PHA03100, PHA03100, ankyrin repeat protein; Provisional.
Length = 422
Score = 46.2 bits (110), Expect = 1e-05
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 226 KDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD 285
IN D G LH+A + + V++L++ GA+ N+ + GD L A + +
Sbjct: 181 YGVPINIKDVYGFTPLHYAVYNNNPEFVKYLLDL-GANPNLVNKYGDTPLHIAILNNNKE 239
Query: 286 LIEYLVNSGA 295
+ + L+N+G
Sbjct: 240 IFKLLLNNGP 249
Score = 28.9 bits (65), Expect = 3.7
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 229 NINQLDENGLNCLHWACDRGH-----LKVVQHLIEKCGADVNVTDSDGDYGLDYA--KAI 281
+IN +N LH+ + + ++V+ L+E GA+VN D++G L YA K
Sbjct: 60 DINSSTKNNSTPLHYLSNIKYNLTDVKEIVKLLLEY-GANVNAPDNNGITPLLYAISKKS 118
Query: 282 EHTDLIEYLVNSGA 295
++EYL+++GA
Sbjct: 119 NSYSIVEYLLDNGA 132
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM1 in hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 78
Score = 42.4 bits (100), Expect = 1e-05
Identities = 17/37 (45%), Positives = 22/37 (59%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
VM D NT S+GFGFVTF + VD + H ++G
Sbjct: 31 VMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDG 67
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 77
Score = 42.4 bits (100), Expect = 1e-05
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS 51
V D TG SKGFGFV F + E KV S H+++G ++ +S
Sbjct: 31 VKKDPKTGQSKGFGFVRFADYEDQVKVLSQ-RHMIDGRWCDVKIPNS 76
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 42.2 bits (99), Expect = 1e-05
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
++ ++ D TG S+GFGFV F++ +V+KV H L+G
Sbjct: 26 VDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLDG 66
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 41.9 bits (98), Expect = 2e-05
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
+ ++ D NTG S+GFGF+ F++ +V+KV H L+G
Sbjct: 28 DCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDG 67
>gnl|CDD|205784 pfam13606, Ank_3, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities.
Length = 30
Score = 40.3 bits (95), Expect = 2e-05
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 236 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV 266
+G LH A G+L++V+ L+E GAD+N
Sbjct: 1 DGNTPLHLAARNGNLELVKLLLEH-GADINA 30
>gnl|CDD|197603 smart00248, ANK, ankyrin repeats. Ankyrin repeats are about 33
amino acids long and occur in at least four consecutive
copies. They are involved in protein-protein
interactions. The core of the repeat seems to be an
helix-loop-helix structure.
Length = 30
Score = 40.3 bits (95), Expect = 3e-05
Identities = 14/31 (45%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 236 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV 266
+G LH A + G+L+VV+ L++K GAD+N
Sbjct: 1 DGRTPLHLAAENGNLEVVKLLLDK-GADINA 30
>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 = 41.4 bits (98), Expect = 3e-05
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKV 31
+A V+ D+ TG S+GFGFV + E +
Sbjct: 28 SARVITDRETGRSRGFGFVEMETAEEANAA 57
>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 = 40.4 bits (95), Expect = 6e-05
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
+ DK T +GF F+TF ++E V K+ T HV+ G ++ ++
Sbjct: 28 EIELPMDKKTNKRRGFCFITFDSEEPVKKILETQFHVIGGKKVEVK 73
>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 = 40.3 bits (95), Expect = 7e-05
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKV------FSTDSHVLEGSRLSIQPS 49
A ++ DK TG SKG FV F+ KE+ K L+G RL + +
Sbjct: 30 ARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 82
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 40.3 bits (94), Expect = 8e-05
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
A V+ DK TG +GFGFV FQN ++ DK H + G R+ ++
Sbjct: 29 AEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHPINGHRVEVK 73
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells, and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1) and has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
It represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 39.6 bits (92), Expect = 9e-05
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSH 37
+A +MFDK T +GFGFVTF++++ V+KV H
Sbjct: 28 DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFH 63
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 40.0 bits (93), Expect = 9e-05
Identities = 17/41 (41%), Positives = 26/41 (63%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
++ ++ D TG S+GFGFV F++ +VDKV H L+G
Sbjct: 27 LDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDG 67
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 11 TGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
G+SKG+GFVTF+ +E +K+ + + G +L+I P
Sbjct: 39 AGVSKGYGFVTFETQEDAEKILAMGNLNFRGKKLNIGP 76
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSIQ 47
+M D TG S+GFGFVTF++ ++A + + LEG + ++
Sbjct: 31 VLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVE 76
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 39.6 bits (92), Expect = 1e-04
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 10/56 (17%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNSQVKKKI 60
+M D+ +G +GF FVTF + ++VDK+ H + G HN +V+K +
Sbjct: 32 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG----------HNCEVRKAL 77
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRL 44
+ ++ D TG SKGF FV F+++E +K + L G L
Sbjct: 26 ESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 38.8 bits (90), Expect = 2e-04
Identities = 18/41 (43%), Positives = 25/41 (60%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
++ ++ D TG S+GFGFV F+ E+VDKV H L G
Sbjct: 26 VDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNG 66
>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 = 38.6 bits (90), Expect = 2e-04
Identities = 14/42 (33%), Positives = 27/42 (64%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR 43
+A VM+D +G S+G+GFV+F++++ + + + GSR
Sbjct: 28 DARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSR 69
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 38.4 bits (89), Expect = 3e-04
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLE 40
VM D T S+GFGFVTF ++ VDKV + H L+
Sbjct: 32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 41.8 bits (98), Expect = 3e-04
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 231 NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 290
N D +G LH AC GH++VV+ L+E GAD + D DG L+ A+ ++++ L
Sbjct: 109 NCRDYDGRTPLHIACANGHVQVVRVLLE-FGADPTLLDKDGKTPLELAEENGFREVVQLL 167
>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 = 38.3 bits (90), Expect = 3e-04
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 8 DKNTGLSKGFGFVTFQNKE 26
DK TG S+GF FVTF +E
Sbjct: 34 DKETGQSRGFAFVTFHTRE 52
>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 = 38.4 bits (90), Expect = 3e-04
Identities = 12/22 (54%), Positives = 18/22 (81%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKE 26
V++D+ TG S+GFGFV F++ E
Sbjct: 31 VVYDQKTGRSRGFGFVYFESVE 52
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 2 (Musashi-2 ) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 76
Score = 38.1 bits (88), Expect = 3e-04
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
VM D T S+GFGFVTF + +VDKV + H L+ +I P
Sbjct: 31 VMRDPTTKRSRGFGFVTFADPASVDKVLAQPHHELDSK--TIDP 72
>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 = 37.8 bits (88), Expect = 5e-04
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDK 30
A V+ D+ TG S+GFG+V F++ E K
Sbjct: 29 ARVITDRETGRSRGFGYVDFESPEDAKK 56
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 37.7 bits (88), Expect = 5e-04
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 8 DKNTGLSKGFGFVTFQNK-EAVDKVFSTDSHVLEGSRLSIQ 47
D+ T S+GF FV F +K +A D + + D L+G L +Q
Sbjct: 33 DRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRVQ 73
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 37.7 bits (87), Expect = 5e-04
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNSQVKKKI 60
VM D+ +G +GF FVTF + + VDK+ H + + HN +VKK +
Sbjct: 32 VMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTI----------NGHNCEVKKAL 77
>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 = 36.9 bits (86), Expect = 9e-04
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 6 MFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ 47
+ G SKGF FV F++ E +K + L+G +L +
Sbjct: 30 IVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, and is an abundant eukaryotic nuclear
RNA-binding protein that may modulate splice site
selection in pre-mRNA splicing. hnRNP A1 has been
characterized as a splicing silencer, often acting in
opposition to an activating hnRNP H. It silences exons
when bound to exonic elements in the alternatively
spliced transcripts of c-src, HIV, GRIN1, and
beta-tropomyosin. hnRNP A1 can shuttle between the
nucleus and the cytoplasm. Thus, it may be involved in
transport of cellular RNAs, including the packaging of
pre-mRNA into hnRNP particles and transport of poly A+
mRNA from the nucleus to the cytoplasm. The cytoplasmic
hnRNP A1 has high affinity with AU-rich elements,
whereas the nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 81
Score = 37.4 bits (86), Expect = 0.001
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
VM D NT S+GFGFVT+ + E VD + H ++G
Sbjct: 34 VMRDPNTKRSRGFGFVTYSSVEEVDAAMNARPHKVDG 70
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 2 (Musashi-2) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 79
Score = 37.0 bits (85), Expect = 0.001
Identities = 18/36 (50%), Positives = 25/36 (69%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSH 37
+A +MFDK T +GFGFVTF+N++ V+KV H
Sbjct: 32 DAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFH 67
>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 = 36.4 bits (85), Expect = 0.002
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 31
+A VM D + G SKGFGFV F+N EA K
Sbjct: 29 TSAKVMKD-DEGKSKGFGFVNFENHEAAQKA 58
>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 = 36.5 bits (85), Expect = 0.002
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
+M D +TG SKGF F+++ + EA D
Sbjct: 34 IMRDPDTGNSKGFAFISYDSFEASDA 59
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 37.7 bits (87), Expect = 0.002
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSDSHNS 54
++A V+ D+ TG S+GFGFV F ++ A S D L G + + P++ S
Sbjct: 62 VDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 38.8 bits (89), Expect = 0.002
Identities = 20/109 (18%), Positives = 40/109 (36%), Gaps = 2/109 (1%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VFSTDSHVLEGSRLSIQPSDSHNSQVKKK 59
++ D+ TG S+GF FV F+++E+ +K + + LEG L +Q + + +
Sbjct: 143 KRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSEL 202
Query: 60 IETKET-ASFSRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQ 107
+ + Y+ +L K L +
Sbjct: 203 SNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGD 251
>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 = 35.7 bits (83), Expect = 0.002
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE 26
+ D TG SKG+GF+ F + E
Sbjct: 27 FVQLQRDPETGRSKGYGFIQFADAE 51
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 35.8 bits (82), Expect = 0.003
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 10/59 (16%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNSQVKKKIETK 63
++ D+ +G +GFGFVTF + + VDK+ H + G HN++V+K + +
Sbjct: 32 IITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTING----------HNAEVRKALSRQ 80
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are 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.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 35.7 bits (83), Expect = 0.003
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI 46
++ DK TG KGF ++ F +K +V+ + G ++ +
Sbjct: 31 ILCDKFTGQPKGFAYIEFLDKSSVENALLLNESEFRGRQIKV 72
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM1 of hnRNP A2/B1 which is an RNA trafficking
response element-binding protein that interacts with
the hnRNP A2 response element (A2RE). Many mRNAs, such
as myelin basic protein (MBP), myelin-associated
oligodendrocytic basic protein (MOBP), carboxyanhydrase
II (CAII), microtubule-associated protein tau, and
amyloid precursor protein (APP) are trafficked by hnRNP
A2/B1. hnRNP A2/B1 also functions as a splicing factor
that regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Moreover, the overexpression of hnRNP A2/B1 has been
described in many cancers. It functions as a nuclear
matrix protein involving in RNA synthesis and the
regulation of cellular migration through alternatively
splicing pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 81
Score = 35.9 bits (82), Expect = 0.003
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
VM D + S+GFGFVTF VD + H ++G
Sbjct: 34 VMRDPASKRSRGFGFVTFSCMNEVDAAMAARPHTIDG 70
>gnl|CDD|165205 PHA02874, PHA02874, ankyrin repeat protein; Provisional.
Length = 434
Score = 38.4 bits (89), Expect = 0.003
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 229 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 288
++N D LH+A +G L+ ++ L E GADVN+ D +G Y + A D+I+
Sbjct: 116 DVNIKDAELKTFLHYAIKKGDLESIKMLFEY-GADVNIEDDNGCYPIHIAIKHNFFDIIK 174
Query: 289 YLVNSGAH 296
L+ GA+
Sbjct: 175 LLLEKGAY 182
Score = 35.3 bits (81), Expect = 0.033
Identities = 30/110 (27%), Positives = 50/110 (45%), Gaps = 9/110 (8%)
Query: 196 ESQLDDNEKN------IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH 249
+ +D N K+ ++ K+G L+ + D NI D+NG +H A
Sbjct: 112 DCGIDVNIKDAELKTFLHYAIKKGDLESIKMLFEYGADVNIE--DDNGCYPIHIAIKHNF 169
Query: 250 LKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGAHSSN 299
+++ L+EK GA NV D++G+ L A I+ L++ G H N
Sbjct: 170 FDIIKLLLEK-GAYANVKDNNGESPLHNAAEYGDYACIKLLIDHGNHIMN 218
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 71
Score = 35.3 bits (82), Expect = 0.004
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 15 KGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI 46
+ F FVTF + E + + H+++G + +
Sbjct: 37 RAFAFVTFADPEVAQSLCG-EDHIIKGVSVHV 67
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 35.0 bits (81), Expect = 0.004
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE 26
+A V+ D TG SKG+GFV+F KE
Sbjct: 28 DARVVKDMQTGKSKGYGFVSFVKKE 52
>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 = 34.9 bits (81), Expect = 0.004
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEA 27
+ ++ D++TG KG+GF F++ E
Sbjct: 27 SFRLVTDRDTGKPKGYGFCEFEDIET 52
>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 = 35.0 bits (81), Expect = 0.005
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRL 44
DK T SKGF FV+F E K +S D + +G RL
Sbjct: 34 DKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQG-RL 70
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 34.9 bits (81), Expect = 0.005
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 13 LSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
L+ GF FVTF++ + + + L G ++S+
Sbjct: 43 LNNGFAFVTFKDASSAENALQLNGTELGGRKISVSL 78
>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 = 34.2 bits (79), Expect = 0.007
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 12 GLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
G SKG+ +V F+N+E+V + D +++G
Sbjct: 37 GKSKGYAYVEFENEESVQEALKLDRELIKG 66
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 34.3 bits (79), Expect = 0.008
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 3 ASVMF--DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI 46
SV DK TG KGFG V F ++E++D D VL G + I
Sbjct: 26 TSVRLATDKETGEFKGFGHVDFADEESLDAALKLDGTVLCGRPIRI 71
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 34.1 bits (79), Expect = 0.009
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKVFSTDSHV-LEGSRLSIQPS 49
K G +GF FV F K+ L G L ++ +
Sbjct: 35 KFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 34.3 bits (79), Expect = 0.010
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS 49
DK T KGF FVT+ E K F+ D V +G L + PS
Sbjct: 37 DKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQGRLLHLLPS 79
>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 = 34.1 bits (79), Expect = 0.011
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE----AVDKVFSTD 35
V+ DK + +GFG+VTF +E A+++ T
Sbjct: 28 RCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTK 65
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 33.9 bits (77), Expect = 0.013
Identities = 17/37 (45%), Positives = 21/37 (56%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG 41
VM D T S+GFGFVT+ E VD S H ++G
Sbjct: 34 VMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDG 70
>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 = 33.8 bits (78), Expect = 0.013
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFST 34
++ +K TG S G+GFV F EA ++ +
Sbjct: 31 IIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
>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 = 33.7 bits (78), Expect = 0.014
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 5 VMFDKNTGLSKGFGFVTFQN----KEAVDKVFSTDSHVLEGSRLSI 46
++ DK TG S+GF FV F + + +D + + D V++G + +
Sbjct: 36 LIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRV 81
>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 = 33.3 bits (77), Expect = 0.015
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
D+N+ SKG +V F ++E+V L G RL QP
Sbjct: 34 DRNSRRSKGVAYVEFYDEESVPLALG-----LTGQRLLGQP 69
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 33.4 bits (77), Expect = 0.016
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKE 26
+++ ++TG SKG+GFV + +K
Sbjct: 31 LVYSESTGESKGYGFVEYASKA 52
>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 = 33.7 bits (78), Expect = 0.017
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQN 24
A V+ DK TG SKG+GFV+F +
Sbjct: 34 QKAKVVRDKRTGKSKGYGFVSFSD 57
>gnl|CDD|222980 PHA03095, PHA03095, ankyrin-like protein; Provisional.
Length = 471
Score = 35.8 bits (83), Expect = 0.021
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 230 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 271
IN + G LH+A + + + LI GAD+N SDG
Sbjct: 250 INARNRYGQTPLHYAAVFNNPRACRRLI-ALGADINAVSSDG 290
Score = 32.3 bits (74), Expect = 0.27
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 229 NINQLDENGLNCLH-WACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD-YAKAIE-HTD 285
++N + G LH + + L V++ LI K GADVN D G L Y +
Sbjct: 75 DVNAPERCGFTPLHLYLYNATTLDVIKLLI-KAGADVNAKDKVGRTPLHVYLSGFNINPK 133
Query: 286 LIEYLVNSGA 295
+I L+ GA
Sbjct: 134 VIRLLLRKGA 143
Score = 29.6 bits (67), Expect = 2.2
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 240 CLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD-YAKAIEHTDLIEYLVNSGA 295
LH++ ++ +V+ L+E GADVN + G L Y D+I+ L+ +GA
Sbjct: 54 YLHYSSEKV-KDIVRLLLEA-GADVNAPERCGFTPLHLYLYNATTLDVIKLLIKAGA 108
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 33.5 bits (77), Expect = 0.021
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQ--PSDS 51
+V+ DK TG+ KG F+T+ +E+ K S + L G IQ P+DS
Sbjct: 36 TVLKDKYTGMHKGCAFLTYCARESALKAQSALHEQKTLPGMNRPIQVKPADS 87
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 33.2 bits (76), Expect = 0.023
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
+++ DK +G KGF ++ F +KE+V + D + G ++ + P
Sbjct: 30 TILCDKFSGHPKGFAYIEFSDKESVRTALALDESLFRGRQIKVMP 74
>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 = 33.1 bits (76), Expect = 0.024
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKE-AVDKVFSTDSHVLEGSRLSIQP 48
V DK +G SKGF +V F + E AV D V +G + I P
Sbjct: 34 VAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHILP 78
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear
molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 32.7 bits (75), Expect = 0.028
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSI 46
N V+ D T KG+GFVT N +EA + S + + L G L +
Sbjct: 30 NVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQV 75
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 32.5 bits (75), Expect = 0.029
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ 47
K TG SKG+ FV F++ E V T ++++L L +
Sbjct: 35 KKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of
Oskar (Osk) expression. It mediates repression by
binding to regulatory Bruno response elements (BREs) in
the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 79
Score = 32.7 bits (74), Expect = 0.032
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQN 24
++A V DK T LSK FGFV++ N
Sbjct: 32 ISAKVFIDKQTNLSKCFGFVSYDN 55
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes.
Since the Hu proteins share high homology with the
Drosophila embryonic lethal abnormal vision (ELAV)
protein, the Hu family is sometimes referred to as the
ELAV family. Drosophila ELAV is exclusively expressed
in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress.
Moreover, HuR has an anti-apoptotic function during
early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Hu proteins
perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 79
Score = 32.7 bits (75), Expect = 0.032
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 2 NASVMFDKNTGLSKGFGFVTF-QNKEAVDKVFSTDSHVLEGS 42
+ ++ D TGLS+G GF+ F + EA + + + + G+
Sbjct: 29 TSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPGA 70
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2
protein homolog alpha (TRA-2 alpha) and similar
proteins. This subgroup corresponds to the RRM of
TRA2-alpha or TRA-2-alpha, also termed transformer-2
protein homolog A, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein (SRp40) that
specifically binds to gonadotropin-releasing hormone
(GnRH) exonic splicing enhancer on exon 4 (ESE4) and is
necessary for enhanced GnRH pre-mRNA splicing. It
strongly stimulates GnRH intron A excision in a
dose-dependent manner. In addition, TRA2-alpha can
interact with either 9G8 or SRp30c, which may also be
crucial for ESE-dependent GnRH pre-mRNA splicing.
TRA2-alpha contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 79
Score = 32.6 bits (74), Expect = 0.033
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 7/50 (14%)
Query: 4 SVMFDKNTGLSKGFGFVTFQ----NKEAVDKVFSTDSHVLEGSRLSIQPS 49
+V++D+ TG S+GF FV F+ +KEA++ + L+G R+ + S
Sbjct: 30 NVVYDQRTGRSRGFAFVYFERIDDSKEAMEH---ANGMELDGRRIRVDYS 76
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 33.4 bits (76), Expect = 0.035
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVD 29
A + DK+TG +KG GFV F+++ +
Sbjct: 31 ALPVIDKSTGRAKGTGFVCFKDQYTYN 57
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 32.8 bits (75), Expect = 0.035
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE 26
N ++ DK TG S GFGFV +Q+ E
Sbjct: 29 NCKIVRDKRTGYSYGFGFVDYQSAE 53
>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 = 32.3 bits (74), Expect = 0.036
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSH 37
D ++G KGFG+V F ++EA
Sbjct: 33 DPDSGRPKGFGYVEFSSQEAAQAALDALGG 62
>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 = 32.3 bits (74), Expect = 0.039
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI 46
++ D+ TG S G+GFV + ++ K +T + + RL +
Sbjct: 32 IVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKV 74
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 32.5 bits (74), Expect = 0.040
Identities = 10/45 (22%), Positives = 24/45 (53%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
+++ DK +G KG+ ++ F +++V+ + D G + + P
Sbjct: 30 TILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSFRGRVIKVLP 74
>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 = 32.5 bits (74), Expect = 0.040
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 9 KNTG--LSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS 49
K G LS GFGFV F+ KE D VL+G L ++ S
Sbjct: 39 KRPGQTLSMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFS 82
>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 = 32.6 bits (75), Expect = 0.042
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSH-VLEGSRLSIQPS 49
LS G+GFV F++KEA K VL+G L ++ S
Sbjct: 40 GPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHALELKLS 82
>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 = 32.7 bits (74), Expect = 0.042
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFSTDSHVLEGS 42
+N+ V+ D+ TGLS+G F+ F + EA + + S + H GS
Sbjct: 28 INSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGS 70
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 32.5 bits (74), Expect = 0.042
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVD 29
V+ D+ T S+GFGFVTF+N +
Sbjct: 32 VVKDRETQRSRGFGFVTFENPDDAK 56
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate
nucleolin. This subfamily corresponds to the RRM4 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 78
Score = 32.3 bits (73), Expect = 0.042
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKE 26
+ A ++ D++TG SKGFGFV F ++E
Sbjct: 25 IAARIVTDRDTGSSKGFGFVDFSSEE 50
>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 = 32.2 bits (74), Expect = 0.045
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKE 26
A VM D+ G SKGFGFV F + E
Sbjct: 31 AKVMTDEK-GRSKGFGFVCFSSPE 53
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 32.2 bits (74), Expect = 0.046
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
+ DK T KG+GFV F + EA K
Sbjct: 32 AILDKKTNKCKGYGFVDFDSPEAALK 57
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of
specific mRNAs during gametogenesis. .
Length = 81
Score = 32.5 bits (74), Expect = 0.048
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 11 TGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPS 49
G+SKG+GFVTF+ +E K+ + +L+I +
Sbjct: 39 AGVSKGYGFVTFETQEDAQKILQEANRLCFRDKKLNIGQA 78
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM2 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 = 80
Score = 32.1 bits (73), Expect = 0.050
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 3 ASVMFDKNTGLSKGFGFVTF 22
A +M D TG+S+G+GFV F
Sbjct: 32 AKIMTDPVTGVSRGYGFVRF 51
>gnl|CDD|165157 PHA02795, PHA02795, ankyrin-like protein; Provisional.
Length = 437
Score = 34.6 bits (79), Expect = 0.053
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 229 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 278
+INQLD G L+ A G++ +V L+E GA+VN S+G LD A
Sbjct: 213 DINQLDAGGRTLLYRAIYAGYIDLVSWLLEN-GANVNAVMSNGYTCLDVA 261
>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 = 34.8 bits (80), Expect = 0.054
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 34
A VM D+ G+S+GFGFV F N E ++ +
Sbjct: 315 AKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345
Score = 30.9 bits (70), Expect = 0.93
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 14/85 (16%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKE----AVDKVFSTD-SHVLEGSRLSIQPSDSHNSQVK 57
A+VM D + G S+GF FV F+ E AV+++ EG +L + + +
Sbjct: 208 AAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGR---AQKRAE 263
Query: 58 KKIETKETASFSRMAENMEDRFNQA 82
++ E + + E ++R +A
Sbjct: 264 REAELRR-----KFEELQQERKMKA 283
Score = 27.8 bits (62), Expect = 8.0
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
V D+N G S+G+GFV F+ +E+
Sbjct: 120 VATDEN-GKSRGYGFVHFEKEESAKA 144
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 34.8 bits (80), Expect = 0.056
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 244 ACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGA 295
A R L ++ L+ K G +V+ D G L A A +H D++ L+ +GA
Sbjct: 629 AAKRNDLTAMKELL-KQGLNVDSEDHQGATALQVAMAEDHVDMVRLLIMNGA 679
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 85
Score = 32.3 bits (73), Expect = 0.056
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLE--GSRLSIQPSD 50
+M +K++G S+GF FV F + + + + H L G ++S+ SD
Sbjct: 35 LMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLMILGQKVSMHYSD 82
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important
role in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 80
Score = 31.9 bits (72), Expect = 0.063
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
D T +GF F+TF+ ++ V KV H + GS+ I+
Sbjct: 39 DPKTNKRRGFVFITFKEEDPVKKVLEKKFHNVSGSKCEIK 78
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2
and forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3
or NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2
protein. Its message is detected exclusively in
post-mitotic regions of embryonic brain. Like RBFOX1,
both RBFOX2 and RBFOX3 bind to the hexanucleotide
UGCAUG elements and modulate brain and muscle-specific
splicing of exon EIIIB of fibronectin, exon N1 of
c-src, and calcitonin/CGRP. Members in this family also
harbor one RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 76
Score = 31.6 bits (72), Expect = 0.065
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 14 SKGFGFVTFQNKEAVDK 30
SKGFGFVTF N D+
Sbjct: 39 SKGFGFVTFANSADADR 55
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 31.6 bits (72), Expect = 0.081
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 5 VMFDKNTGLSKGFGFVTF 22
+M K TG S+GF FV F
Sbjct: 35 LMRRKTTGASRGFAFVEF 52
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the
RRM of Star-PAP, also termed RNA-binding motif protein
21 (RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs
to the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both,
the poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione
S-transferase (GST)-PIPKIalpha. Star-PAP preferentially
uses ATP as a nucleotide substrate and possesses PAP
activity that is stimulated by PtdIns4,5P2. It contains
an N-terminal C2H2-type zinc finger motif followed by
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
split PAP domain linked by a proline-rich region, a PAP
catalytic and core domain, a PAP-associated domain, an
RS repeat, and a nuclear localization signal (NLS). .
Length = 74
Score = 31.6 bits (72), Expect = 0.081
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
+V+ DK+ G+ + V F +KE VDKV S H L G RL ++P
Sbjct: 30 MNVIMDKDKGV---YAIVEFDSKEGVDKVLSEPQHTLNGHRLRVRP 72
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 31.6 bits (71), Expect = 0.084
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNK 25
+A V+ D TG SKG+GFV+F NK
Sbjct: 30 DARVVKDMATGKSKGYGFVSFYNK 53
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily
corresponds to the RRM2 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 = 79
Score = 31.6 bits (72), Expect = 0.093
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS 49
S+ D+ TG SKGF ++ F++ + V+K D L G L + +
Sbjct: 32 RVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVDEA 79
>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 = 31.1 bits (71), Expect = 0.10
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAV 28
+ D TG SKGF +VT+ N +
Sbjct: 31 LKRDPYTGKSKGFAYVTYSNPASA 54
>gnl|CDD|165207 PHA02876, PHA02876, ankyrin repeat protein; Provisional.
Length = 682
Score = 33.9 bits (77), Expect = 0.11
Identities = 20/78 (25%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 216 DMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL 275
++L+ ++ ++N D + +H+A +RG+ K+V L+ GADVN+ D L
Sbjct: 157 ELLIAEMLLEGGADVNAKDIYCITPIHYAAERGNAKMVNLLLSY-GADVNIIALDDLSVL 215
Query: 276 DYAKAIEHTDLIEYLVNS 293
+ A ++ D I+ ++++
Sbjct: 216 ECAVDSKNIDTIKAIIDN 233
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and
plant flowering time control protein FCA. This
subfamily corresponds to the RRM1 and RRM2 domains of
the CUGBP1 and ETR-3-like factors (CELF) as well as
plant flowering time control protein FCA. CELF, also
termed BRUNOL (Bruno-like) proteins, is a family of
structurally related RNA-binding proteins involved in
regulation of pre-mRNA splicing in the nucleus, and
control of mRNA translation and deadenylation in the
cytoplasm. The family contains six members: CELF-1
(also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP),
CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2,
NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1,
CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5)
and CELF-6 (BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both, sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 31.0 bits (71), Expect = 0.12
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQPSDSHNSQVK 57
+++ DK+TG SKG FV F ++E K + G+ S QVK
Sbjct: 29 VTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGA--------SRPLQVK 77
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 31.0 bits (71), Expect = 0.13
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 6 MFDKNTGLSKGFGFVTFQNKEAVDK 30
M D + GL++G+ FVT+ NKEA +
Sbjct: 34 MMDFS-GLNRGYAFVTYTNKEAAQR 57
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 31.0 bits (71), Expect = 0.13
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
V D+N G SKG+GFV F+ +EA +
Sbjct: 34 VATDEN-GGSKGYGFVHFETEEAAVR 58
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog
of DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. 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 = 82
Score = 30.9 bits (70), Expect = 0.14
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 11 TGLSKGFGFVTFQNKEAVDKVFSTDSHV-LEGSRLSIQPS 49
TG+SKG+GFV+F + V K+ +S + G +L + P+
Sbjct: 42 TGVSKGYGFVSFYDDVDVQKI--VESQINFHGKKLKLGPA 79
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 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,
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 = 79
Score = 30.7 bits (69), Expect = 0.15
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
+M D TGL++G+ FVTF KEA +
Sbjct: 33 LMMDPLTGLNRGYAFVTFCTKEAAQE 58
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM3 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR),
both of which belong to the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) family of
RNA-binding proteins that have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contain
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are important for localization in
the cytoplasm. The splicing activation or repression
activity of CELF-2 on some specific substrates is
mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2,
can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 31.2 bits (70), Expect = 0.16
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-STDSHVLEGSRLSIQPSDSHNS 54
++A V DK T LSK FGFV++ N + + + + RL +Q S N
Sbjct: 35 VSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSKND 89
>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 = 30.8 bits (70), Expect = 0.16
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
DK TG SKG FV F EA+ K +L+G +++++
Sbjct: 35 DKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKINVE 74
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 31.0 bits (70), Expect = 0.16
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 3 ASVMFDKNTGLSKGFGFVTF----QNKEAVDKVFSTDSHVLEGSRLSI 46
A V+ D TG S+G+GFVTF +EA+ K+ + L G L +
Sbjct: 29 AVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNK---KLHGRILRL 73
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 30.8 bits (69), Expect = 0.17
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNK 25
+A V+ D TG SKG+GFV+F NK
Sbjct: 30 DARVVKDMATGKSKGYGFVSFFNK 53
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 30.2 bits (69), Expect = 0.18
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKEAVDKVF-STDSHVLEGSRL 44
V +N +GF FV F + E + + VL+G L
Sbjct: 27 GVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68
>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 = 32.9 bits (75), Expect = 0.19
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSH-NSQVKKKIET 62
D+N+ SKG +V F + E+V K + +L G + +Q S + N K
Sbjct: 124 DRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQ 179
Score = 32.2 bits (73), Expect = 0.35
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 5 VMFDKNTGLSKGFGFVTF----QNKEAVDKV 31
+ D TG SKGFGF+ F + KEA++ +
Sbjct: 218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
>gnl|CDD|241083 cd12639, RRM3_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
RRM3 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,
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 contains three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
strongly expressed in kidney, brain, and testis, is
also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in an muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element,
MSE2. CELF-6 also promotes skipping of exon 11 of
insulin receptor, a known target of CELF activity that
is expressed in kidney. In 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 = 79
Score = 30.6 bits (69), Expect = 0.19
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQN 24
++A V D+ T SK FGFV+F N
Sbjct: 32 ISAKVFVDRATNQSKCFGFVSFDN 55
>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 = 30.6 bits (69), Expect = 0.21
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFSTDSHVLEGSRLSIQ 47
+ +++ DK+TGL +G FV + + EA + S + + GS + +
Sbjct: 28 VQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGSTMPLS 75
>gnl|CDD|238242 cd00423, Pterin_binding, Pterin binding enzymes. This family
includes dihydropteroate synthase (DHPS) and
cobalamin-dependent methyltransferases such as
methyltetrahydrofolate, corrinoid iron-sulfur protein
methyltransferase (MeTr) and methionine synthase (MetH).
DHPS, a functional homodimer, catalyzes the
condensation of p-aminobenzoic acid (pABA) in the de
novo biosynthesis of folate, which is an essential
cofactor in both nucleic acid and protein biosynthesis.
Prokaryotes (and some lower eukaryotes) must synthesize
folate de novo, while higher eukaryotes are able to
utilize dietary folate and therefore lack DHPS.
Sulfonamide drugs, which are substrate analogs of pABA,
target DHPS. Cobalamin-dependent methyltransferases
catalyze the transfer of a methyl group via a methyl-
cob(III)amide intermediate. These include MeTr, a
functional heterodimer, and the folate binding domain of
MetH.
Length = 258
Score = 32.2 bits (74), Expect = 0.22
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 264 VNVTD---SDGDYGLDYAKAIEHTDLIEYLVNSGAH 296
+NVT SDG L KA+EH +V GA
Sbjct: 7 LNVTPDSFSDGGKFLSLDKALEH---ARRMVEEGAD 39
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 29.9 bits (67), Expect = 0.26
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 9 KNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSIQ 47
++ L +GFGFV F + ++A D V+ D L R++I+
Sbjct: 27 RDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERVTIE 66
>gnl|CDD|222939 PHA02878, PHA02878, ankyrin repeat protein; Provisional.
Length = 477
Score = 32.2 bits (73), Expect = 0.32
Identities = 30/120 (25%), Positives = 56/120 (46%), Gaps = 15/120 (12%)
Query: 187 VNVSSMINDESQLDDNEKNIY-----EWAKEGKLDMLVKQLTKL---KDFNINQLDENGL 238
V + +I L + KNI K+ K D++ ++TKL +IN D +
Sbjct: 114 VEIFKII-----LTNRYKNIQTIDLVYIDKKSKDDIIEAEITKLLLSYGADINMKDRHKG 168
Query: 239 NC-LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGAHS 297
N LH+A + ++ + L+ GA+VN+ D + L +A + ++ L+ +GA +
Sbjct: 169 NTALHYATENKDQRLTELLLSY-GANVNIPDKTNNSPLHHAVKHYNKPIVHILLENGAST 227
>gnl|CDD|202118 pfam02126, PTE, Phosphotriesterase family.
Length = 308
Score = 31.7 bits (72), Expect = 0.39
Identities = 22/115 (19%), Positives = 42/115 (36%), Gaps = 13/115 (11%)
Query: 187 VNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQL-----DENGLNCL 241
V++S ++ D+ K + E A G T+L + ++ D+ + +
Sbjct: 181 VDLSRVVIGHCDDIDDLKYLLELAALGCYLGYDLFGTELLGYQLSPDIDIPPDQKRIRRV 240
Query: 242 HWACDRGHLK--VVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 294
H DRG+ ++ H I G Y+ + T++I L G
Sbjct: 241 HALVDRGYEDRILLSHDIT-TKFRSMKYG-----GHGYSHILLLTNVIPKLRQRG 289
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a CCCH class of
zinc finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 29.3 bits (66), Expect = 0.40
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 15 KGFGFVTFQNKEAVDKVFSTDS-HVLEGSRLSI 46
+ FGFVTF+N E V ++ S + H + GSR+ +
Sbjct: 37 RMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 29.3 bits (66), Expect = 0.44
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 3 ASVMFDKNTGLSKGFGFVTF 22
S++ DKNTG SKGFG+V F
Sbjct: 30 VSIVKDKNTGESKGFGYVKF 49
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 29.2 bits (66), Expect = 0.46
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 9 KNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSIQPS 49
+ L GFGFV F++ ++A D V+ + L G R+ ++ +
Sbjct: 27 REINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHA 68
>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 = 29.1 bits (66), Expect = 0.48
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 16 GFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSIQPS 49
GF FV F++ ++A D V + D + G+R+ ++ S
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELS 71
>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 = 28.2 bits (64), Expect = 0.68
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS 49
+ K GF FV F +EA +K + + G L + S
Sbjct: 15 KLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 86
Score = 29.3 bits (65), Expect = 0.68
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSR---LSIQPSDSH 52
N V+ D NT KGFGFVT N EA + S + + L G R +S + + +H
Sbjct: 32 NVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRL-GDRVLQVSFKTNKTH 85
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 28.8 bits (65), Expect = 0.70
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
D N G K F FVTF+++ +V ++ +L G RL
Sbjct: 36 DPN-GKPKSFAFVTFKHEVSVP--YAIQ--LLNGIRL 67
>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 = 28.9 bits (65), Expect = 0.71
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
DK TG S G+GFV + + E +K +T L G RL
Sbjct: 36 DKVTGQSLGYGFVNYVDPEDAEKAINT----LNGLRL 68
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 28.7 bits (65), Expect = 0.76
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVD---KVFS 33
D+ T +G+GFV F ++E D K+ +
Sbjct: 33 DRVTQAHQGYGFVEFLSEEDADYAIKIMN 61
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise
role of PPIase remains unclear. PPIase contains a
conserved N-terminal peptidyl-prolyl cistrans isomerase
(PPIase) motif, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 28.8 bits (65), Expect = 0.79
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 32
+ V+ DK TG S + F+ F+ KE ++ +
Sbjct: 32 SCEVIRDKKTGDSLQYAFIEFETKEDCEEAY 62
>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 = 0.82
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKV-FSTDSHVLEGSRLSI 46
G +GF FV + E ++ + + H L+GS + +
Sbjct: 38 APNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 30.8 bits (70), Expect = 0.82
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 159 EDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLD 216
+D + EE W+ ++ S + W++V S ES ++E+ E AK+ K D
Sbjct: 95 DDDDDEEEEWEVEEDEDSDDEGE----WIDVESDKEIESSDSEDEEEKDEAAKKAKED 148
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 28.6 bits (64), Expect = 0.87
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE 26
N V K TG SK +GF+ F N E
Sbjct: 28 NVRVARSKKTGNSKHYGFIQFLNPE 52
>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 = 28.9 bits (64), Expect = 0.87
Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
N V+ D NT KGFGFVT N E ++ L G RL
Sbjct: 30 NVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS----LNGYRL 68
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 80
Score = 28.6 bits (63), Expect = 1.00
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 34
++ + DKNT KG+GFV F + A K ++
Sbjct: 32 VSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 28.5 bits (64), Expect = 1.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKV 31
K+TG KGF F+ F+ E K
Sbjct: 35 KHTGDIKGFAFIEFETPEEAQKA 57
>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 = 28.4 bits (64), Expect = 1.0
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVD 29
D TGLSKG+ F + + D
Sbjct: 35 DSATGLSKGYAFCEYLDPSVTD 56
>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 = 28.8 bits (65), Expect = 1.1
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 8 DKNTGLSKGFGFVTFQNKE----AVD 29
DK TG SKGF F+ ++++ AVD
Sbjct: 44 DKKTGKSKGFAFLAYEDQRSTILAVD 69
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 28.4 bits (64), Expect = 1.1
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 3 ASVMFDKNTGLSKGFGFVTFQNKE 26
A V+ D+N G S+G+GFV F ++
Sbjct: 32 AKVVLDQN-GNSRGYGFVRFSDES 54
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds 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. It 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, and 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; it binds RNA through its RRM domains. .
Length = 79
Score = 28.4 bits (63), Expect = 1.2
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEA 27
+M D +G ++G+ F+TF KEA
Sbjct: 33 LMMDPLSGQNRGYAFITFCGKEA 55
>gnl|CDD|227845 COG5558, COG5558, Transposase [DNA replication, recombination, and
repair].
Length = 261
Score = 30.3 bits (68), Expect = 1.3
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 17/97 (17%)
Query: 19 FVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNSQVKKK------------IETKETA 66
F+ +E V FS D G+ S+ + + S K+K I+T
Sbjct: 76 FILLLREEGVSGDFSGD-----GTGYSLTITKHYRSNPKRKGKDFRYVFRIIDIDTGMYV 130
Query: 67 SFSRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYA 103
F + +D F +A L S+ K++S +L K+Y+
Sbjct: 131 GFGYSDRSEKDAFEKALGMLKSMGVKVNSISLDKYYS 167
>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 = 28.4 bits (64), Expect = 1.3
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKV 31
G +G+ FVTF+ KE +K
Sbjct: 38 PLKGQPRGYCFVTFETKEEAEKA 60
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 28.5 bits (63), Expect = 1.3
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKE 26
+ S+++D+ + S+GF FV F+N +
Sbjct: 38 DVSIVYDQQSRRSRGFAFVYFENVD 62
>gnl|CDD|240987 cd12543, RRM2_PAR14, RNA recognition motif 2 in vertebrate poly
[ADP-ribose] polymerase 14 (PARP-14). This subgroup
corresponds to the RRM2 of PARP-14, also termed
aggressive lymphoma protein 2, a member of the B
aggressive lymphoma (BAL) family of
macrodomain-containing PARPs. It is expressed in B
lymphocytes and interacts with the IL-4-induced
transcription factor Stat6. It plays a fundamental role
in the regulation of IL-4-induced B-cell protection
against apoptosis after irradiation or growth factor
withdrawal. It mediates IL-4 effects on the levels of
gene products that regulate cell survival,
proliferation, and lymphomagenesis. PARP-14 acts as a
transcriptional switch for Stat6-dependent gene
activation. In the presence of IL-4, PARP-14 activates
transcription by facilitating the binding of Stat6 to
the promoter and release of HDACs from the promoter
with an IL-4 signal. In contrast, in the absence of a
signal, PARP-14 acts as a transcriptional repressor by
recruiting HDACs. Absence of PARP-14 protects against
Myc-induced developmental block and lymphoma. Thus,
PARP-14 may play an important role in Myc-induced
oncogenesis. Additional research indicates that PARP-14
is also a binding partner with phosphoglucose isomerase
(PGI)/ autocrine motility factor (AMF). It can inhibit
PGI/AMF ubiquitination, thus contributing to its
stabilization and secretion. PARP-14 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), three tandem macro domains, and C-terminal
region with sequence homology to PARP catalytic domain.
.
Length = 74
Score = 27.8 bits (62), Expect = 1.4
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 20 VTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
+TF++ E V KV H ++ +S+ P
Sbjct: 45 ITFKDGEDVQKVLKK-QHSIKKEPISVYP 72
>gnl|CDD|238380 cd00739, DHPS, DHPS subgroup of Pterin binding enzymes. DHPS
(dihydropteroate synthase), a functional homodimer,
catalyzes the condensation of p-aminobenzoic acid (pABA)
in the de novo biosynthesis of folate, which is an
essential cofactor in both nucleic acid and protein
biosynthesis. Prokaryotes (and some lower eukaryotes)
must synthesize folate de novo, while higher eukaryotes
are able to utilize dietary folate and therefore lack
DHPS. Sulfonamide drugs, which are substrate analogs of
pABA, target DHPS.
Length = 257
Score = 29.9 bits (68), Expect = 1.5
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 264 VNVTD---SDGDYGLDYAKAIEHTDLIEYLVNSGAH 296
+NVT SDG L KA+ H E ++ GA
Sbjct: 7 LNVTPDSFSDGGRFLSLDKAVAH---AEKMIAEGAD 39
>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 = 27.8 bits (62), Expect = 1.6
Identities = 10/42 (23%), Positives = 16/42 (38%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI 46
+M +++G KGF FV F+ E R+
Sbjct: 30 MMTFEDSGKCKGFAFVDFEEIEFATNALKGKHLNGRALRVEY 71
>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 = 27.6 bits (62), Expect = 1.8
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDK 30
K G KGF FV F +K +K
Sbjct: 34 KPDGKKKGFAFVQFTSKADAEK 55
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 28.1 bits (63), Expect = 1.8
Identities = 7/31 (22%), Positives = 17/31 (54%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 31
++ ++ +K TG G+ FV F ++ ++
Sbjct: 28 LSVKIIRNKLTGGPAGYCFVEFADEATAERC 58
>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 = 27.8 bits (62), Expect = 1.8
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKE 26
++ +++D+ TG KG+GF ++++E
Sbjct: 26 VSFRLVYDRETGKPKGYGFCEYKDQE 51
>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 = 27.5 bits (62), Expect = 1.8
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDK 30
D+ L +G+ +V F++ E +K
Sbjct: 33 DREVNLPRGYAYVEFESPEDAEK 55
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 28.0 bits (63), Expect = 1.9
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 5 VMFDK------NTGLSKGFGFVTFQNKE 26
+M D G SKG+GFV F N E
Sbjct: 41 IMRDLKRVDPNGKGKSKGYGFVEFTNHE 68
>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 = 27.6 bits (62), Expect = 2.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 8 DKNTGLSKGFGFVTFQNKEAV 28
D +TG K FGF F++ E
Sbjct: 35 DPSTGKLKAFGFCEFEDPEGA 55
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 27.5 bits (61), Expect = 2.3
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
++ D T + KGF +V F+++ AV+K
Sbjct: 31 IVRDPKTNVGKGFAYVQFKDENAVEK 56
>gnl|CDD|218658 pfam05616, Neisseria_TspB, Neisseria meningitidis TspB protein.
This family consists of several Neisseria meningitidis
TspB virulence factor proteins.
Length = 502
Score = 29.6 bits (66), Expect = 2.3
Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 196 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQ--LDENGLNCL 241
ESQ++ + +E ++ + D +++N ++ + NG NC
Sbjct: 172 ESQMERLARPYWEMVRKNRNDSY-----YFRNYNFSRCYFNWNGGNCN 214
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 27.3 bits (60), Expect = 2.5
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
N + D T +GF FVT+ ++E V K+ + H + + I+
Sbjct: 28 NIELPMDTKTNERRGFCFVTYTDEEPVQKLLESRYHQIGSGKCEIK 73
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 29.5 bits (66), Expect = 2.6
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVD 29
D TGLSKG+ F +++ D
Sbjct: 330 DIATGLSKGYAFCEYKDPSVTD 351
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 27.3 bits (61), Expect = 2.6
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 9 KNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
+TG +G F+TF+ +EA + + D + G L ++
Sbjct: 34 PDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFLKVE 72
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells. And it also regulates the neurite elongation and
morphological differentiation. HuD specifically bound
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 27.4 bits (60), Expect = 2.7
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
N V+ D NT KGFGFVT N + ++ L G RL
Sbjct: 32 NVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS----LNGYRL 70
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 27.4 bits (61), Expect = 2.7
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 11 TGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQ 47
TG +GFGFV F K+ + F S L G RL ++
Sbjct: 39 TGSHRGFGFVDFITKQDAKRAFKALCHSTHLYGRRLVLE 77
>gnl|CDD|222931 PHA02798, PHA02798, ankyrin-like protein; Provisional.
Length = 489
Score = 29.0 bits (65), Expect = 2.9
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 225 LKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT 284
+INQ+DE G N L+++ + K+ ++L++ G D+N+ G+ L A E+
Sbjct: 246 FSYIDINQVDELGFNPLYYSVSHNNRKIFEYLLQL-GGDINIITELGNTCL--FTAFENE 302
Query: 285 DLIEYLVNS 293
++ NS
Sbjct: 303 SK--FIFNS 309
>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 = 26.8 bits (60), Expect = 3.1
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 8 DKNTGLSKGFGFVTFQNKE 26
D T +GF FV F+ E
Sbjct: 33 DYETQKHRGFAFVEFEEPE 51
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif
2 in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized
to the nuclear and cytoplasmic compartments. In
addition to PARP activity, PARP-10 is also involved in
the control of cell proliferation by inhibiting c-Myc-
and E1A-mediated cotransformation of primary cells.
PARP-10 may also play a role in nuclear processes
including the regulation of chromatin, gene
transcription, and nuclear/cytoplasmic transport.
PARP-10 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two overlapping C-terminal
domains composed of a glycine-rich region and a region
with homology to catalytic domains of PARP enzymes
(PARP domain). In addition, PARP-10 contains two
ubiquitin-interacting motifs (UIM). PARP-14, also
termed aggressive lymphoma protein 2, is a member of
the B aggressive lymphoma (BAL) family of
macrodomain-containing PARPs. Like PARP-10, PARP-14
also includes two RRMs at the N-terminus. Nmi, also
termed N-myc and STAT interactor, is an interferon
inducible protein that interacts with c-Myc, N-Myc, Max
and c-Fos, and other transcription factors containing
bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc
proteins, Nmi also associates with all the Stat family
of transcription factors except Stat2. In response to
cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can
enhance Stat-mediated transcriptional activity through
recruiting the Stat1 and Stat5 transcriptional
coactivators, CREB-binding protein (CBP) and p300. IFP
35 is an interferon-induced leucine zipper protein that
can specifically form homodimers. Distinct from known
bZIP proteins, IFP 35 lacks a basic domain critical for
DNA binding. In addition, IFP 35 may negatively
regulate other bZIP transcription factors by
protein-protein interaction. For instance, it can form
heterodimers with B-ATF, a member of the AP1
transcription factor family. Both Nmi and IFP35 harbor
one RRM. RBM43 is a putative RNA-binding protein
containing one RRM, but its biological function remains
unclear. .
Length = 74
Score = 26.9 bits (60), Expect = 3.2
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 15 KGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
KG VTF + + ++V H L G++LS++P
Sbjct: 41 KGSALVTFADFKVAERVVKQKKHPLNGTQLSVRP 74
>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 = 29.1 bits (65), Expect = 3.2
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSRLSI 46
N ++ D T KG+GFV+ N EA + S + + L L +
Sbjct: 298 NVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343
Score = 28.4 bits (63), Expect = 4.7
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 5 VMFDKNTGLSKGFGFVTFQNKEAVDK 30
++ D TGLSKG GF+ F ++ D+
Sbjct: 121 ILSDNVTGLSKGVGFIRFDKRDEADR 146
Score = 27.6 bits (61), Expect = 8.8
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL 44
DK TG S G+GFV + E +K ++ L G RL
Sbjct: 38 DKVTGQSLGYGFVNYVRPEDAEKAVNS----LNGLRL 70
>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 = 27.2 bits (61), Expect = 3.2
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVF-STDSHVLEGSRL 44
D TG SKG+ FV ++++ + + V++GS +
Sbjct: 38 DIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEI 75
>gnl|CDD|239362 cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) family,
NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily; Nuo, also called respiratory chain Complex 1,
is the entry point for electrons into the respiratory
chains of bacteria and the mitochondria of eukaryotes.
It is a multisubunit complex with at least 14 core
subunits. It catalyzes the electron transfer of NADH to
quinone coupled with the transfer of protons across the
membrane, providing the proton motive force required for
energy-consuming processes. Electrons are transferred
from NADH to quinone through a chain of iron-sulfur
clusters in Nuo, including the [2Fe-2S] cluster present
in NuoE core subunit, also called the 24 kD subunit of
Complex 1. This subfamily also include formate
dehydrogenases, NiFe hydrogenases and NAD-reducing
hydrogenases, that contain a NuoE domain. A subset of
these proteins contain both NuoE and NuoF in a single
chain. NuoF, also called the 51 kD subunit of Complex 1,
contains one [4Fe-4S] cluster and also binds the NADH
substrate and FMN.
Length = 80
Score = 27.1 bits (61), Expect = 3.3
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 240 CLHWACD-RGHLKVVQHLIEKCGADVNVTDSDGDYGLD 276
C AC RG +++ L +K G T DG + L+
Sbjct: 7 CTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLE 44
>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 = 27.0 bits (60), Expect = 3.3
Identities = 8/39 (20%), Positives = 22/39 (56%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI 46
+ G +GFG+ F++++++ + S + L+ R+ +
Sbjct: 36 PGDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRIRV 74
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 26.7 bits (60), Expect = 3.6
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 1 MNASVMFDKNTGLSKGFGFVTFQNKEAVDK 30
++ V D T S G+ +V FQN ++
Sbjct: 27 LSIRVCRDLITRRSLGYAYVNFQNPADAER 56
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), in the middle and
an RGG box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 26.9 bits (59), Expect = 3.7
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 47
D T +GF F+TF+ +E V K+ H + S+ I+
Sbjct: 34 DNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 73
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 26.5 bits (59), Expect = 4.7
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP 48
K G SKGF +V F ++ A V + G + +
Sbjct: 35 HKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 26.7 bits (59), Expect = 4.9
Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKEA 27
+V+ D+N G S+G FVTF +++
Sbjct: 32 TVLRDQN-GQSRGCAFVTFASRQC 54
>gnl|CDD|240990 cd12546, RRM_RBM43, RNA recognition motif in vertebrate
RNA-binding protein 43 (RBM43). This subgroup
corresponds to the RRM of RBM43, a putative RNA-binding
protein containing one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). Although its biological
function remains unclear, RBM43 shows high sequence
homology to poly [ADP-ribose] polymerase 10 (PARP-10),
which is a novel oncoprotein c-Myc-interacting protein
with poly(ADP-ribose) polymerase activity. .
Length = 77
Score = 26.5 bits (59), Expect = 5.1
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 15 KGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP 48
KG +VTF+ +E + V HVL+ L ++
Sbjct: 45 KGVAYVTFEEEEDAENVLK-KKHVLQDKSLGVKL 77
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 85
Score = 26.6 bits (58), Expect = 5.2
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 2 NASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDSHVLEGSR---LSIQPSDSHNS 54
N V+ D T KGFGFVT N EA + S + + L G R +S + S H +
Sbjct: 30 NVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRL-GDRVLQVSFKTSKQHKA 85
>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 = 26.2 bits (58), Expect = 6.1
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 15 KGFGFVTFQNKEAVDKVF-STDSHVLEGSRLSIQP 48
FGFV F + EAV K+ + + RL+++
Sbjct: 45 PNFGFVVFDDPEAVQKILANKPIYFRGDHRLNVEE 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 = 26.1 bits (58), Expect = 6.7
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 4 SVMFDKNTGLSKGFGFVTFQNKE-AVDKVFSTDSHVLEGSRL 44
+++ DK T SKG F+ F ++E A V + ++ L G L
Sbjct: 32 TIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73
>gnl|CDD|211417 cd11576, GH99_GH71_like_2, Uncharacterized glycoside hydrolase
family 99-like domain. This family of putative
glycoside hydrolases resembles glycosyl hydrolase
families 71 and 99 (following the CAZY nomenclature) and
may share a similar catalytic site and mechanism. The
domain may co-occur with other domains involved in the
binding/processing of glycans.
Length = 378
Score = 28.0 bits (63), Expect = 7.0
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 119 SWYNMEAKSKYNA---------WNSLGQMAKSEAMSKYIALLNEVDAG 157
SW+N++ S N W K+ A Y+A+ +E D G
Sbjct: 283 SWHNLKGGSPLNQIPRLGGDFLWRQAYNAKKAGAKMIYVAMFDEYDEG 330
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM1 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. Moreover, hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 25.8 bits (57), Expect = 7.3
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 6 MFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ 47
+F G S+G G V F++KE+V K T + + L+G +L ++
Sbjct: 32 LFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVVK 74
>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 = 26.0 bits (58), Expect = 7.5
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 10 NTGLSKGFGFVTFQNKEAVDKV 31
TG +KG+ FV F E +
Sbjct: 45 ETGKTKGYAFVEFATPEEAKEA 66
>gnl|CDD|184134 PRK13549, PRK13549, xylose transporter ATP-binding subunit;
Provisional.
Length = 506
Score = 28.0 bits (63), Expect = 8.2
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 217 MLVKQLTKLKDFNI---NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY 273
LVK+L+ L+ NI N++ G+ + + D +L+ Q L+ + D+N G+
Sbjct: 92 ALVKELSVLE--NIFLGNEITPGGI--MDY--DAMYLRA-QKLLAQLKLDINPATPVGNL 144
Query: 274 GLDYAKAIE 282
GL + +E
Sbjct: 145 GLGQQQLVE 153
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 27.6 bits (62), Expect = 9.4
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 185 GWVNVSSMINDESQ--LDDNEKNIYEWAKEGKLDMLV 219
G V S +E Q L+ +++ E A+EGKLD ++
Sbjct: 137 GGNEVDSKNAEEDQDALEKYTRDLTELAREGKLDPVI 173
>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 = 25.8 bits (56), Expect = 9.5
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 8 DKNTGLSKGFGFVTFQNKEAVDKVFST 34
DK TG S G+GFV + + DK +T
Sbjct: 38 DKITGQSLGYGFVNYVDPNDADKAINT 64
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
0.310 0.127 0.368
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,234,055
Number of extensions: 1274040
Number of successful extensions: 1190
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1170
Number of HSP's successfully gapped: 240
Length of query: 300
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 204
Effective length of database: 6,679,618
Effective search space: 1362642072
Effective search space used: 1362642072
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.4 bits)