RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2347
(207 letters)
>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 = 92.3 bits (230), Expect = 7e-25
Identities = 40/73 (54%), Positives = 53/73 (72%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L K +LE EFEK+G L SVWVA NPPGFAFVEF + DAE A +++ +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60
Query: 71 LMGSKLRVEISRG 83
+ G+++RVE+SRG
Sbjct: 61 ICGNRVRVELSRG 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 74.6 bits (184), Expect = 4e-18
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
++VG L +E+L F KFGK+ SV + + GFAFVEF ++ DAE A ++
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 66 MNDQDLMGSKLRV 78
+N ++L G L+V
Sbjct: 61 LNGKELDGRPLKV 73
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes
including mRNA and rRNA processing, RNA export, and RNA
stability. This domain is 90 amino acids in length and
consists of a four-stranded beta-sheet packed against
two alpha-helices. RRM usually interacts with ssRNA,
but is also known to interact with ssDNA as well as
proteins. RRM binds a variable number of nucleotides,
ranging from two to eight. The active site includes
three aromatic side-chains located within the conserved
RNP1 and RNP2 motifs of the domain. The RRM domain is
found in a variety heterogeneous nuclear
ribonucleoproteins (hnRNPs), proteins implicated in
regulation of alternative splicing, and protein
components of small nuclear ribonucleoproteins
(snRNPs).
Length = 72
Score = 72.3 bits (178), Expect = 3e-17
Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMN 67
++VG L +EDL F KFG++ SV + + GFAFVEF + DAE A +++N
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 68 DQDLMGSKLRVE 79
++L G KL+V
Sbjct: 61 GKELDGRKLKVS 72
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 73.4 bits (179), Expect = 1e-15
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
++VG L V +EDL F+KFG + V + + GFAFVEF ++ AE A +
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175
Query: 65 SMNDQDLMGSKLRVEISRGRGRGR 88
+N ++L G LRV+ ++ + R
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPR 199
>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 = 65.7 bits (161), Expect = 1e-14
Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 4/70 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMN 67
++VG L +EDL+ F KFG + S+ + + GFAFVEF ++ DAE A +++N
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 68 DQDLMGSKLR 77
++L G +LR
Sbjct: 61 GKELGGRELR 70
>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 = 64.2 bits (157), Expect = 5e-14
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 5/79 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAAC 63
G +++V GL+ +++LE F KFG++ V + +P GF FV F + DA+AA
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60
Query: 64 DSMNDQDLMGSKLRVEISR 82
+N ++L G ++VE ++
Sbjct: 61 RDLNGKELEGRVIKVEKAK 79
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 62.8 bits (152), Expect = 2e-13
Identities = 37/76 (48%), Positives = 47/76 (61%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L K +LE F +G L SVWVA NPPGFAFVEF + DA A ++ +
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 65
Query: 71 LMGSKLRVEISRGRGR 86
L G ++RVE+S G R
Sbjct: 66 LCGCRVRVELSNGEKR 81
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 61.4 bits (150), Expect = 5e-13
Identities = 30/69 (43%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMND 68
+YV L +V +EDL F +GK+ V + N P GFAFVEF++ DAEAA +N
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 69 QDLMGSKLR 77
L G LR
Sbjct: 61 LVLDGRTLR 69
>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 = 59.5 bits (145), Expect = 3e-12
Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
+YVGGL E V ++ L F FG + + + + GFAFVEF DA AA D+M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 67 NDQDLMGSKLRV 78
N+ +L G +RV
Sbjct: 61 NESELFGRTIRV 72
>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 = 57.5 bits (140), Expect = 8e-12
Identities = 21/53 (39%), Positives = 27/53 (50%)
Query: 29 EFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
F FG + + + PGFAFVEFS + AE A +N G LRV+ S
Sbjct: 4 LFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 56.6 bits (136), Expect = 4e-11
Identities = 36/76 (47%), Positives = 49/76 (64%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+VYVG L K +LE F +G L +VW+A NPPGFAFVEF + DAE A ++ +
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60
Query: 71 LMGSKLRVEISRGRGR 86
+ GS++RVE+S G R
Sbjct: 61 ICGSRVRVELSTGMPR 76
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 56.7 bits (137), Expect = 4e-11
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
+++V GL +V KE+LE F+K G + SV + N P G A+VE+ N+ A A M
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 67 NDQDLMGSKLRVEIS 81
+ ++ + V IS
Sbjct: 64 DGTEIKEKTISVAIS 78
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation
factor (ACF). hnRNP R is a ubiquitously expressed
nuclear RNA-binding protein that specifically bind
mRNAs with a preference for poly(U) stretches and has
been implicated in mRNA processing and mRNA transport,
and also acts as a regulator to modify binding to
ribosomes and RNA translation. hnRNP Q is also a
ubiquitously expressed nuclear RNA-binding protein. It
has been identified as a component of the spliceosome
complex, as well as a component of the apobec-1
editosome, and has been implicated in the regulation of
specific mRNA transport. ACF is an RNA-binding subunit
of a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. This
family also includes two functionally unknown
RNA-binding proteins, RBM46 and RBM47. All members
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains).
Length = 72
Score = 55.7 bits (135), Expect = 8e-11
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
+YV L + +E L F ++G++ V +AFV F + DA A + MN ++L
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERV---KKIKDYAFVHFEERDDAVKAMEEMNGKEL 60
Query: 72 MGSKLRV 78
GS + V
Sbjct: 61 EGSPIEV 67
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 52.4 bits (126), Expect = 1e-09
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 20 TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
T ++ED+E FE FG L + FAFVEF + DA A ++++ + GS L VE
Sbjct: 11 TTREEDIEKLFEPFGPLVRCDIRKT---FAFVEFEDSEDATKALEALHGSRIDGSVLTVE 67
>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 = 52.6 bits (127), Expect = 1e-09
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
+YVG L V +EDL+ F +FG++ S V + GF FVE +A AA +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 66 MNDQDLMGSKLRVEISR 82
+N D G L V +R
Sbjct: 61 LNGTDFGGRTLTVNEAR 77
>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 = 52.0 bits (125), Expect = 2e-09
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
++VG L+ + E L F FG+++ V + G+ FV F + DAE A SM
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 67 NDQDLMGSKLR 77
N Q L G +R
Sbjct: 62 NGQWLGGRAIR 72
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 51.6 bits (124), Expect = 3e-09
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP---PGFAFVEFSNQIDAEAACDSMND 68
++VG L+ V KE+L F + GK+ V + FAF++F + A A +S N
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 69 QDLMGSKLRVE 79
L + V+
Sbjct: 66 SMLKNKTMHVQ 76
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 50.6 bits (122), Expect = 6e-09
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN 67
YVG L V + L F G + S+ V + G+A+V F N DAE A D++N
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 68 DQDLMGSKLRV 78
+ G +R+
Sbjct: 63 FDVIKGKPIRI 73
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to
the RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
TRBP-interacting domain. RBM4 is a ubiquitously
expressed splicing factor with two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may also function as a translational
regulator of stress-associated mRNAs as well as play a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RRMs, a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. This family also includes Drosophila
RNA-binding protein lark (Dlark), a homolog of human
RBM4. It plays an important role in embryonic
development and in the circadian regulation of adult
eclosion. Dlark shares high sequence similarity with
RBM4 at the N-terminal region. However, Dlark has three
proline-rich segments instead of three alanine-rich
segments within the C-terminal region. .
Length = 66
Score = 50.3 bits (121), Expect = 7e-09
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+++VG L + E+L FEK+G + V N + FV + DAE A ++N +
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN---YGFVHMEEEEDAEDAIKALNGYE 57
Query: 71 LMGSKLRVE 79
MG ++ VE
Sbjct: 58 FMGKRINVE 66
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins.
This subgroup corresponds to the RRM1 of SF2, also
termed SR1 protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal domain rich in proline, serine
and lysine residues (PSK domain), a composition
reminiscent of histones. This PSK domain harbors a
putative phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 50.2 bits (120), Expect = 8e-09
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF--NPPGFAFVEFSNQIDAEAACDSMND 68
VYVG L +++ ++E F K+G + + + PPG+AF+EF + DAE A +
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60
Query: 69 QDLMGSKLRVEI 80
D G +LRVE+
Sbjct: 61 YDFDGQRLRVEL 72
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 50.1 bits (120), Expect = 9e-09
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-PGFAFVEFSNQIDAEAACDSMNDQ 69
VY G + D++ FE G + V + AF+ F N A+ A +++N
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60
Query: 70 DLMGSKLRVE 79
+ G+ ++V+
Sbjct: 61 SVDGNCIKVQ 70
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 49.9 bits (120), Expect = 1e-08
Identities = 29/67 (43%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 11 RVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
RV+VG L T+ V KEDLE F K+GK+ + + G+ FV+F N+ DA AA N +
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH---KGYGFVQFDNEEDARAAVAGENGR 58
Query: 70 DLMGSKL 76
++ G KL
Sbjct: 59 EIAGQKL 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 = 50.1 bits (120), Expect = 1e-08
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----------NPPGFAFVEFSNQIDAEA 61
VYV L + E L+ F K+G V + + GFAF+EF +A+
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGT-----VVYVSLPRYKHTGDIKGFAFIEFETPEEAQK 56
Query: 62 ACDSMNDQD 70
AC +N+
Sbjct: 57 ACKHLNNPP 65
>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 = 48.9 bits (117), Expect = 2e-08
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
RVY+G L ++ D+E F+ +G++ + + GF FVEF + DA+ A +N ++
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINLKN---GFGFVEFEDPRDADDAVYELNGKE 57
Query: 71 LMGSKLRVEISRG 83
L G ++ VE +RG
Sbjct: 58 LCGERVIVEHARG 70
>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 = 49.2 bits (118), Expect = 2e-08
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
++V L E LE F + G + +V + GF +V F+ + DA+ A +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 67 NDQDLMGSKLRVEISRGR 84
G K+ VE ++ +
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds
to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share
high sequence similarity and are expressed in a wide
variety of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains. This subfamily also
includes a yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1, termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein, which has been identified as
both a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP).
It may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. PUB1 is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it
is one of the major cellular proteins cross-linked by
UV light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there
is no strong evidence implicating PUB1 in the mechanism
of DNA replication. PUB1 contains three RRMs, and a GAR
motif (glycine and arginine rich stretch) that is
located between RRM2 and RRM3. .
Length = 73
Score = 48.8 bits (117), Expect = 2e-08
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
T VYVG L + +E+L+ F FG + V V F G+AFV F A A ++N
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV-FKDKGYAFVRFDTHEAAATAIVAVNGT 59
Query: 70 DLMGSKLRV 78
+ G ++
Sbjct: 60 SINGQTVKC 68
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 48.9 bits (117), Expect = 3e-08
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSV--WVAFNPPGFAFVEFSNQIDAEAACDSMND 68
R+YVG L +++ D+E F K+G + ++ P FAFVEF + DAE A +
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 69 QDLMGSKLRVE 79
D G +LRVE
Sbjct: 61 YDFDGYRLRVE 71
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 77
Score = 48.0 bits (115), Expect = 5e-08
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
R+YV + + ++D++ FE FGK+ S +A +P G+ F+E+ N A+ A
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 65 SMNDQDLMGSKLRV 78
SMN DL G +LRV
Sbjct: 61 SMNLFDLGGQQLRV 74
>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 = 48.0 bits (115), Expect = 6e-08
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 15/80 (18%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----------GFAFVEFSNQIDAE 60
+YV L + ++DL F KFG++ S+ + P GFAFV F + AE
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRI---PKKQDEKQGRLNNGFAFVTFKDASSAE 59
Query: 61 AACDSMNDQDLMGSKLRVEI 80
A +N +L G K+ V +
Sbjct: 60 NAL-QLNGTELGGRKISVSL 78
>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 = 47.7 bits (114), Expect = 7e-08
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
VYV L ++ DL F K+GK+ V + + G AF+ F ++ DA ++
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 67 NDQDLMGSKLRVEIS 81
N+++L G L+ I+
Sbjct: 64 NNKELFGRTLKCSIA 78
>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 = 47.4 bits (113), Expect = 9e-08
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDS 65
R++V L + K++DLE F KFG+L+ V VA GFA+V F + DA A
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Query: 66 MNDQDLMGSKLRV 78
++ + G + +
Sbjct: 64 LDGKVFQGRLIHI 76
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia 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. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 47.5 bits (114), Expect = 1e-07
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 23 KEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMN 67
KED+ E KFG + + V +P G +V+F A+ ++N
Sbjct: 25 KEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALN 70
>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 = 47.1 bits (113), Expect = 1e-07
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
+ V L+E ++DL F FG ++ V++A + GFAFV F + DAE A +
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 66 MNDQDLMGSKLRVEISR 82
+N L VE ++
Sbjct: 61 LNGFGYDNLILSVEWAK 77
>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 = 50.6 bits (121), Expect = 1e-07
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAA 62
++ T +YV L +V ++ L F KFG++ S V + GFAFV F DA A
Sbjct: 176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235
Query: 63 CDSMNDQDLMGSKLRVEISRGRGRGR 88
+ MN + + +K ++ GR + R
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKR 261
Score = 47.1 bits (112), Expect = 2e-06
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 4/84 (4%)
Query: 5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAE 60
M +G +YV L +TV E L F + G++ S V + GF FV FSN +A
Sbjct: 281 MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEAN 340
Query: 61 AACDSMNDQDLMGSKLRVEISRGR 84
A M+ + L G L V +++ +
Sbjct: 341 RAVTEMHGRMLGGKPLYVALAQRK 364
Score = 41.7 bits (98), Expect = 1e-04
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
+YVG L V + L F+ FG + SV V + G+ +V F N DAE A ++M
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 67 NDQDLMGSKLRV 78
N + L G +R+
Sbjct: 63 NFKRLGGKPIRI 74
Score = 33.2 bits (76), Expect = 0.080
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDS 65
++V L ++V + L F KFG + S VA + G+ FV F + A+AA
Sbjct: 89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148
Query: 66 MN 67
+N
Sbjct: 149 VN 150
>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 = 46.5 bits (111), Expect = 2e-07
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
R++V L T +E+L FE FG+++ V + + GFAFV F A A
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 66 MNDQDLMGSKLRV 78
++ G L V
Sbjct: 61 LDGSIFQGRLLHV 73
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein
orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which
is a putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 46.1 bits (110), Expect = 3e-07
Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWV--------AFNPPGFAFVEFSNQIDAEA 61
T +YVG L V +E L EF +FG L SV + FV F N+ DAE
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61
Query: 62 ACDSMNDQDLMGSKLRV 78
A D ++ +D+MG +L++
Sbjct: 62 ALDELDGKDVMGYELKL 78
>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 = 46.0 bits (110), Expect = 3e-07
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
T VYV L E + E L+ F K+GK+ S V + G F FV F N A+ A +
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61
Query: 66 MNDQDLMGSKLRV 78
+N +++ G KL V
Sbjct: 62 LNGKEVNGKKLYV 74
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 45.9 bits (109), Expect = 3e-07
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDSM 66
+Y+G L +++L+ F +FG + +V VA N + F++F N A A SM
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 67 NDQDLMGSKLRVEI 80
N+ LMG L+V +
Sbjct: 62 NNYLLMGKVLQVHV 75
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 45.7 bits (109), Expect = 3e-07
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-------GFAFVEFSNQIDAEAAC 63
R+ V L + DL+ F FG VW P GFAFV+F+++ DAE A
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGF---VWEVTIPRKPDGKKKGFAFVQFTSKADAEKAI 57
Query: 64 DSMNDQDLMGSKLRVEIS 81
+N + + G + V+ +
Sbjct: 58 KGVNGKKIKGRPVAVDWA 75
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 45.5 bits (108), Expect = 4e-07
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R+YV + + F +G + V + N FAFVEF + A A DS++ +
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISN---FAFVEFESLESAIRAKDSVHGKV 57
Query: 71 LMGSKLRV 78
L + L V
Sbjct: 58 LNNNPLYV 65
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 49.3 bits (117), Expect = 4e-07
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
R+YV + + + D++ FE FG++ +A P G+ F+E++N A S
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265
Query: 66 MNDQDLMGSKLRV 78
MN DL G LRV
Sbjct: 266 MNLFDLGGQYLRV 278
Score = 47.0 bits (111), Expect = 2e-06
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
RVYVG ++ ++++ + F+ FG + S+ ++++P GFAFVE+ A+ A +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 66 MNDQDLMGSKLRV 78
MN Q L G ++V
Sbjct: 169 MNGQMLGGRNIKV 181
>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 = 45.7 bits (109), Expect = 4e-07
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMN 67
YVG L + ++DL FE FG++ V + +P G+ F++F++ DA+ A + +N
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61
Query: 68 DQDLMGSKLRV 78
+L G ++V
Sbjct: 62 GFELAGRPIKV 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 = 45.5 bits (108), Expect = 5e-07
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
++VG L+ +V E L+ EFEKFG + V + GF +V+F + DA+ A ++
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 66 MNDQDLMGSKLRVEIS 81
M+ ++L G + V+ S
Sbjct: 61 MDGKELDGRPINVDFS 76
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 48.6 bits (116), Expect = 5e-07
Identities = 36/62 (58%), Positives = 36/62 (58%), Gaps = 10/62 (16%)
Query: 100 RGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGG 159
GG GG RGGG G GGGG R GG R GG G GRG RG GG GGR GGG GG
Sbjct: 3 GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG-------RGRGGGGGGR---GGGGGG 52
Query: 160 GG 161
G
Sbjct: 53 GP 54
Score = 48.2 bits (115), Expect = 6e-07
Identities = 35/64 (54%), Positives = 35/64 (54%), Gaps = 9/64 (14%)
Query: 87 GRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGY 146
G GGG GGR RGG GG GGGG GGG GGGRGRG GG G RGGGG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGG---------RGGGRGRGRGGGGGGRGGGGG 51
Query: 147 RGGR 150
G
Sbjct: 52 GGPG 55
Score = 48.2 bits (115), Expect = 6e-07
Identities = 28/52 (53%), Positives = 29/52 (55%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
G GRG G GG GG GGRGG RGGG G G GG G GGGG G+
Sbjct: 5 GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 44.0 bits (104), Expect = 2e-05
Identities = 29/64 (45%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 101 GGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGG 160
G GG+ GG GG GGG GGGGRG G G G G RGG GG GGG
Sbjct: 1 GMGGGFGGGRGGGRGGG--------GGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGG 52
Query: 161 GYRG 164
G
Sbjct: 53 GPGK 56
Score = 44.0 bits (104), Expect = 2e-05
Identities = 25/55 (45%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
G G GGGRGG G GG GG GG G G GG G GG G G G
Sbjct: 3 GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG--RGGGGGGRGGGGGGGPG 55
Score = 42.4 bits (100), Expect = 5e-05
Identities = 35/63 (55%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 129 GRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGG 188
G G G GG RG GGG GGR GGGRGGG RGG RG GG GG GG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRG--GGGRGGG--RGGGRGRGRGGGG-----GGRGGGGG 51
Query: 189 GGR 191
GG
Sbjct: 52 GGP 54
Score = 42.0 bits (99), Expect = 8e-05
Identities = 28/55 (50%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 121 GGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGK 175
G FGGG G GG G RGGGG GGR G GRG GG GGR G G
Sbjct: 2 MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGG-GRGRGRGGGGGGRGGGGGGGPG 55
Score = 40.5 bits (95), Expect = 2e-04
Identities = 30/60 (50%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 132 RGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
GGF G RGGG GG GGGRGGGG GGR G G+ G GGG GGG
Sbjct: 1 GMGGGFGGGRGGGRGGGG----GGGRGGGGRGGGRG-GGRGRGRGGGGGGRGGGGGGGPG 55
Score = 28.5 bits (64), Expect = 2.4
Identities = 20/47 (42%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 154 GGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQR 200
G G G GG RGG G GG GGG GG GR R R
Sbjct: 1 GMGGGFGGGRGGG-RGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGR 46
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 45.3 bits (108), Expect = 6e-07
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDS 65
TR+ V L V +EDLE F + G++ V + ++ G A V F + DAE A
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 66 MNDQDLMGSKLRVEI 80
N L G ++VE+
Sbjct: 61 FNGVLLDGQPMQVEL 75
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins from plants. This
subgroup corresponds to the RRM2 in a family that
represents a novel group of arginine/serine (RS) or
serine/arginine (SR) splicing factors existing in
plants, such as A. thaliana RSp31, RSp35, RSp41 and
similar proteins. Like vertebrate RS splicing factors,
these proteins function as plant splicing factors and
play crucial roles in constitutive and alternative
splicing in plants. They all contain two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
at their N-terminus, and an RS domain at their
C-terminus.
Length = 70
Score = 45.2 bits (107), Expect = 6e-07
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 22 KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
+ DLE FE +GKL +V + N FAFV++ Q DA A +S N ++ + VE
Sbjct: 13 RTRDLERHFEPYGKLVNVRIRRN---FAFVQYETQEDATKALESTNMSKVLDRVISVE 67
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 48.7 bits (117), Expect = 6e-07
Identities = 30/114 (26%), Positives = 33/114 (28%), Gaps = 3/114 (2%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
R R R D + G G RDG DR R +GD R
Sbjct: 161 AERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD---RREE 217
Query: 142 GGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSR 195
G G R R RG + D G GG RG R R R
Sbjct: 218 RGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDR 271
Score = 46.8 bits (112), Expect = 3e-06
Identities = 28/110 (25%), Positives = 29/110 (26%), Gaps = 10/110 (9%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
RG GR R R G G RDGGDR G R
Sbjct: 184 EAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDN 243
Query: 142 GGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
D+ G G G R R G GG GG R
Sbjct: 244 REDRGDRDGDDGEGRGGRRGRRFRDRDR----------RGRRGGDGGNER 283
Score = 43.7 bits (104), Expect = 3e-05
Identities = 24/116 (20%), Positives = 30/116 (25%), Gaps = 1/116 (0%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGS 140
+ R R + R G R G R R D +G
Sbjct: 154 TEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD 213
Query: 141 RGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGG-GGRFRSR 195
R R + G R R R + + G G G G RFR R
Sbjct: 214 RREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
Score = 43.0 bits (102), Expect = 5e-05
Identities = 28/91 (30%), Positives = 29/91 (31%), Gaps = 3/91 (3%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGR-GRGDGGFRGS 140
RGR R G R GG G RD D G R RGD
Sbjct: 196 RGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG 255
Query: 141 RGGGGYRGGRDEYG--GGRGGGGYRGGRDSR 169
G GG RG R GR GG R+
Sbjct: 256 EGRGGRRGRRFRDRDRRGRRGGDGGNEREPE 286
Score = 35.6 bits (83), Expect = 0.013
Identities = 23/128 (17%), Positives = 32/128 (25%), Gaps = 7/128 (5%)
Query: 79 EISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFR 138
+ R RG R GG + D G
Sbjct: 126 QARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQ--A 183
Query: 139 GSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPV 198
+ G R G R + R + G+ D GG R G R R R
Sbjct: 184 EAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRD-----GGDRRGRRRRRDRRDA 238
Query: 199 QRRYNVDE 206
+ N ++
Sbjct: 239 RGDDNRED 246
Score = 32.6 bits (75), Expect = 0.14
Identities = 26/69 (37%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 77 RVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
R + RGR R R R D G R G G G GG R G RF R R G
Sbjct: 220 RRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRR--GRRF----RDRDRRG 273
Query: 137 FRGSRGGGG 145
RG GG
Sbjct: 274 RRGGDGGNE 282
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 44.9 bits (107), Expect = 9e-07
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
+R+ V L + V ++ L FE G++ V V G F FV F ++ DA+ A
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 66 MNDQDLMGSKLRVEI 80
N + SK+ VE+
Sbjct: 61 FNKTFIDTSKISVEL 75
>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 = 44.6 bits (106), Expect = 9e-07
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
+V+VG LTE + +EDL F +FG++ V++ FAFV F++ A++ C D
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCG--EDH 58
Query: 70 DLMGSKLRVEISR 82
+ G + V +
Sbjct: 59 IIKGVSVHVSNAE 71
>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 = 44.5 bits (106), Expect = 1e-06
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
++VG LT V K+ L+ F +G + V + + G+A+VEF + DAE A M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 67 NDQDLMGSKLRVE 79
+ + G ++ VE
Sbjct: 61 DGGQIDGQEVTVE 73
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 44.5 bits (106), Expect = 1e-06
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 29 EFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
F KFG + ++ V +NP A V+FS +A+ A S
Sbjct: 22 HFSKFGTIVNIQVNYNPES-ALVQFSTSEEAKKAYRS 57
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the
RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. SRSF12, also
termed 35 kDa SR repressor protein (SRrp35), or
splicing factor, arginine/serine-rich 13B (SFRS13B), or
splicing factor, arginine/serine-rich 19 (SFRS19), is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice
site of the adenovirus E1A pre-mRNA in vivo. Both,
SRSF10 and SRSF12, contain a single N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a C-terminal RS domain rich in serine-arginine
dipeptides. .
Length = 84
Score = 44.7 bits (106), Expect = 1e-06
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
T +YV + + + +DL F K+G + V++ + P GFA+V+F + DAE A
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 65 SMNDQDLMGSKLRVEISRG 83
++ +G ++ ++ ++G
Sbjct: 61 YLDRTRFLGREIEIQFAQG 79
>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 = 44.2 bits (105), Expect = 1e-06
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF--------NPPGFAFVEFSNQIDAEAA 62
R+++G L + + L F K+GK+ F P G+ FV F + +AE A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 63 CDSMNDQDLMGSKLRV 78
S+N + +G KL V
Sbjct: 61 LKSLNGKTALGKKLVV 76
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 44.0 bits (104), Expect = 2e-06
Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVA-FNPPGFAFVEFSNQIDAEAACDSMNDQ 69
R+YVG L ++ +D+E F K+G + + + P FAFVEF + DAE A +
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 70 DLMGSKLRVEISR 82
D G +LRVE R
Sbjct: 61 DYDGYRLRVEFPR 73
>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 = 44.1 bits (105), Expect = 2e-06
Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 12 VYVGGLTETVKKEDL-ELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAACDS 65
VYVG L E V +E L EL F + G + +V V G+ FVEF ++ DA+ A
Sbjct: 1 VYVGNLDEKVTEELLWEL-FIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59
Query: 66 MNDQDLMGSKLRV 78
MN L G +RV
Sbjct: 60 MNMIKLYGKPIRV 72
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 43.4 bits (103), Expect = 2e-06
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 12 VYVGGLTETVKKEDLELE-FEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMND 68
+YVG L TV EDL E F + G + S + +AFVE+ + A AA +MN
Sbjct: 1 LYVGNLDRTVT-EDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNG 59
Query: 69 QDLMGSKLRV 78
+ ++G +++V
Sbjct: 60 RLILGQEIKV 69
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 43.7 bits (104), Expect = 2e-06
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVA----FNPP-GFAFVEFSNQIDAEAACDS 65
R++VGGL+ +V + DLE F +FG ++ V + P GFA+++ C S
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 66 -MNDQDLMGSKLRVE 79
+N GS L++E
Sbjct: 61 TLNGTKWKGSVLKIE 75
>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 = 43.8 bits (104), Expect = 2e-06
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSV-----WVAFNPPGFAFVEFSNQIDAEAACDSMN 67
+V L EDLE+ F +FGK+ S + +AF+EF + D E A M+
Sbjct: 7 FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 43.4 bits (102), Expect = 3e-06
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQD 70
V L+ + ++ L+ E F K S+ + N P G+AFVEF + DA+ A +S N+ +
Sbjct: 6 VNNLSYSASEDSLQ---EVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62
Query: 71 LMGSKLRVE 79
+ G +R+E
Sbjct: 63 IEGRSIRLE 71
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 43.5 bits (103), Expect = 3e-06
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
+R+ V L + +K++ L FE FG + V + + G F FV + + +A+ A
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60
Query: 66 MNDQDLMGSKLRVEI 80
N+ + SK+ VEI
Sbjct: 61 FNNSFIDTSKITVEI 75
>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 = 43.4 bits (103), Expect = 3e-06
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 10/71 (14%)
Query: 21 VKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAAC---DSMNDQDLM 72
+E+L+ F +FG++ + + G AFV+F + A+ D+ D L
Sbjct: 12 ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLS 71
Query: 73 --GSKLRVEIS 81
G +L V ++
Sbjct: 72 LDGRRLIVTLA 82
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 43.1 bits (102), Expect = 3e-06
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMN 67
T V+VGGL V +++L F FG++ V + PPG FV+F ++ AEAA +
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPGKGCGFVQFVHRAAAEAAIQQLQ 58
Query: 68 DQDLMGSKLR 77
+ GS++R
Sbjct: 59 GTIIGGSRIR 68
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 43.3 bits (103), Expect = 4e-06
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 23 KEDLELEFEKFGKLNSVWVAFNPP--------GFAFVEFSNQIDAEAACDSMN 67
ED++ E K+GK+ SV + G FVEF++ DA+ A ++
Sbjct: 25 LEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 42.9 bits (101), Expect = 4e-06
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWV--AFNPP--GFAFVEFSNQIDAEAACDS 65
T++ V L K+D+ F +G+L SV V F+ GFAFVEFS +A A ++
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60
Query: 66 MNDQDLMGSKL 76
+ D L+G +L
Sbjct: 61 LKDTHLLGRRL 71
>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 = 42.9 bits (101), Expect = 5e-06
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
+ +++VGGL L F ++GKL V +P GF F+ FS+ +A+ A
Sbjct: 1 QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60
Query: 63 CDSM 66
++
Sbjct: 61 MEAQ 64
>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 = 42.6 bits (101), Expect = 5e-06
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
T VY+ GL EDLE + FGK+ S + G+ FV+F + A A +
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 65 SMNDQDLMGS 74
+N + +
Sbjct: 61 GLNGRGVQAQ 70
>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 = 42.3 bits (100), Expect = 7e-06
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 5/70 (7%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMND 68
V LT +DL FEK+G++ V++ + GFAFV F ++ DAE A D+M+
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 69 QDLMGSKLRV 78
++L G +LRV
Sbjct: 63 KELDGRELRV 72
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM3 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B) and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and is a
novel component of the NXF1 pathway. It binds to NXF1
and serves as receptor for the RNA export element RTE.
It also possess mRNA export activity and can facilitate
the access of DEAD-box protein DBP5 to mRNA at the
nuclear pore complex (NPC). RNA-binding protein 15B
(RBM15B), also termed one twenty-two 3 (OTT3), is a
paralog of RBM15 and therefore has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF.
Members in this family belong to the Spen (split end)
protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 72
Score = 42.2 bits (100), Expect = 7e-06
Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-PGFAFVEFSNQIDAEAACDSMNDQD 70
++VGGL +LE EF++FG + + ++P +A++E+ + A+AA +++
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRI--DYDPGRNYAYIEYESIEAAQAAKEALRGFP 58
Query: 71 L--MGSKLRVEISR 82
L G +LRV+ +
Sbjct: 59 LGGPGRRLRVDFAD 72
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 42.0 bits (99), Expect = 8e-06
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
RVYVG ++ + ++ + F FG + S+ ++++P GFAFVE+ A+ A +
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61
Query: 66 MNDQDLMGSKLRV 78
MN L G ++V
Sbjct: 62 MNGVMLGGRNIKV 74
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 42.6 bits (101), Expect = 8e-06
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN 67
+V L + L EFE++G + + + + P G+AF+EF ++ D +AA +
Sbjct: 5 FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64
Query: 68 DQDLMGSKLRVEISRGR 84
+ + G ++ V++ RGR
Sbjct: 65 GKKIDGRRVLVDVERGR 81
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 42.1 bits (100), Expect = 9e-06
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 13 YVGGLTETVKKED----LELEFEKFGKLNSVWVAFNPP---GFAFVEFSNQIDAEAACDS 65
Y+ L E +KK++ L F +FG + + VA G AFV F + A A +
Sbjct: 3 YINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKTLKMRGQAFVVFKDVESATNALRA 61
Query: 66 MNDQDLMGSKLRVEISR 82
+ +R++ ++
Sbjct: 62 LQGFPFYDKPMRIQYAK 78
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 42.2 bits (100), Expect = 9e-06
Identities = 18/72 (25%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
++V G+ E ++ED+ +F +FG++ ++ + + G+A +E+ + +A+AA + +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 67 NDQDLMGSKLRV 78
N ++L+G + V
Sbjct: 69 NGKELLGQTISV 80
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in
vertebrate. It has been reported to be involved in
pre-splicesome assembly and to interact with the
Ca2+-signaling protein ALG-2. It also plays an
important role in embryogenesis. RBM22 contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a zinc finger of the unusual type
C-x8-C-x5-C-x3-H, and a C-terminus that is unusually
rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 41.5 bits (98), Expect = 1e-05
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE-AACDSMND 68
T +YVGGL E V ++DL F +FG++ S+ V AFV F+ + AE AA N
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-QQCAFVTFTTREAAEKAAERLFNK 60
Query: 69 QDLMGSKLRV 78
+ G +L++
Sbjct: 61 LIINGRRLKL 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 = 41.6 bits (98), Expect = 1e-05
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
R +++VGGL V + DL F +FG + V V ++ P GF F+ F ++ +
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60
Query: 63 CDSMNDQDLMGSKLRVEISR 82
+ + D+ G K VE+ R
Sbjct: 61 V-NEHFHDINGKK--VEVKR 77
>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 = 41.0 bits (97), Expect = 2e-05
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA-----FNPPGFAFVEFSNQIDAEAACDSM 66
VY+G L + +L F +FG + + ++ G+AFVEF + A+ ++M
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 67 NDQDLMGSKLRVE 79
N+ L L+ +
Sbjct: 62 NNYLLFERLLKCK 74
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 41.2 bits (96), Expect = 2e-05
Identities = 22/79 (27%), Positives = 46/79 (58%), Gaps = 5/79 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
T ++V + + + EDL EF ++G + V+V + P GFA+++F + DAE A
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60
Query: 65 SMNDQDLMGSKLRVEISRG 83
++N + + G ++ ++ ++G
Sbjct: 61 NLNRKWVCGRQIEIQFAQG 79
>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 = 40.8 bits (95), Expect = 2e-05
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
+++VGGL+ ED++ FE+FGK++ + F+ GF FV F ++ E C+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMND 68
V GL+ + DL F ++G + V V ++ GF FV F + DA+ A + +N
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63
Query: 69 QDLMGSKLRVEIS 81
++ G ++RV+ S
Sbjct: 64 MEIDGRRIRVDYS 76
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 40.8 bits (95), Expect = 3e-05
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
++V L TV +E LE F +FGKL V +AFV F + A A D MN +++
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVK---KLKDYAFVHFEERDAAVRAMDEMNGKEI 60
Query: 72 MGSKLRVEISR 82
G ++ + +++
Sbjct: 61 EGEEIEIVLAK 71
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDSM 66
++VG + E+L+ F+ G +N + + P GFA++EF ++ E A +
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60
Query: 67 NDQDLMGSKLRV 78
N+ + G +++V
Sbjct: 61 NESEFRGRQIKV 72
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM,
but unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might
share similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 40.4 bits (95), Expect = 3e-05
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPG--FAFVEFSNQIDAEAACDSM 66
++V GL+ T K DL+ F K+GK+ + N P F FV ++ +A +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 67 NDQDLMGSKLRVE 79
+ +L G + VE
Sbjct: 62 HRTELHGRVISVE 74
>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 = 40.5 bits (95), Expect = 3e-05
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
+++VGGL+ ++D++ F +FGK+ + F+ GF FV F ++ + C+
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 40.7 bits (95), Expect = 3e-05
Identities = 21/79 (26%), Positives = 46/79 (58%), Gaps = 5/79 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
+ ++V + + + EDL EF ++G + V+V + P GFA+V+F + DAE A
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60
Query: 65 SMNDQDLMGSKLRVEISRG 83
+++ + + G ++ ++ ++G
Sbjct: 61 NLDRKWICGRQIEIQFAQG 79
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar
proteins. This subfamily corresponds to the RRM1 of
RBM19 and MRD1. RBM19, also termed RNA-binding domain-1
(RBD-1), is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 77
Score = 40.3 bits (95), Expect = 4e-05
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKF-GKLNSVWVAFNPPG----FAFVEFSNQIDAEAACD 64
+R+ V L ++ + +L+ F K G++ V + G AF+ + + +A+ A D
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60
Query: 65 SMNDQDLMGSKLRVE 79
N+ + SK+ VE
Sbjct: 61 YFNNTYINTSKISVE 75
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed
in all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64
at U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation
in a more limited set of tissues and cell types,
largely in meiotic and postmeiotic male germ cells, and
to a lesser extent in brain. The loss of CSTF2T will
cause male infertility, as it is necessary for
spermatogenesis and fertilization. Moreover, CSTF2T is
required for expression of genes involved in
morphological differentiation of spermatids, as well as
for genes having products that function during
interaction of motile spermatozoa with eggs. It
promotes germ cell-specific patterns of polyadenylation
by using its RRM to bind to different sequence elements
downstream of polyadenylation sites than does CstF64.
The family also includes yeast ortholog mRNA
3'-end-processing protein RNA15 and similar proteins.
RNA15 is a core subunit of cleavage factor IA (CFIA),
an essential transcriptional 3'-end processing factor
from Saccharomyces cerevisiae. RNA recognition by CFIA
is mediated by an N-terminal RRM, which is contained in
the RNA15 subunit of the complex. The RRM of RNA15 has
a strong preference for GU-rich RNAs, mediated by a
binding pocket that is entirely conserved in both yeast
and vertebrate RNA15 orthologs.
Length = 75
Score = 40.3 bits (95), Expect = 4e-05
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
V+VG + +E L F + G + S + + P G+ F EF + A +A ++
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 67 NDQDLMGSKLRVE 79
N + G LRV+
Sbjct: 61 NGYEFNGRALRVD 73
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 40.0 bits (93), Expect = 4e-05
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
+RV++G L T VKK D+E F K+GK+ V GFAFV++ N+ +A AA +
Sbjct: 2 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDG 58
Query: 69 QDLMGSKLRVEIS 81
+ + G L + ++
Sbjct: 59 RMIAGQVLDINLA 71
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 39.6 bits (93), Expect = 6e-05
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
TR+ V L +V ++D+ F G L + PG A V + + DA A D N++
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARL--VRPGVAEVVYVRKDDALTAIDKYNNR 58
Query: 70 DLMGSKLRVEI 80
+L G ++ ++
Sbjct: 59 ELDGQPMKCKL 69
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM2 of U1A/U2B"/SNF protein family,
containing Drosophila sex determination protein SNF and
its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs) connected by a variable, flexible linker.
SNF is an RNA-binding protein found in the U1 and U2
snRNPs of Drosophila where it is essential in sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). U1A is an RNA-binding protein associated with
the U1 snRNP, a small RNA-protein complex involved in
pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent on U2 snRNA binding. .
Length = 72
Score = 39.5 bits (93), Expect = 6e-05
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 16 GLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-G 73
L E KE LE+ F +F V V G AFVEF + A A ++ + G
Sbjct: 9 NLPEETTKEMLEMLFNQFPGFKEVRLVP--RRGIAFVEFETEEQATVALQALQGFKITPG 66
Query: 74 SKLRV 78
+++
Sbjct: 67 HAMKI 71
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 40.0 bits (94), Expect = 6e-05
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 21 VKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQIDAEAACDSMNDQDL--MG 73
V ++DL F FG++ +WV G A+V+F+ A A + MN + L
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
Query: 74 SKLRVEI 80
L+V I
Sbjct: 74 KPLKVLI 80
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 39.7 bits (93), Expect = 6e-05
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM 72
Y+G L+ V + DL FE+ K+ V G+AFV+ +Q A+ A + +N + L
Sbjct: 2 YIGNLSSDVNESDLRQLFEE-HKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQ 60
Query: 73 GSKLRVEIS 81
G + VE S
Sbjct: 61 GKVIEVEHS 69
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 39.6 bits (93), Expect = 6e-05
Identities = 22/78 (28%), Positives = 47/78 (60%), Gaps = 5/78 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
++VG L+ + +++DLE F++ G++ V +A + GF VEF+ + A+ A
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59
Query: 67 NDQDLMGSKLRVEISRGR 84
+ ++L+G ++RV+++ R
Sbjct: 60 SGEELLGREIRVDLATER 77
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein
44 (RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 39.5 bits (92), Expect = 6e-05
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
V+VGGL+ +V + DL F+K+ +++ + + + +A + F DA A MN
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGGV 60
Query: 71 LMGSKLRV 78
L G ++V
Sbjct: 61 LSGLSIKV 68
>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 = 39.5 bits (93), Expect = 8e-05
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA----------FNPPGFAFVEFSNQIDAEA 61
++V L +E L+ FEK G + SV +A G+ FVEF ++ A+
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 62 ACDSMNDQDLMGSKLRVEIS 81
A + L G L +++S
Sbjct: 63 ALKRLQGTVLDGHALELKLS 82
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 39.9 bits (94), Expect = 8e-05
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 23 KEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
++DL E EKFG++ V V +P G A V+F +A+ +++N + G +L E
Sbjct: 26 RDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAERW 85
Query: 82 RGR 84
G+
Sbjct: 86 DGK 88
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 39.5 bits (93), Expect = 1e-04
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 30 FEKFGKLNSVWVAFNP-PGF-AFVEFSNQIDAEAACDSMNDQD-LMGS-KLRVEISR 82
F +G + + + F G A V+F + AE A ++N ++ G L ++ SR
Sbjct: 22 FSPYGAVEKI-LIFEKNTGVQALVQFDSVESAENAKKALNGRNIYDGCCTLDIQFSR 77
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM2 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and is highly conserved between
plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 39.0 bits (91), Expect = 1e-04
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
+GT V V L +V +DL F +G++ + N F+EF + AEAA ++N
Sbjct: 1 QGTLV-VFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALN 59
Query: 68 DQDLMGSKLRVE 79
++ G ++++E
Sbjct: 60 RSEIAGKRIKLE 71
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSN 55
+++VGGL E V +EDL F ++G + SV + + GFAFV F +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD 50
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 41.8 bits (98), Expect = 1e-04
Identities = 23/61 (37%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 98 DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFR-GSRGGGGYRGGRDEYGGG 156
D++ GG R GGG GG R+GG F G R G G R S R R + G
Sbjct: 562 DAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTG 621
Query: 157 R 157
R
Sbjct: 622 R 622
Score = 41.8 bits (98), Expect = 1e-04
Identities = 22/65 (33%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 141 RGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQR 200
GG RGG +GG R GG + R GG+ D G R G R S +R
Sbjct: 566 HTGGERRGGGRGFGGERREGGRNFSGERRE--GGRGDGRRFSGERREGRAPRRDDSTGRR 623
Query: 201 RYNVD 205
R+ D
Sbjct: 624 RFGGD 628
Score = 34.4 bits (79), Expect = 0.037
Identities = 21/62 (33%), Positives = 22/62 (35%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
G RGGG G GGR G G G R G+R G R D R
Sbjct: 566 HTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGRRRF 625
Query: 142 GG 143
GG
Sbjct: 626 GG 627
Score = 34.1 bits (78), Expect = 0.046
Identities = 21/52 (40%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 113 YGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRG 164
+ GG R GG FGG R G F G R GG GR G R G R
Sbjct: 566 HTGGERRGGGRGFGGERRE-GGRNFSGERREGGRGDGRRFSGERREGRAPRR 616
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 38.4 bits (90), Expect = 1e-04
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R++VG L + +E+ + F K+G+++ V++ GF F+ + +AE A ++
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN-KEKGFGFIRLDTRTNAEKAKAELDGIM 61
Query: 71 LMGSKLRV 78
G +LRV
Sbjct: 62 RKGRQLRV 69
>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 = 1e-04
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
++VG L+ V L F F + V ++ G+ FV F +Q DAE A + M
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 67 NDQDLMGSKLRV 78
N + L +R
Sbjct: 62 NGKWLGSRPIRC 73
>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 = 38.7 bits (90), Expect = 1e-04
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
++V L +V +EDL F + V +P G+ FV F+ DA+ A +
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 67 NDQDLMGSKLRVEISRGR 84
++ L G LR++I+ R
Sbjct: 62 KNKKLHGRILRLDIAERR 79
>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 = 38.7 bits (91), Expect = 1e-04
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 16/66 (24%)
Query: 17 LTETVKKEDLELEFEKFG--KLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQD 70
L + ++K F KFG K+ +++ + G+AFVEF+ +A+ A ++N
Sbjct: 20 LKKVLRKI-----FSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALN--- 71
Query: 71 LMGSKL 76
G KL
Sbjct: 72 --GYKL 75
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 39.2 bits (92), Expect = 1e-04
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSV-----WVAFNPPGFAFVEFSNQIDAEAACDSM 66
++VG L+ +E L F ++G + + V G+AFVE+ ++ DA A
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 67 NDQDLMGSKLRVEISRGR 84
+ + GS++ V+ R R
Sbjct: 66 HKLVIDGSEIFVDFERER 83
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM1 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single-
and double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. It forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manneras well as with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 38.7 bits (90), Expect = 1e-04
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
+R++VG L + +E++ FEK+GK +++ GF F+ + AE A +++
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNM 60
Query: 70 DLMGSKLRV 78
L G +LRV
Sbjct: 61 PLRGKQLRV 69
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 38.5 bits (90), Expect = 2e-04
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFA-FVEFSNQIDAEAACDSMN 67
++ + + V+ EDL+ +G + + V V + + A+ A + +N
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLN 60
Query: 68 DQDLMGSKLRVE 79
+ GSKL+V
Sbjct: 61 GHEYEGSKLKVS 72
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 41.5 bits (97), Expect = 2e-04
Identities = 50/183 (27%), Positives = 70/183 (38%), Gaps = 26/183 (14%)
Query: 12 VYVGGLTETVKKEDLELEFEKF--GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
+YV L T +E +E F +F GK+ V + +AFV F ++ DA A D +N +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD---YAFVHFEDREDAVKAMDELNGK 292
Query: 70 DLMGSKLRVEISR----------GRGRGRGGGGRGGRFDSRGGRGG----YRGGGGGYGG 115
+L GS++ V +++ RG G G R S G Y
Sbjct: 293 ELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYH 352
Query: 116 GGYRDGGDRFGG----GGRGRGDGGFR--GSRGGGGYRGGRDEYGGGRGGGGYRGGRDSR 169
Y GRGRG R G RG Y G YG G YRG + +
Sbjct: 353 PPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPY-GYEAYYGDYYGYHDYRGKYEDK 411
Query: 170 GFD 172
+
Sbjct: 412 YYG 414
Score = 30.4 bits (68), Expect = 0.77
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----NPPGFAFVEFSNQIDAEAA 62
RG V+VG + + +++L FEK G + + + G+AFV F + +A+ A
Sbjct: 56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEA 115
Query: 63 CDSMNDQDLMGSKL 76
+N+ ++ +L
Sbjct: 116 VKLLNNYEIRPGRL 129
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACD 64
G +YV L +++ E L EF FG + S V + GF FV FS+ +A A
Sbjct: 1 GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60
Query: 65 SMNDQDLMGSK 75
MN + ++G K
Sbjct: 61 EMNGR-IIGGK 70
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFG-----KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
++VG L + +++L+ F++FG ++NS P F FV F + + +
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65
Query: 67 NDQDLMGSKLRVE 79
+L VE
Sbjct: 66 PIYFRGDHRLNVE 78
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 38.2 bits (89), Expect = 2e-04
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMND 68
R+YVG L V+++DLE F K+G++ + + FAFV F + DAE A N
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60
Query: 69 QDLMGSKLRVE 79
D +LRVE
Sbjct: 61 YDFGQCRLRVE 71
>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 = 38.5 bits (89), Expect = 2e-04
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
R +++VGGL+ ED++ FE+FGK+ + F+ GF FV F N+ E
Sbjct: 2 RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
Query: 63 CD 64
C+
Sbjct: 62 CE 63
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 38.4 bits (90), Expect = 2e-04
Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 5/59 (8%)
Query: 15 GGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQDL 71
GGL V +E+L FEK+G + + + PPG + FV +S+ DA AA D++N ++L
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVM---PPGKPYCFVSYSSIEDAAAAYDALNGKEL 64
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 24 EDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
+DL F FG + S V + F FV + N A+AA +MN + G +L+V
Sbjct: 13 QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72
Query: 79 E 79
+
Sbjct: 73 Q 73
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 12 VYVGGLTETVKKEDL-ELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDSM 66
++VG L V +E L EL F + G L V + +P G FAFV F +++ A +
Sbjct: 4 LFVGNLDARVTEEILYEL-FLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLL 62
Query: 67 NDQDLMGSKLRVE 79
N L G +LR++
Sbjct: 63 NGIRLFGRELRIK 75
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 30 FEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
F + GK +A P GFAFVE++ DAE A ++N L GS +RV
Sbjct: 24 FSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 38.0 bits (88), Expect = 2e-04
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
RVY+G L+ V+++D++ F +GKL + + G+ FVEF + DA+ A +N +D
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLK---NGYGFVEFEDSRDADDAVYELNGKD 57
Query: 71 LMGSKLRVEISRG 83
L G ++ VE +RG
Sbjct: 58 LCGERVIVEHARG 70
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 37.7 bits (88), Expect = 3e-04
Identities = 16/55 (29%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 26 LELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
LE F +FG L V++ PG + + +++++ AE A +++ +++ G KL+V
Sbjct: 16 LEDVFCRFGGLIDVYLV---PGKNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67
>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 = 37.8 bits (88), Expect = 3e-04
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMN 67
R++V + + DL F +FG + V + FN GF FV F+N DA+ A + ++
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61
Query: 68 DQDLMGSKLRV 78
+ G K+ V
Sbjct: 62 GTVVEGRKIEV 72
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 37.7 bits (88), Expect = 3e-04
Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-GFAFVEFSNQIDAEAACDSMND 68
T +++G L++ V +EDL+ FE++G++ S+ PP G A+V + DA A + +
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSI--DMIPPRGCAYVCMETRQDAHRALQKLRN 60
Query: 69 QDLMGSKLRVEISRGRG 85
L G K++V + +G
Sbjct: 61 VKLAGKKIKVAWAPNKG 77
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 37.5 bits (87), Expect = 3e-04
Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
+++VG ++ T ++L FE+FG++ +AFV + +A AA +++N +
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGK 57
Query: 70 DLMGSKLRVEI 80
++ G ++ VE+
Sbjct: 58 EVKGRRINVEL 68
>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 = 37.5 bits (88), Expect = 3e-04
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
V+VG L +++E+L FE G + +V + + GF +V F + A +
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60
Query: 67 NDQDLMGSKLRVE 79
N L G K+RV+
Sbjct: 61 NGIKLKGRKIRVK 73
>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 = 40.3 bits (94), Expect = 3e-04
Identities = 27/124 (21%), Positives = 51/124 (41%), Gaps = 23/124 (18%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
++YVG L + +++L FE FG + V + +P GF F++F + +A+ A +
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247
Query: 66 MNDQDLMGSKLRV-----------------EISRGRGRGRGGGGRG-GRFDSRGGRGGYR 107
MN +L G ++V +I + + G+ + + R
Sbjct: 248 MNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGD 307
Query: 108 GGGG 111
GG
Sbjct: 308 GGLL 311
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 37.7 bits (87), Expect = 4e-04
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
++V L TV +E LE F +FGKL V +AF+ F + A A + MN ++L
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGKEL 60
Query: 72 MGSKLRVEISR 82
G + + ++
Sbjct: 61 EGENIEIVFAK 71
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 37.5 bits (88), Expect = 4e-04
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+YVG L+ +E + F + G + + + + P GF FVE+ + DAE A +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 67 NDQDLMGSKLRVEISRG 83
N L +RV+ G
Sbjct: 61 NGTKLDDRIIRVDWDAG 77
>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 = 37.4 bits (87), Expect = 4e-04
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
R+++ L T +EDLE F K+G L+ V + + P GFAFV + A A
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 66 MNDQDLMGSKLRV 78
++ G L +
Sbjct: 64 LDGTVFQGRLLHL 76
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 37.7 bits (88), Expect = 5e-04
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQ 69
+YVG + + +L F+ FG++ + + F G + FV + DA A + ND
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGNDD 64
Query: 70 D 70
Sbjct: 65 P 65
>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 = 37.2 bits (87), Expect = 5e-04
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 30 FEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK 75
F + G++ SV + N G+ FVEF+ AE A S+N + + ++
Sbjct: 20 FAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQ 70
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM1 of nucleolysin TIAR, also termed TIA-1-related
protein, and a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 81
Score = 37.0 bits (85), Expect = 6e-04
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 12 VYVGGLTETVKKEDLELE-FEKFGKLNSVWV----AFNPPGFAFVEFSNQIDAEAACDSM 66
+YVG L+ V E L L+ F + G S + N P + FVEF DA AA +M
Sbjct: 2 LYVGNLSRDVT-EVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 59
Query: 67 NDQDLMGSKLRV 78
N + ++G +++V
Sbjct: 60 NGRKILGKEVKV 71
>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 = 36.8 bits (86), Expect = 6e-04
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMN 67
+++ L +++ + L F FG + S VA + G+ FV F + A A + +N
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64
>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 = 36.8 bits (86), Expect = 7e-04
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAAC 63
T+++VGGL + L F +FG++ V + G+ FV F ++ AE AC
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 36.9 bits (86), Expect = 8e-04
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF---NPPGFAFVEFSNQIDAEAACDSMND 68
+YVG L T + L F + G++ V +A P +AFVEF+ Q A +N
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLNG 65
Query: 69 QDLMGSKLRVEISR 82
G L+V S
Sbjct: 66 AMFGGRPLKVNHSN 79
>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 = 36.8 bits (85), Expect = 8e-04
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
++++GGL+ ++ LE F K+G+++ V V + GF FV F N DA+ A +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 66 MNDQDLMGSKLRVE 79
MN + + G ++RV+
Sbjct: 62 MNGKSVDGRQIRVD 75
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 36.6 bits (85), Expect = 8e-04
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 13/83 (15%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLN--------SVWVAFN-----PPGFAFVEFSNQID 58
V+V L ++DL F G + +W+ + P G A V + +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 59 AEAACDSMNDQDLMGSKLRVEIS 81
A AA + N++D MG+ ++V ++
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 36.5 bits (84), Expect = 8e-04
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
+RV++G L T VKK D+E F K+GK+ V G+AFV++ ++ A AA N
Sbjct: 2 SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSVH---KGYAFVQYISERHARAAVAGENA 58
Query: 69 QDLMGSKLRV 78
+ + G L +
Sbjct: 59 RIIAGQPLDI 68
>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 = 36.6 bits (85), Expect = 9e-04
Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
++VG L+ ++ + F ++G+++SV + +P GF +VEFS+Q A+AA D++
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 67 NDQDLMGSKLRVE 79
DL+G +R++
Sbjct: 61 GGTDLLGRPVRLD 73
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 36.6 bits (84), Expect = 9e-04
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
+RV++G L T VKK D+E F K+G++ V G+AFV++SN+ A A N
Sbjct: 2 SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSVH---KGYAFVQYSNERHARGAVIGENG 58
Query: 69 QDLMGSKLRVEIS 81
+ L G L + ++
Sbjct: 59 RVLAGQTLDINMA 71
>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 = 36.5 bits (85), Expect = 9e-04
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
R++VGG+ +E+L F +FG + V + + G+ FV F Q DAE M
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA-M 62
Query: 67 NDQDLMGSKLRV 78
+ + G KL +
Sbjct: 63 GNLNFRGKKLNI 74
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 36.3 bits (84), Expect = 0.001
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDA 59
VY+G L E+ +E+L + EKFG ++ + + AFV F + +A
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKI-VKEKNIAFVHFLSIANA 52
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 36.5 bits (85), Expect = 0.001
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVAFNPP------GFAFVEFSNQIDAEAA 62
R++VGG+ +T KE++ EF K + + V V +P GFAFVE+ + A A
Sbjct: 2 CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 37.7 bits (87), Expect = 0.001
Identities = 40/118 (33%), Positives = 56/118 (47%), Gaps = 14/118 (11%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
T++++GGL+ L F FG + V + GF FV F+++ A AA
Sbjct: 35 TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94
Query: 65 SMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGG 122
M+ ++L G +RV + R + GG GGY GGGGGYGGGG GG
Sbjct: 95 EMDGKELNGRHIRVNPANDRPSAP---------RAYGGGGGYSGGGGGYGGGGDGGGG 143
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4
is a splicing regulatory serine/arginine (SR) protein
that plays an important role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
For instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, it activates splicing of the cardiac troponin
T (cTNT) alternative exon by direct interactions with
the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between
the nucleus and cytoplasm. It contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 36.1 bits (83), Expect = 0.001
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 3/76 (3%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
RVY+G L+ ++ D+E F+ +GK+ V + G+ FVEF + DA+ A +N +D
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLK---NGYGFVEFDDLRDADDAVYELNGKD 57
Query: 71 LMGSKLRVEISRGRGR 86
L G ++ VE +RG R
Sbjct: 58 LCGERVIVEHARGPRR 73
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 38.1 bits (89), Expect = 0.001
Identities = 16/35 (45%), Positives = 17/35 (48%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGG 117
GR R G G G GG+ GGGG GGGG
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGG 266
Score = 37.3 bits (87), Expect = 0.003
Identities = 22/51 (43%), Positives = 24/51 (47%)
Query: 80 ISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGR 130
+ GR R G GR G GG G GGG GGG+ GG GGGG
Sbjct: 217 LYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGA 267
Score = 31.9 bits (73), Expect = 0.16
Identities = 21/65 (32%), Positives = 22/65 (33%)
Query: 100 RGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGG 159
R G G Y G + G R G G GGG GG GG GG
Sbjct: 205 RAIISGPMFGRSLYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGG 264
Query: 160 GGYRG 164
GG G
Sbjct: 265 GGASG 269
Score = 31.6 bits (72), Expect = 0.25
Identities = 20/55 (36%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 97 FDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFR---GSRGGGGYRG 148
GR R G G G GG G G GGF GS GGGG G
Sbjct: 215 RSLYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG 269
Score = 27.7 bits (62), Expect = 4.2
Identities = 20/56 (35%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 132 RGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRG 187
G + R G G R G G GG GG GF GG GGGG G
Sbjct: 216 SLYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSS--GGGGASG 269
Score = 26.9 bits (60), Expect = 6.8
Identities = 15/34 (44%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYG 114
S G G G GG GG GG GGGG G
Sbjct: 237 SSGSGGSGGSGGGSSGGGFSGG-GGSSGGGGASG 269
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 36.2 bits (83), Expect = 0.001
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
+YV L + +E +E EF K +V +AFV FSN+ DA A +++N + +
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSI-KPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVI 69
Query: 72 MGSKLRVEISR 82
GS + V +++
Sbjct: 70 DGSPIEVTLAK 80
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 35.6 bits (82), Expect = 0.001
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+++VG + E +E+L FE +G + S V FAFV + A+ A + +N ++
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ---FAFVHLRGEAAADRAIEELNGRE 58
Query: 71 LMGSKLRVEIS 81
L G KL VE S
Sbjct: 59 LHGRKLVVEHS 69
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 36.2 bits (84), Expect = 0.002
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF----------AFVEFSNQIDAE 60
RVY+ L+ + +EDLE + F ++ + + GF A+ EFS+ AE
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 61 AACDSMNDQDLMGSKLRV 78
+N + KL V
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78
>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 = 36.2 bits (83), Expect = 0.002
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMND 68
V GL+ + DL F K+G + V + ++ GFAFV F N DA+ A + N
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73
Query: 69 QDLMGSKLRVEIS 81
+L G ++RV+ S
Sbjct: 74 MELDGRRIRVDFS 86
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT
motif responsible for docking many substrates to
calcineurin, and an unrecognized C-terminal TxxP motif
of unknown function. .
Length = 75
Score = 35.6 bits (83), Expect = 0.002
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 23 KEDLELEFEKFGKLNSVWVAFNP-PGF--AFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
K LE F +G++ F P F A V FS+ +A A ++ GS LRV
Sbjct: 17 KAALESLFSSYGEI----ATFVYLPSFRRARVVFSSPEEAALARIELHGTVFEGSVLRV 71
>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 = 35.8 bits (82), Expect = 0.002
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
V+VG L+ + ED++ F FGK++ V + G+ FV F N++DAE A M
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 67 NDQDLMGSKLR 77
Q L G ++R
Sbjct: 64 GGQWLGGRQIR 74
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 38.2 bits (89), Expect = 0.002
Identities = 35/87 (40%), Positives = 38/87 (43%), Gaps = 19/87 (21%)
Query: 88 RGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYR 147
GGG G RFD GG GG+ GG G + D F GRG G GG G
Sbjct: 79 AGGGFGGRRFDGGGGFGGFGTGGDGAE----FNLNDLFDAAGRGGG--------GGIG-- 124
Query: 148 GGRDEYGG--GRGGGGYRGGRDSRGFD 172
D +GG RGGG R R RG D
Sbjct: 125 ---DLFGGLFNRGGGSARPSRPRRGND 148
Score = 33.9 bits (78), Expect = 0.042
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 137 FRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGG 189
R GGG+ G R + GG G GG+ G D F+ D ++ G G GGG
Sbjct: 74 TRRLFAGGGFGGRR--FDGGGGFGGFGTGGDGAEFNLN--DLFDAAGRGGGGG 122
Score = 27.4 bits (61), Expect = 5.2
Identities = 21/49 (42%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 113 YGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGG 161
+ GGG+ GG RF GGG G GGF G + GRGGGG
Sbjct: 78 FAGGGF--GGRRFDGGG---GFGGFGTGGDGAEFNLNDLFDAAGRGGGG 121
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 35.6 bits (82), Expect = 0.002
Identities = 16/66 (24%), Positives = 38/66 (57%), Gaps = 4/66 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSM 66
+++VG L + ++++E F +G++ +++ + G AFV++S++ A+AA ++
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60
Query: 67 NDQDLM 72
N M
Sbjct: 61 NGVYTM 66
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. Moreover, CPEB-2 impedes target RNA
translation at elongation; it directly interacts with
the elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a Zn-finger
motif. In addition, they do have conserved nuclear
export signals that are not present in CPEB-1. .
Length = 92
Score = 35.9 bits (83), Expect = 0.002
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVW-------VAFNPPGFAFVEFSNQIDAEAAC 63
+V+VGGL + ++++ F +FG L W F P G+AF+ F + +A
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 61
Query: 64 DS 65
D+
Sbjct: 62 DA 63
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for
growth. Srp1p is closely related to the SR protein
family found in metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. Some family members also contain another RRM
domain.
Length = 78
Score = 35.5 bits (82), Expect = 0.002
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV----AFNPPGFAFVEFSNQIDAEAACDSMN 67
+YV G + DL EFE++G+L + F FAFVE+ + DAE A + M+
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61
Query: 68 DQDLMGSK--LRVEISR 82
+ + L V+ ++
Sbjct: 62 GRRFPDTGDTLHVQWAK 78
>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 = 35.4 bits (82), Expect = 0.002
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACD 64
T + V L + + +E+L FE G + S + G+ FV++ ++ DA+ A +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 65 SMNDQDLMGSKLRV 78
++N ++ +L+V
Sbjct: 61 TLNGFEIRNKRLKV 74
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 35.3 bits (82), Expect = 0.002
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 23 KEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAAC 63
+++L F K+G ++ V V+ G A VEF+++ AEAA
Sbjct: 18 EDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAV 58
>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 = 35.2 bits (81), Expect = 0.003
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
VYVG + E+LE F G +N V + + P GFA++EFS++ A +
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA-L 60
Query: 67 NDQDLMGSKLRVEISR 82
++ G +++V R
Sbjct: 61 DESLFRGRQIKVMPKR 76
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 35.3 bits (82), Expect = 0.003
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMN 67
VG L E FG + ++ ++ G+ FVE++++ A A + ++
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62
Query: 68 DQDLMGSKLRV 78
+ + G KL+V
Sbjct: 63 GKQIGGRKLQV 73
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 36.9 bits (86), Expect = 0.003
Identities = 28/61 (45%), Positives = 31/61 (50%)
Query: 107 RGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGR 166
RGGGGG GGGG+ GG GGGG G G GG G G D + GG+ GG
Sbjct: 122 RGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGD 181
Query: 167 D 167
D
Sbjct: 182 D 182
Score = 32.7 bits (75), Expect = 0.081
Identities = 32/67 (47%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 86 RGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGG 145
RG GGGG GG F GG GG GGGGG GGGG GG G D + + GG
Sbjct: 122 RGGGGGGGGGGF---GGGGGGSGGGGGGGGGGGAPGG--GGAQASAPADDPWSSAPASGG 176
Query: 146 YRGGRDE 152
+ GG DE
Sbjct: 177 FGGGDDE 183
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 35.0 bits (80), Expect = 0.003
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
+YV L + +E ++ EF KF K V +AFV F N+ DA AA MN + +
Sbjct: 4 LYVRNLMISTTEETIKAEFNKF-KPGVVERVKKLRDYAFVHFFNREDAVAAMSVMNGKCI 62
Query: 72 MGSKLRVEISR 82
G+ + V +++
Sbjct: 63 DGASIEVTLAK 73
>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 = 35.0 bits (81), Expect = 0.003
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
+YV GL +T+ +++LE F +G++ + + + G F+ F +I+AE A ++
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 67 NDQDLMGS 74
N G+
Sbjct: 63 NGTIPPGA 70
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast
pre-mRNA-splicing factor Cwc2 and similar proteins.
This subfamily corresponds to the RRM of yeast protein
Cwc2, also termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and an intervening loop,
also termed RNA-binding loop or RB loop, between ZnF
and RRM, all of which are necessary and sufficient for
RNA binding. The ZnF is also responsible for mediating
protein-protein interaction. The C-terminal flexible
region of Cwc2 interacts with the WD40 domain of Prp19.
Length = 78
Score = 34.9 bits (81), Expect = 0.003
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 12 VYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
+YVGG+ + +E F ++G + + V G AFV + + AE A ++M
Sbjct: 4 LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRV-LPSKGIAFVRYKYRASAEFAKEAMA 62
Query: 68 DQDL 71
DQ L
Sbjct: 63 DQSL 66
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family
of histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes
Set1A and Set1B that are ubiquitously expressed
vertebrates histone methyltransferases exhibiting high
homology to yeast Set1. Set1A and Set1B proteins
exhibit a largely non-overlapping subnuclear
distribution in euchromatic nuclear speckles, strongly
suggesting that they bind to a unique set of target
genes and thus make non-redundant contributions to the
epigenetic control of chromatin structure and gene
expression. With the exception of the catalytic
component, the subunit composition of the Set1A and
Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The
genomic targeting of these complexes is determined by
the identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast
to Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 35.0 bits (81), Expect = 0.004
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 16 GLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMNDQD 70
L + + + L+ +K+G++ V + F+P G A V F + A+ + +N
Sbjct: 9 NLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTS 68
Query: 71 LMGSKLRVEI 80
+MG ++V +
Sbjct: 69 VMGKIIKVFL 78
>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 = 34.5 bits (80), Expect = 0.004
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGS 74
E KKE EL F FG++ SV + GFAFVEF + +A+ A +++ L G
Sbjct: 11 EATKKELREL-FSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGR 69
Query: 75 KLRVE 79
L +E
Sbjct: 70 HLVLE 74
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and
similar proteins. This subfamily corresponds to the
RRM of Nab3p, an acidic nuclear polyadenylated
RNA-binding protein encoded by Saccharomyces cerevisiae
NAB3 gene that is essential for cell viability. Nab3p
is predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA
processing. Nab3p contains an N-terminal
aspartic/glutamic acid-rich region, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal region rich in glutamine and proline
residues. .
Length = 71
Score = 34.3 bits (79), Expect = 0.004
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 11 RVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
R+++G L T+ V KEDL F +G+L + + + FV+F + A + +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNA---YGFVQFDSPESCANAINCEQGK 57
Query: 70 DLMGSKLRVEISR 82
+ G KL +E+S+
Sbjct: 58 MIRGRKLHLEVSK 70
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 34.6 bits (79), Expect = 0.004
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----NPPGFAFVEFSNQIDAEAACD 64
G +++G L + +++L EK GK+ + + N G+AFV FSN+ +A+ A
Sbjct: 1 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60
Query: 65 SMNDQDLMGSKL 76
+N+ ++ +L
Sbjct: 61 QLNNYEIRNGRL 72
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 37.2 bits (86), Expect = 0.004
Identities = 34/124 (27%), Positives = 44/124 (35%), Gaps = 16/124 (12%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
R RGRG G RG R + R G R +R + + G +G R
Sbjct: 445 RPVSRGRGRGQRGPRSQPQNQRRQQNRGRQSSQPP--RQQQNRSNQNNQRQSQGPNQGPR 502
Query: 142 GGGGYRGGRD-----EYGGGRGGGG----YR-----GGRDSRGFDGGKPDYYNGGGGGRG 187
G GGY YGGG+G YR + + + + G GRG
Sbjct: 503 GQGGYNLRPRTYQPQRYGGGQGRRWNPNPYRQSGQGRSQQQQPQPEARGNQSRTPGPGRG 562
Query: 188 GGGR 191
GGR
Sbjct: 563 QGGR 566
Score = 29.5 bits (66), Expect = 1.4
Identities = 14/63 (22%), Positives = 18/63 (28%), Gaps = 4/63 (6%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRG 142
G G+GR R +G + G G R GG + R R
Sbjct: 520 GGGQGRRWNPNPYRQSGQGRSQQQQPQPEARGNQSRTPGPGRGQGGRGNQN----RNQRS 575
Query: 143 GGG 145
G
Sbjct: 576 GNN 578
Score = 29.5 bits (66), Expect = 1.5
Identities = 26/105 (24%), Positives = 33/105 (31%), Gaps = 20/105 (19%)
Query: 82 RGRGRGRGGGGRGGRFD------SRGGRGGYRGGGG-----------GYGGG---GYRDG 121
RGR + + R + S+G G RG GG YGGG +
Sbjct: 471 RGRQSSQPPRQQQNRSNQNNQRQSQGPNQGPRGQGGYNLRPRTYQPQRYGGGQGRRWNPN 530
Query: 122 GDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGR 166
R G GR + +RG G GGRG
Sbjct: 531 PYRQSGQGRSQQQQPQPEARGNQSRTPGPGRGQGGRGNQNRNQRS 575
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 34.5 bits (79), Expect = 0.005
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
+YV GL +T+ +++LE F ++G++ + + + G F+ F +I+AE A
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 65 SMNDQDLMGS 74
+N Q G+
Sbjct: 61 GLNGQKPEGA 70
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 36.7 bits (85), Expect = 0.005
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 80 ISRGR-GRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFR 138
I GR RG GG G+GG + G+ GG + R G + G+ R
Sbjct: 387 IQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRR 446
Query: 139 G 139
Sbjct: 447 R 447
Score = 35.9 bits (83), Expect = 0.009
Identities = 23/76 (30%), Positives = 28/76 (36%), Gaps = 10/76 (13%)
Query: 124 RFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGG 183
R GG GRG GG RG + G RG GG + + SR KP
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGE----GGAKSASAKPAEKPSRRLGDAKP------A 440
Query: 184 GGRGGGGRFRSRSPVQ 199
G + R R + Q
Sbjct: 441 GEQQRRRRPRKPAAAQ 456
Score = 35.6 bits (82), Expect = 0.015
Identities = 17/72 (23%), Positives = 20/72 (27%), Gaps = 12/72 (16%)
Query: 126 GGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGG 185
G RG G G G RG + R E G R G
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRR------------LGDA 437
Query: 186 RGGGGRFRSRSP 197
+ G + R R P
Sbjct: 438 KPAGEQQRRRRP 449
Score = 34.8 bits (80), Expect = 0.022
Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 99 SRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGG 149
RGG G +GGG G G R G GG + SR G +
Sbjct: 393 QRGGGGRGQGGGRGQQQGQPRRGE---GGAKSASAKPAEKPSRRLGDAKPA 440
Score = 34.8 bits (80), Expect = 0.027
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 85 GRGRGGGGRGGRFDSRG-GRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRG 142
GR + GGG G+ RG +G R G GG + G + G + R
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRR 448
Score = 34.4 bits (79), Expect = 0.036
Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 7/68 (10%)
Query: 102 GRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGG 161
GR GGG G GGG + G RG+GG + + G + G
Sbjct: 390 GRQQRGGGGRGQGGGRGQ------QQGQPRRGEGGAKSASAKPA-EKPSRRLGDAKPAGE 442
Query: 162 YRGGRDSR 169
+ R R
Sbjct: 443 QQRRRRPR 450
Score = 33.2 bits (76), Expect = 0.071
Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 3/61 (4%)
Query: 73 GSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
G + R RG+G GRG R RG G R G + G + R
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPR---RGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRR 446
Query: 133 G 133
Sbjct: 447 R 447
Score = 27.5 bits (61), Expect = 6.2
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 155 GGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYN 203
RGGGG RG RG G+P G GG + + + P +R +
Sbjct: 392 QQRGGGG-RGQGGGRGQQQGQPR--RGEGGAKSASAK-PAEKPSRRLGD 436
>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 = 34.2 bits (78), Expect = 0.005
Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
RV++G L +++D+E F+ +G++ + + GF FVEF + DA+ A ++ ++
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLK---RGFGFVEFDDPRDADDAVYELDGKE 57
Query: 71 LMGSKLRVEISR 82
L ++ +E +R
Sbjct: 58 LCNERVTIEHAR 69
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 34.8 bits (79), Expect = 0.006
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
R +YV GL +T+ +++LE F ++G++ + + + G F+ F +I+AE A
Sbjct: 4 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63
Query: 63 CDSMNDQDLMGS 74
+N Q G+
Sbjct: 64 IKGLNGQKPPGA 75
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM1 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 33.7 bits (77), Expect = 0.006
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+++VG L ++++ FE++GK+ + N + FV ++ A+ A +++
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN---YGFVHMDDKTAADEAIRNLHHYK 58
Query: 71 LMGSKLRVE 79
L G + VE
Sbjct: 59 LHGVAINVE 67
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 36.2 bits (84), Expect = 0.007
Identities = 35/124 (28%), Positives = 39/124 (31%), Gaps = 7/124 (5%)
Query: 80 ISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDG------GDRFGGGGRGRG 133
+S G RG R G + GG GG GGGGG G G G G G G
Sbjct: 178 LSCGGVRGGPRPERAG-YGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSG 236
Query: 134 DGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFR 193
G G GG+ G G G GY G Y +G
Sbjct: 237 YGSGGTRSGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGSPSYSPSSSSNS 296
Query: 194 SRSP 197
S S
Sbjct: 297 SSSS 300
Score = 30.9 bits (70), Expect = 0.45
Identities = 38/111 (34%), Positives = 41/111 (36%), Gaps = 13/111 (11%)
Query: 93 RGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDE 152
G R R R GY GGGGG GGGG GG G G GF+ S G
Sbjct: 181 GGVRGGPRPERAGYGGGGGGGGGGGGG------GGSGPGPPPPGFKSSFPPPYGPGAGPS 234
Query: 153 YGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYN 203
G G GG G G P ++ G G G G F SR Y
Sbjct: 235 SGYGSGGTR-------SGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYG 278
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM1 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 91
Score = 34.2 bits (79), Expect = 0.007
Identities = 27/89 (30%), Positives = 38/89 (42%), Gaps = 23/89 (25%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVW--------------VAFNPPGF--------A 49
V+VG L T KK+DL+ F++FG + SV VA F A
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 50 FVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
+V F + AE A +N + G +RV
Sbjct: 63 YVVFKEEESAEKAL-KLNGTEFEGHHIRV 90
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 82
Score = 34.1 bits (79), Expect = 0.008
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 11/78 (14%)
Query: 11 RVYVGGLTETVKKEDLELEF----EKFGKLNS-----VWVAFNPPG-FAFVEFSNQIDAE 60
R+YVG L + +E+L F G + + V NP FAFVEF +A
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEAT 62
Query: 61 AACDSMNDQDLMGSKLRV 78
AA +++ G L++
Sbjct: 63 AAL-ALDGIIFKGQPLKI 79
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 33.7 bits (78), Expect = 0.008
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 17 LTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAA 62
L +E+L FEKFG L + + PP A VEF DA A
Sbjct: 8 LPFGTTEEELRELFEKFGSLGRLLL---PPSRTIALVEFLEPSDARKA 52
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 33.9 bits (78), Expect = 0.008
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 12 VYVGGLTETVKKEDLEL----EFEKFGKLNSVWV---AFNPPGFAFVEFSNQIDAEAACD 64
V+V L + ++LE F K+G L V V P +AFV+F+N DA+ A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRP-YAFVQFTNDDDAKNALA 63
Query: 65 SMNDQDLMGSKLRVEISRG 83
L G +R E ++
Sbjct: 64 KGQGTILDGRHIRCERAKV 82
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 33.9 bits (78), Expect = 0.008
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 4/66 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSM 66
+++VG L++ ++D+ FE FG + + P G AFV+FS+ +A+AA +++
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINAL 62
Query: 67 NDQDLM 72
+ M
Sbjct: 63 HGSQTM 68
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 33.8 bits (78), Expect = 0.009
Identities = 19/69 (27%), Positives = 34/69 (49%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM 72
+V + V+ E+L FE+FG + +++ A GF V + + A A ++ +L
Sbjct: 5 FVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTELG 64
Query: 73 GSKLRVEIS 81
G KL + S
Sbjct: 65 GRKLDIHFS 73
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 33.5 bits (76), Expect = 0.009
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG---FAFVEFSNQIDAEAACDSMND 68
+YVG L+ V + + F + G S + + G + FVEF A A+ +MN
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMNG 61
Query: 69 QDLMGSKLRV 78
+ +MG +++V
Sbjct: 62 RKIMGKEVKV 71
>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 = 33.8 bits (77), Expect = 0.009
Identities = 24/78 (30%), Positives = 48/78 (61%), Gaps = 6/78 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA----FNPPGFAFVEFSNQIDAEAACDSMN 67
++V GL+E +E L+ F+ G + + V + GF FV+FS++ DA+AA ++M
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60
Query: 68 DQDLMGSKLRVEISRGRG 85
D ++ G+K+ ++ ++ +G
Sbjct: 61 DGEIDGNKVTLDFAKPKG 78
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 33.4 bits (77), Expect = 0.010
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 8 RGTRVYVGG--LTETVKKEDLELEFEKFGKLNSVWVAFNPP-GFAFVEFSNQIDAEAACD 64
+G +YV G LTE + L+ F FG + ++ + FV F A+ A
Sbjct: 3 KGNTLYVHGYGLTEEI----LKKAFSPFGNIINI--SMEKEKNCGFVTFEKMESADRAIA 56
Query: 65 SMNDQDLMGSKLRVEISR 82
+N + G +L+V ++R
Sbjct: 57 ELNGTTVQGVQLKVSLAR 74
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells and also regulates the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 33.5 bits (76), Expect = 0.011
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
R +YV GL +T+ +++LE F ++G++ + + + G F+ F +I+AE A
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60
Query: 63 CDSMNDQDLMGS 74
+N Q G+
Sbjct: 61 IKGLNGQKPSGA 72
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 33.3 bits (77), Expect = 0.011
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 50 FVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
FVEF + AEAA D++N + +G +L+V+
Sbjct: 42 FVEFYDIRAAEAALDALNGRPFLGGRLKVK 71
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 33.4 bits (77), Expect = 0.011
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 18 TETVKKEDLELEFEKFGKLNSVWVA-FNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKL 76
++T K+ L EF+K GK+ SV V +A V F DAE A + + G+++
Sbjct: 12 SDTSLKDGLFHEFKKHGKVTSVKVHGTGSERYAIVFFRKPEDAEKALEVSKGKLFFGAEI 71
Query: 77 RVE 79
V
Sbjct: 72 EVT 74
>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate
regulator of differentiation 1 (Rod1). This subgroup
corresponds to the RRM3 of ROD1 coding protein Rod1, a
mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. Rod1 contains four repeats
of RNA recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and
does have RNA binding activities. .
Length = 76
Score = 33.4 bits (76), Expect = 0.012
Identities = 16/64 (25%), Positives = 31/64 (48%)
Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
+ + L + F +G ++ V + FN A V+ ++ A+ A +N Q L G +R
Sbjct: 11 DAITPHGLFILFGVYGDVHRVKIMFNKKENALVQMADATQAQLAMSHLNGQRLYGKVIRA 70
Query: 79 EISR 82
+S+
Sbjct: 71 TLSK 74
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there
is an unusual and conserved interdomain interaction
between RRM3 and RRM4. It is widely held that only RRMs
3 and 4 are involved in RNA binding and RRM2 mediates
PTB homodimer formation. However, new evidence show
that the RRMs 1 and 2 also contribute substantially to
RNA binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 33.8 bits (77), Expect = 0.013
Identities = 19/64 (29%), Positives = 32/64 (50%)
Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
E V + L + F +G + V + FN A V+ ++ A+ A +N Q L G LR+
Sbjct: 10 ERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPLRI 69
Query: 79 EISR 82
+S+
Sbjct: 70 TLSK 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 = 33.5 bits (76), Expect = 0.013
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
V+VG L+ + +D++ F FG+++ V + G+ FV F N+ DAE A M
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 67 NDQDLMGSKLR 77
Q L G ++R
Sbjct: 64 GGQWLGGRQIR 74
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 35.6 bits (82), Expect = 0.013
Identities = 31/160 (19%), Positives = 47/160 (29%), Gaps = 29/160 (18%)
Query: 30 FEKFGKLNSVWVAFNPPGF--AFVEFSNQIDAEAACDSMNDQDLMGS--KLRVEISR--- 82
F +GK+ + V F A VEF + A+ A ++N D+ L++E ++
Sbjct: 117 FNPYGKVLRI-VTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTR 175
Query: 83 -------------------GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYG--GGGYRDG 121
GR R + G+ G GY GG
Sbjct: 176 LNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPL 235
Query: 122 GDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGG 161
G +R + YG GG G
Sbjct: 236 AGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPG 275
>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 = 33.5 bits (76), Expect = 0.014
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEAAC 63
G +++ L + +DL F FG + S V + F FV + N + A+AA
Sbjct: 7 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66
Query: 64 DSMNDQDLMGSKLRVEISRGR 84
+MN + +L+V++ R +
Sbjct: 67 QAMNGFQIGMKRLKVQLKRSK 87
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich
splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or
SRp55). The second subgroup is composed of
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C) and plant pre-mRNA-splicing factor SF2
(SR1). These SR proteins are mainly involved in
regulating constitutive and alternative pre-mRNA
splicing. They also have been implicated in
transcription, genomic stability, mRNA export and
translation. All SR proteins in this family, except
SRSF5, undergo nucleocytoplasmic shuttling, suggesting
their widespread roles in gene expression. These SR
proteins share a common domain architecture comprising
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal
RS domains rich in serine-arginine dipeptides. Both
domains can directly contact with RNA. The RRMs appear
to determine the binding specificity and the SR domain
also mediates protein-protein interactions. In
addition, this subfamily includes the yeast nucleolar
protein 3 (Npl3p), also termed mitochondrial targeting
suppressor 1 protein, or nuclear polyadenylated
RNA-binding protein 1. It is a major yeast RNA-binding
protein that competes with 3'-end processing factors,
such as Rna15, for binding to the nascent RNA,
protecting the transcript from premature termination
and coordinating transcription termination and the
packaging of the fully processed transcript for export.
It specifically recognizes a class of G/U-rich RNAs.
Npl3p is a multi-domain protein with two RRMs,
separated by a short linker and a C-terminal domain
rich in glycine, arginine and serine residues. .
Length = 71
Score = 33.0 bits (76), Expect = 0.015
Identities = 22/69 (31%), Positives = 34/69 (49%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
RV V GL E +DL+ + G + V + G VEF++Q D E A ++ +
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTE 61
Query: 71 LMGSKLRVE 79
G ++RVE
Sbjct: 62 FRGRRVRVE 70
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 32.9 bits (76), Expect = 0.016
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 14/80 (17%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFNPPG--------FAFVEFSNQIDAEAA 62
++V + + D+ FE++G++ S+ + P F +V+F++ A AA
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRF-----PSLRFNKTRRFCYVQFTSPESAAAA 57
Query: 63 CDSMNDQDLMGSKLRVEISR 82
+N + G KL V+IS
Sbjct: 58 VALLNGKLGEGYKLVVKISD 77
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic
RNA-binding protein 25 and similar proteins. This
subfamily corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or
protein S164, or RNA-binding region-containing protein
7, an evolutionary-conserved splicing coactivator
SRm160 (SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif.
It localizes to the nuclear speckles and associates
with multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors.
It can activate proapoptotic Bcl-xS 5'ss by binding to
the exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.0 bits (76), Expect = 0.016
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVW------VAFNPPGFAFVEFSNQIDAEAAC 63
T V+VG + E V + + EK GK+ S W F F EF + A A
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLS-WKRVKDPSTGKLKAFGFCEFEDPEGALRAL 59
Query: 64 DSMNDQDLMGSKLRV 78
+N +L G KL V
Sbjct: 60 RLLNGLELGGKKLLV 74
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM2 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 32.9 bits (75), Expect = 0.017
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEAACDSM 66
+YV G T+++ +E L+ F + L ++++ + + F++F A AA D +
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60
Query: 67 N-DQDLMGSKL 76
+ +L G +
Sbjct: 61 TGEWELKGRRA 71
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 33.0 bits (76), Expect = 0.017
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 23 KEDLELEFEKFGKLNSVWVAFNPPGFA------FVEFSNQIDAEAACDSMNDQDLMGSKL 76
K+++E E EK+GK+ +V V A FVEFS+ +A A ++N + G K+
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGRKV 79
Query: 77 RVE 79
Sbjct: 80 TAR 82
>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 = 32.9 bits (75), Expect = 0.017
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
VYVG + E+LE F G +N V + + P G+A++EF+ + EAA ++
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-AL 60
Query: 67 NDQDLMGSKLRV 78
++ G ++V
Sbjct: 61 DESSFRGRVIKV 72
>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 = 35.3 bits (81), Expect = 0.018
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 13/87 (14%)
Query: 2 SDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---------PPGFAFVE 52
S +++ R+Y+G L + ++ ++ E FG L AFN G+AF E
Sbjct: 288 STTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLK----AFNLIKDIATGLSKGYAFCE 343
Query: 53 FSNQIDAEAACDSMNDQDLMGSKLRVE 79
+ + + A ++N +D +KL V+
Sbjct: 344 YKDPSVTDVAIAALNGKDTGDNKLHVQ 370
>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 = 33.0 bits (76), Expect = 0.020
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVAFNP-----PGFAFVEFSNQIDAEAA 62
G +++G L V ++ L F FG L + + +P GFAF+ + + ++AA
Sbjct: 1 GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60
Query: 63 CDSMNDQDLMGSKLRVE 79
++MN Q L + V
Sbjct: 61 IEAMNGQYLCNRPITVS 77
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 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 = 81
Score = 33.0 bits (75), Expect = 0.020
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+YV GL +T+ ++++E F ++G++ + + + G F+ F +I+AE A +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 67 NDQDLMGS 74
N Q +G+
Sbjct: 64 NGQKPLGA 71
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 34.8 bits (80), Expect = 0.021
Identities = 29/63 (46%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 102 GRGGYRGGGGGYGGGGYR-DGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGG 160
G GG+R G GG GGGG+ D GD FGGG +G G G G G D +GG G
Sbjct: 79 GNGGFRPGPGGGGGGGFNFDLGDLFGGGAQGGGGAGGGGGLG--------DVFGGLFNRG 130
Query: 161 GYR 163
G R
Sbjct: 131 GRR 133
>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 = 0.021
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
+Y+ GL T+ ++D+E F +FG++ + V + G AF+ F + +AE A S
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 67 NDQDLMGS 74
N GS
Sbjct: 63 NGHKPPGS 70
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 34.9 bits (80), Expect = 0.022
Identities = 13/33 (39%), Positives = 13/33 (39%)
Query: 110 GGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRG 142
GGG G G GGGGR G G R
Sbjct: 433 GGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRP 465
Score = 33.4 bits (76), Expect = 0.083
Identities = 15/33 (45%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 84 RGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGG 116
RG GR G G G R G GG R G G G
Sbjct: 432 RGGGRSGPGGGSR-SGSVGGGGRRDGAGADGKP 463
Score = 29.9 bits (67), Expect = 1.0
Identities = 17/35 (48%), Positives = 17/35 (48%)
Query: 124 RFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRG 158
R GGG G G G GS GGGG R G G R
Sbjct: 431 RRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRP 465
Score = 29.5 bits (66), Expect = 1.2
Identities = 17/45 (37%), Positives = 17/45 (37%), Gaps = 8/45 (17%)
Query: 88 RGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
R GGGR G G G GGGG RDG G R
Sbjct: 431 RRGGGRSG--------PGGGSRSGSVGGGGRRDGAGADGKPRPRR 467
Score = 28.8 bits (64), Expect = 2.5
Identities = 11/26 (42%), Positives = 11/26 (42%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRG 108
G G G G GGR D G G R
Sbjct: 440 GGGSRSGSVGGGGRRDGAGADGKPRP 465
Score = 26.8 bits (59), Expect = 9.7
Identities = 14/50 (28%), Positives = 14/50 (28%), Gaps = 6/50 (12%)
Query: 138 RGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRG 187
R R R G G G G G R DG D G R
Sbjct: 422 REQRAAEEQRRGGGRSGPGGGSRSGSVGGGGRR-DGAGAD-----GKPRP 465
>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 = 32.8 bits (75), Expect = 0.022
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPP------GFAFVEFSNQIDAEAACDSMNDQD-L 71
E KE EL F FG+L +V + GF FV+F + DA+ A ++ L
Sbjct: 11 EATVKELREL-FSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHL 69
Query: 72 MGSKLRVE 79
G +L +E
Sbjct: 70 YGRRLVLE 77
>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 = 32.5 bits (75), Expect = 0.022
Identities = 19/67 (28%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
+++VG L +T +ED+ FE++G + V + + G AFV+FS++ +A+ A ++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 66 MNDQDLM 72
++ + M
Sbjct: 61 LHGKVTM 67
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in
RNA-binding protein MRN1 and similar proteins. This
subgroup corresponds to the RRM2 and RRM4 of MRN1, also
termed multicopy suppressor of RSC-NHP6 synthetic
lethality protein 1, or post-transcriptional regulator
of 69 kDa, and is an RNA-binding protein found in
yeast. Although its specific biological role remains
unclear, MRN1 might be involved in translational
regulation. Members in this family contain four copies
of conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 82
Score = 32.9 bits (75), Expect = 0.022
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 12 VYVGGLT-----ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
VY+G ++ + +++L E EK+G++ S+ + AF+ F N +A AA ++
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRI-LREKACAFINFMNIPNAIAALQTL 63
Query: 67 NDQDLMGSKLRVEISRGR 84
N + + +R+ + R
Sbjct: 64 NGKKPYDTIVRINYGKDR 81
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 32.6 bits (75), Expect = 0.022
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 12 VYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
+ V L E V + L F +G + V + FN A ++ ++ A+ A +N
Sbjct: 2 LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61
Query: 71 LMGSKLRVEISRG 83
L G KLRV +S+
Sbjct: 62 LHGKKLRVTLSKH 74
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 34.8 bits (80), Expect = 0.024
Identities = 23/51 (45%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 108 GGGGGYGGGGYRDG------GDRFGGGGRGRG--DGGFRGSRGGGGYRGGR 150
GGG GYGGGG D FGGG R G GF GGGG R
Sbjct: 80 GGGPGYGGGGGDFNDIFSAFNDMFGGGARRGGGSPFGFEDVFGGGGRRRRA 130
Score = 30.5 bits (69), Expect = 0.49
Identities = 26/62 (41%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 81 SRGRGRGRGGGGRGGRF-DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGG-RGRGDGGFR 138
S G G G GG GG F D GGG GGG D FGGGG R R G
Sbjct: 76 SAASGGGPGYGGGGGDFNDIFSAFNDMFGGGARRGGGSPFGFEDVFGGGGRRRRASAGIP 135
Query: 139 GS 140
G+
Sbjct: 136 GT 137
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast
RNA-binding protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or
modifier of damage tolerance Mdt1, a novel
phosphothreonine (pThr)-containing protein that
specifically interacts with the pThr-binding site of
the Rad53 FHA1 domain. It is encoded by gene MDT1
(YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is
involved in normal G2/M cell cycle progression in the
absence of DNA damage and functions as a novel target
of checkpoint-dependent cell cycle arrest pathways. It
contains an N-terminal RRM, a nuclear localization
signal, a coiled coil, and a total of 15 SQ/TQ motifs.
cip1 (Csx1-interacting protein 1) and cip2
(Csx1-interacting protein 2) are novel cytoplasmic
RRM-containing proteins that counteract Csx1 function
during oxidative stress. They are not essential for
viability in fission yeast Schizosaccharomyces pombe.
Both cip1 and cip2 contain one RRM. Like PIN4, Cip2
also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 32.4 bits (74), Expect = 0.025
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR 82
G AF F + +A+ +++N ++ G +LRVE R
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 34.0 bits (78), Expect = 0.025
Identities = 32/63 (50%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 101 GGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGG 160
GGRGG GGGGG GGY GGGG G G G SR GGG GGG GGG
Sbjct: 109 GGRGGSGGGGGGGDEGGY-------GGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGG 161
Query: 161 GYR 163
R
Sbjct: 162 ASR 164
Score = 31.3 bits (71), Expect = 0.22
Identities = 31/67 (46%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 94 GGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEY 153
GGR S GG GG GG G GGGG G GG R G GG GGGG GG
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGGGGY---GGESRSGGGGGRASGGGGGGAGGGASRP 165
Query: 154 GGGRGGG 160
GGG
Sbjct: 166 SAPAGGG 172
Score = 31.3 bits (71), Expect = 0.22
Identities = 34/63 (53%), Positives = 35/63 (55%), Gaps = 8/63 (12%)
Query: 85 GRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGG 144
GRG GGG GG G GGY GGGGG GGG GG+ GGG GR GG G GGG
Sbjct: 110 GRGGSGGGGGG-----GDEGGYGGGGGGGGGGY---GGESRSGGGGGRASGGGGGGAGGG 161
Query: 145 GYR 147
R
Sbjct: 162 ASR 164
Score = 29.0 bits (65), Expect = 1.2
Identities = 24/58 (41%), Positives = 28/58 (48%)
Query: 126 GGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGG 183
GGGG G +GG+ G GGGG G + GG GG GG G +P GGG
Sbjct: 115 GGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGGG 172
Score = 29.0 bits (65), Expect = 1.5
Identities = 30/63 (47%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRG 142
GRG GGGG G GG GG GG GG G GG GGGG G G G R S
Sbjct: 110 GRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSG-GGGGRASGGGGGGAGGGASRPSAP 168
Query: 143 GGG 145
GG
Sbjct: 169 AGG 171
Score = 28.2 bits (63), Expect = 2.5
Identities = 24/46 (52%), Positives = 24/46 (52%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGG 128
G G G GGGG GG S GG G GGGGG GGG GGG
Sbjct: 127 GGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGGG 172
Score = 27.8 bits (62), Expect = 2.9
Identities = 22/57 (38%), Positives = 23/57 (40%)
Query: 145 GYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRR 201
G RGG GGG GGY GG G G GGGG GGG + R
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRP 165
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 32.3 bits (73), Expect = 0.026
Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
T+++VG ++ + ++L +FE++G + + + +AFV DA A +++
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEAIRGLDNT 57
Query: 70 DLMGSKLRVE 79
+ G ++ V+
Sbjct: 58 EFQGKRMHVQ 67
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 34.7 bits (80), Expect = 0.028
Identities = 14/51 (27%), Positives = 15/51 (29%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
GRGRG G + G R G G G G G R
Sbjct: 528 TGRGRGGPGQRPAADQHAAGAAAVARAGDGRPAAGRGDRAGAGVHAAGVHR 578
Score = 29.3 bits (66), Expect = 1.8
Identities = 16/55 (29%), Positives = 16/55 (29%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
R RGR G GRGG G G R R G G G
Sbjct: 521 RPEHRGRTGRGRGGPGQRPAADQHAAGAAAVARAGDGRPAAGRGDRAGAGVHAAG 575
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus
(HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and
enhancing HCV internal ribosome entry site
(IRES)-mediated translation initiation via the 3'-UTR.
IGF2BP1 contains four hnRNP K-homology (KH) domains,
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. It also
contains two putative nuclear export signals (NESs) and
a putative nuclear localization signal (NLS). .
Length = 77
Score = 32.3 bits (73), Expect = 0.028
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ- 69
++Y+G L E+V DLE FE K++ G+AFV+ ++ A A ++ + +
Sbjct: 3 KLYIGNLNESVTPADLEKVFEDH-KISYSGQFLVKSGYAFVDCPDEQWAMKAIETFSGKV 61
Query: 70 DLMGSKLRVEIS 81
+L G +L +E S
Sbjct: 62 ELHGKRLEIEHS 73
>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 = 34.5 bits (79), Expect = 0.028
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
+G +YV GL +T+ + +LE F FG++ + + + G F+ F + +A+ A
Sbjct: 88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA 147
Query: 63 CDSMNDQ 69
++N
Sbjct: 148 IKTLNGT 154
Score = 29.9 bits (67), Expect = 0.81
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEA 61
E T + V L +T+ +E++ F G++ S V G+ FV + DAE
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Query: 62 ACDSMNDQDLMGSKLRVEISR 82
A +S+N L ++V +R
Sbjct: 61 AVNSLNGLRLQNKTIKVSYAR 81
Score = 29.5 bits (66), Expect = 1.2
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 30 FEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
F FG + +V + + G+ FV +N +A A S+N L L+V
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343
>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 = 32.5 bits (75), Expect = 0.028
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 10/78 (12%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGK--LNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
+ + GL +ED+ + V + + GFAFVEF + DA D
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64
Query: 65 SMNDQDLM---GSKLRVE 79
++N+ D G +RV
Sbjct: 65 ALNNLDPFVIDGRVVRVS 82
>gnl|CDD|172774 PRK14286, PRK14286, chaperone protein DnaJ; Provisional.
Length = 372
Score = 34.6 bits (79), Expect = 0.029
Identities = 24/50 (48%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 102 GRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGD--GGFRGSRGGGGYRGG 149
G+ G G GG+G G Y D D FG G GD GG RG GGG R G
Sbjct: 70 GKAGVNAGAGGFGQGAYTDFSDIFGDFGDIFGDFFGGGRGGGSGGGRRSG 119
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 32.4 bits (74), Expect = 0.030
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDSMND 68
+VG L T+ +E+L FE++G + V + P G +AFV+F N A A +M+
Sbjct: 6 FVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSG 65
Query: 69 Q 69
Q
Sbjct: 66 Q 66
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 31.9 bits (73), Expect = 0.032
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSMN 67
++V L +V +DL+ F + G + V + GF V F + DA+ A + N
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 68 DQDLMGSKLRV 78
DL G +L V
Sbjct: 61 GYDLEGRELEV 71
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 34.6 bits (79), Expect = 0.032
Identities = 25/105 (23%), Positives = 36/105 (34%), Gaps = 15/105 (14%)
Query: 30 FEKFGKLNSVW-VAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRGR 88
F+ + W V N + F + A +++ + S + + G G
Sbjct: 451 FKHDLAIVLSWIVPKNNKLGKPITFGGKRPANGKGNNVPAKKSRPSNDQKQYVNKSGEGI 510
Query: 89 GGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRG 133
G+ GGRG RG G G GGG G G RG
Sbjct: 511 SKVGQSY-----GGRGRTRGRGRGGGGG---------RGRGYNRG 541
Score = 33.9 bits (77), Expect = 0.046
Identities = 21/68 (30%), Positives = 26/68 (38%), Gaps = 9/68 (13%)
Query: 113 YGGGGYRDGGDRFGGGGRGRGDG--------GFRG-SRGGGGYRGGRDEYGGGRGGGGYR 163
+GG +G + R G S+ G Y G G GRGGGG R
Sbjct: 475 FGGKRPANGKGNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGR 534
Query: 164 GGRDSRGF 171
G +RGF
Sbjct: 535 GRGYNRGF 542
Score = 33.1 bits (75), Expect = 0.096
Identities = 16/43 (37%), Positives = 16/43 (37%), Gaps = 9/43 (20%)
Query: 93 RGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDG 135
G G G RG G G GG GGGRGRG
Sbjct: 506 SGEGISKVGQSYGGRGRTRGRGRGG---------GGGRGRGYN 539
Score = 28.9 bits (64), Expect = 2.4
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 10/79 (12%)
Query: 125 FGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGG 184
FGG G G ++ + +Y G G + G+ G + G G
Sbjct: 475 FGGKRPANGKGNNVPAKKSRP-SNDQKQYVNKSGEGISKVGQSYGGRGRTR------GRG 527
Query: 185 GRGGGGRFRSRSPVQRRYN 203
GGGGR R + R +
Sbjct: 528 RGGGGGRGRGYN---RGFW 543
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment
factor B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described
functions in transcriptional repression, RNA splicing
and metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1
has been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
nuclear localization signal (NLS). The C-terminus of
SAFB1 contains Glu/Arg- and Gly-rich regions that might
be involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously
coexpressed and share very high sequence similarity,
suggesting that they might function in a similar
manner. However, unlike SAFB1, exclusively existing in
the nucleus, SAFB2 is also present in the cytoplasm.
The additional cytoplasmic localization of SAFB2
implies that it could play additional roles in the
cytoplasmic compartment which are distinct from the
nuclear functions shared with SAFB1.
Length = 76
Score = 32.0 bits (72), Expect = 0.033
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPG---FAFVEFSNQIDAEAAC 63
G ++V GL+ T + DL+ F K+GK+ V N PG + FV S +A
Sbjct: 1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60
Query: 64 DSMNDQDLMGSKLRVE 79
+ ++ +L G + VE
Sbjct: 61 NHLHRTELHGRMISVE 76
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 32.0 bits (73), Expect = 0.034
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 11 RVYVGGLTETVKKEDLELE----FEKFGKLNSVWVAFNPPGF-----AFVEFSNQIDAEA 61
+YV G++ + +E++ F +FG L SV V N AFV+F + A
Sbjct: 2 TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61
Query: 62 ACDSMNDQDLMGS 74
A + N + L
Sbjct: 62 AQKACNGKWLFQG 74
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the
formation of D-loops in superhelical duplex DNA, and is
involved in cell proliferation. PSF can also interact
with multiple factors. It is an RNA-binding component
of spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions,
such as DNA recombination and RNA synthesis,
processing, and transport. PSF contains two conserved
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for interactions with RNA and for
the localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 71
Score = 31.8 bits (72), Expect = 0.034
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R++VG L + +++ + F K+G+ V++ GF F++ ++ AE A ++D
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTP 61
Query: 71 LMGSKLRV 78
+ G +LRV
Sbjct: 62 MRGRQLRV 69
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 31.8 bits (73), Expect = 0.037
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP--GFAFVEFSNQIDAEAACDSMNDQ 69
+YV L + E+L F K+G + + + G AFV + + DA+ ACD ++
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64
Query: 70 DLMGSKLRV 78
++ L V
Sbjct: 65 NVANRYLVV 73
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 31.9 bits (72), Expect = 0.037
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR 82
+AFV F+++ DA A +++N +L GS + V +++
Sbjct: 39 YAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAK 73
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 32.0 bits (72), Expect = 0.038
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
VY GG+T + ++ + F FG++ V V F G++FV F++ A A S+N +
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRV-FPDKGYSFVRFNSHESAAHAIVSVNGTTI 61
Query: 72 MG 73
G
Sbjct: 62 EG 63
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 34.1 bits (78), Expect = 0.041
Identities = 26/61 (42%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 132 RGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
R G G R GGG GGGY GG S G G P GGGGG G GG
Sbjct: 48 RSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGF-PFIIPGGGGGGGFGGI 106
Query: 192 F 192
F
Sbjct: 107 F 107
Score = 33.4 bits (76), Expect = 0.066
Identities = 22/56 (39%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 110 GGGYGGGGYRDGGDRFGG-GGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRG 164
GG GGG +R G G G GG+ G GG G GG GGGG+ G
Sbjct: 50 GGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGG 105
Score = 31.1 bits (70), Expect = 0.38
Identities = 27/68 (39%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 76 LRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRF----GGGGRG 131
L V + G GGG G G GGGY GGGY GG F GGG G
Sbjct: 41 LSVAAAARSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGG 100
Query: 132 RGDGGFRG 139
G GG G
Sbjct: 101 GGFGGIFG 108
>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 = 32.0 bits (72), Expect = 0.042
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
+++VGG+ E ++ L FE++GK++++ + + GF FV F +
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDH 52
>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 = 31.4 bits (72), Expect = 0.052
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
++++GGL + ++ ++ E FGKL + + + G+AF E+ + + A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 66 MNDQDLMGSKLRV 78
+N L KL V
Sbjct: 62 LNGMQLGDKKLTV 74
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 31.5 bits (72), Expect = 0.054
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
+++VG L TV ++L+ F +FGK+ S V F+ G+ FV FS++
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 31.3 bits (71), Expect = 0.054
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
V+ G ++ ++E F K+G+++ V + GFAFV ++ DAE A +++ +
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDMK---SGFAFVYMEDERDAEDAIRGLDNFEF 59
Query: 72 --MGSKLRVE 79
+LRVE
Sbjct: 60 GRQRRRLRVE 69
>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 = 31.6 bits (72), Expect = 0.057
Identities = 16/65 (24%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACD 64
+++VG + ++++DL FE+FGK+ + V + G AF+ + + A A
Sbjct: 6 IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65
Query: 65 SMNDQ 69
++++Q
Sbjct: 66 ALHEQ 70
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 31.6 bits (71), Expect = 0.059
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF---AFVEFSNQIDAEAAC 63
V+V GL E+V + DL EKFG + +V P F A VEF +++ C
Sbjct: 6 VHVRGLCESVVEADLVEALEKFGPI--CYVMMMP--FKRQALVEFEM-VESAKKC 55
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 33.7 bits (76), Expect = 0.059
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFAFVEFS 54
G R++VGGL E+V ++DL F G +++V +V FA+++FS
Sbjct: 10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFS 56
>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM2 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 80
Score = 31.6 bits (71), Expect = 0.061
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
+++ L E + L + F +F V + AFVEF N++ + AA +++
Sbjct: 8 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEVQSAAAKEAL 62
>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 = 31.6 bits (71), Expect = 0.063
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
++++GGL+ +E L +E++GKL V +P GF FV FS + +AA
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60
>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM1 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 31.5 bits (71), Expect = 0.063
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
++Y+G L+E DLE F+ + F+ P G+AFV+ ++ A A D+
Sbjct: 3 KLYIGNLSENASPLDLESIFKDSK------IPFSGPFLVKSGYAFVDCPDESWAMKAIDT 56
Query: 66 MNDQ-DLMGSKLRVEIS 81
++ + +L G + VE S
Sbjct: 57 LSGKVELHGKVIEVEHS 73
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 33.6 bits (77), Expect = 0.064
Identities = 16/69 (23%), Positives = 20/69 (28%)
Query: 100 RGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGG 159
R G G G + + G+ GG+R G Y GG GG
Sbjct: 2 RSTDGSSSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANHQDNYGGFRPGYGNYSGGYGG 61
Query: 160 GGYRGGRDS 168
G S
Sbjct: 62 FGMNSYGSS 70
Score = 29.0 bits (65), Expect = 1.7
Identities = 13/68 (19%), Positives = 17/68 (25%), Gaps = 3/68 (4%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGG---RGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGF 137
S G + G GG+R G + GG G G +
Sbjct: 8 SSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANHQDNYGGFRPGYGNYSGGYGGFGMNSY 67
Query: 138 RGSRGGGG 145
S G
Sbjct: 68 GSSTLGKR 75
Score = 28.6 bits (64), Expect = 2.8
Identities = 15/67 (22%), Positives = 17/67 (25%), Gaps = 4/67 (5%)
Query: 123 DRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGG 182
R G G S Y Y G + G +P Y N
Sbjct: 1 MRSTDGSSSNGSVSSGPSNNYNSYG----PYPDSSNPYGNYQANHQDNYGGFRPGYGNYS 56
Query: 183 GGGRGGG 189
GG G G
Sbjct: 57 GGYGGFG 63
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1),
a ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response; it binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
Meanwhile, HuR also has pro-apoptotic function by
promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Like other Hu proteins, HuR contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 81
Score = 31.2 bits (70), Expect = 0.071
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAACD 64
T + V L + + +++L F G++ S VA + G+ FV + N DAE A +
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 65 SMNDQDLMGSKLRVEISR 82
++N L ++V +R
Sbjct: 62 TLNGLRLQSKTIKVSYAR 79
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 31.2 bits (71), Expect = 0.072
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG---FAFVEFSNQIDAEAACDSMN- 67
++VGG+ ++ ++DL+ F G++ V + + FAFVEF+ DAE+A ++N
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFA---DAESALSALNL 59
Query: 68 DQDLMGSK-LRVEISR 82
L+G LRV S+
Sbjct: 60 SGTLLGGHPLRVSPSK 75
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 33.2 bits (77), Expect = 0.072
Identities = 19/39 (48%), Positives = 22/39 (56%), Gaps = 6/39 (15%)
Query: 108 GGGGGYGG-GGYRDG-----GDRFGGGGRGRGDGGFRGS 140
GGGGG+GG GG+ D GD FGGG G RG+
Sbjct: 78 GGGGGFGGGGGFGDIFGDIFGDIFGGGRGGGRQRARRGA 116
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 that interacts
specifically with a highly serine-phosphorylated form
of the carboxy-terminal domain (CTD) of the largest
subunit of RNA polymerase II (pol II) and may play a
direct role in coupling with both, transcription and
pre-mRNA processing, processes. SCAF4 and SCAF8 both
contain a conserved N-terminal CTD-interacting domain
(CID), an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and serine/arginine-rich
motifs.
Length = 81
Score = 31.2 bits (70), Expect = 0.073
Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
T ++VG L + ++D+ E+FG + S+ + P G A++ ++ DA A ++
Sbjct: 5 TTLWVGQLDKRTTQQDVTSLLEEFGPIESINM-IPPRGCAYIVMVHRQDAYRALQKLSRG 63
Query: 70 DLMGSKLRVEISRGRGRG 87
++ ++ ++I+ +G
Sbjct: 64 NVKVNQKSIKIAWALNKG 81
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a
specific inhibitory effect on oestrogen action, SLTM is
shown to exert a generalized inhibitory effect on gene
expression associated with induction of apoptosis in a
wide range of cell lines. .
Length = 74
Score = 31.2 bits (70), Expect = 0.078
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPG---FAFVEFSNQIDAEAACDSM 66
++V GL+ K DL+ F K+GK+ S V N PG + V S+ + +
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 67 NDQDLMGSKLRVE 79
+ +L G ++ VE
Sbjct: 62 HRTELHGQQISVE 74
>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative
RNA-binding protein 15B (RBM15B) from vertebrate. This
subgroup corresponds to the RRM3 of RBM15B, also termed
one twenty-two 3 (OTT3), a paralog of RNA binding motif
protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 76
Score = 31.1 bits (70), Expect = 0.085
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
TR++VGGL L EF++FG + ++ FA++++ + A+AAC M
Sbjct: 3 TRLWVGGLGPNTSLAALAREFDRFGSIRTI-DYVKGDSFAYIQYESLDAAQAACAQMRGF 61
Query: 70 DLMGSKLRVEI 80
L G R+ +
Sbjct: 62 PLGGPDRRLRV 72
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 32.9 bits (75), Expect = 0.088
Identities = 22/112 (19%), Positives = 28/112 (25%), Gaps = 2/112 (1%)
Query: 98 DSRGGRGGYRGGGGGYGG-GGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGG 156
D + R +R G G GG GR RG G YG
Sbjct: 299 DKKRRRRRWRNMGHDSRGPYNANYGGQFNSRSGRTGSSESIRGFTYDSSTTYGGSSYGTS 358
Query: 157 RG-GGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYNVDEY 207
+ G R + G GG G S + V +
Sbjct: 359 QTDSTSTYGSRSTFDSSTGGGSQSGGGSTYGGSSTFDGSSRGSSDSFGVSYF 410
Score = 32.5 bits (74), Expect = 0.14
Identities = 25/104 (24%), Positives = 30/104 (28%), Gaps = 7/104 (6%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRG--RGDGG--F 137
R G G R G G G Y D +GG G + D +
Sbjct: 308 RNMGHDSRGPYNANYGGQFNSRSGRTGSSESIRGFTY-DSSTTYGGSSYGTSQTDSTSTY 366
Query: 138 RGSRGGGGYRGGRDEYGGGRGGGGYRG-GRDSRG-FDGGKPDYY 179
GG + GGG GG SRG D Y+
Sbjct: 367 GSRSTFDSSTGGGSQSGGGSTYGGSSTFDGSSRGSSDSFGVSYF 410
Score = 26.7 bits (59), Expect = 9.3
Identities = 16/63 (25%), Positives = 21/63 (33%), Gaps = 6/63 (9%)
Query: 109 GGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDS 168
YG D GGG + G + GS G G + G Y G + +
Sbjct: 362 STSTYGSRSTFDS--STGGGSQSGGGSTYGGSSTFDGSSRGSSDSFGVS----YFGPQQT 415
Query: 169 RGF 171
GF
Sbjct: 416 VGF 418
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 33.1 bits (76), Expect = 0.10
Identities = 15/41 (36%), Positives = 18/41 (43%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGG 122
R + RG+G G+ G R RGG R G G R G
Sbjct: 104 RTQRRGQGPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGA 144
Score = 32.7 bits (75), Expect = 0.11
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 117 GYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGR-DEYGGGRGGGGYRGGRDS 168
G + R G G +G+ R ++ GG + R GGR G +R R++
Sbjct: 100 GKQTRTQRRGQGPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGARHRRLREA 152
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 32.6 bits (74), Expect = 0.12
Identities = 29/65 (44%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 108 GGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRD 167
G GGG G GG GGD GG G GG G GGGG GG E GG G + G
Sbjct: 84 GDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSE-GGSTGKSLTKEGVG 142
Query: 168 SRGFD 172
+ FD
Sbjct: 143 AGDFD 147
Score = 28.7 bits (64), Expect = 2.2
Identities = 24/62 (38%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 127 GGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGR 186
GGG G G G GGG GG GGG GG GG D G +GG G
Sbjct: 86 GGGTGEGGSDTGGDTGGGNTGGGS---GGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVG 142
Query: 187 GG 188
G
Sbjct: 143 AG 144
Score = 28.7 bits (64), Expect = 2.3
Identities = 21/58 (36%), Positives = 22/58 (37%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGS 140
G G G GG GG GG GG G GGG DGG GG G+
Sbjct: 86 GGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGA 143
Score = 27.2 bits (60), Expect = 5.8
Identities = 22/70 (31%), Positives = 23/70 (32%), Gaps = 2/70 (2%)
Query: 76 LRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDG 135
G G G G GG D+ G G GG GG GG GG GG G
Sbjct: 77 TGSADKDGDGGGTGEGGSDTGGDT--GGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGK 134
Query: 136 GFRGSRGGGG 145
G G
Sbjct: 135 SLTKEGVGAG 144
Score = 26.8 bits (59), Expect = 9.3
Identities = 20/56 (35%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 85 GRGRGGGGRGGRFDSRGGRGGYRGGG---GGYGGGGYRDGGDRFGGGGRGRGDGGF 137
G GG G ++ GG GG GG GG GGG G G G G F
Sbjct: 91 EGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGAGDF 146
Score = 26.8 bits (59), Expect = 9.4
Identities = 23/64 (35%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 98 DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGR 157
D GG G G G GG GG GG G G GG GGG GG +
Sbjct: 83 DGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGG----SDGGGSEGGSTGKSLTK 138
Query: 158 GGGG 161
G G
Sbjct: 139 EGVG 142
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 32.8 bits (74), Expect = 0.12
Identities = 33/89 (37%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 111 GGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSR- 169
G GGG GG+R GGGR GGF R G G R D R GR +
Sbjct: 108 GRLGGGFRSYGGNRSYGGGRRPYGGGFDDDRRGWGPRVS-DFPQPSRADEIDDWGRGKKS 166
Query: 170 ----GFDGGKPDYYNGGGGGRGGGGRFRS 194
FD G+ Y GGG GGGG
Sbjct: 167 TPLPSFDQGRQGRYPSGGGAFGGGGGGGG 195
Score = 27.7 bits (61), Expect = 5.6
Identities = 34/119 (28%), Positives = 40/119 (33%), Gaps = 14/119 (11%)
Query: 81 SRGRGRGRGGGGR--GGRFDSRGGRGGYRGGG----------GGYGGGGYRDGGDRFGGG 128
S G R GGG R GG FD G R +G G F G
Sbjct: 116 SYGGNRSYGGGRRPYGGGFDDDRRGWGPRVSDFPQPSRADEIDDWGRGKKSTPLPSFDQG 175
Query: 129 GRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRG 187
+GR G GGGG GG + GG G DS + K + + G G
Sbjct: 176 RQGRYPSGGGAFGGGGGGGGGGERRSGGFRDSP--GADDSDRWGRKKVETFGSAFGENG 232
>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 = 0.12
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAAC 63
GT ++VG + + +++L FEK G + + + +P G+AFV F + A+ A
Sbjct: 1 GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60
Query: 64 DSMNDQDLMGSK 75
N+ ++ K
Sbjct: 61 KLYNNHEIRPGK 72
>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 = 30.7 bits (69), Expect = 0.12
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQ 56
+++VGG+ E ++ L FEK+GK+ ++ V + GFAFV F +
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDH 52
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 30.2 bits (69), Expect = 0.13
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV------AFNPPGFAFVEFSNQIDAEAACDS 65
VYV G + +D++ FEKFGK+N++ + F G FVEF + DA+ +
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFK--GSVFVEFKTEEDAKKFLE- 58
Query: 66 MNDQDLMGSKLRVE 79
+L V
Sbjct: 59 KEKLKYKEKELTVM 72
>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 = 30.5 bits (69), Expect = 0.15
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSV-----WVAFNPPGFAFVEFSNQIDAEAACD 64
T + V L + + ++++ F G++ S V G+ FV + + DAE A +
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 65 SMNDQDLMGSKLRV 78
++N L ++V
Sbjct: 62 TLNGLRLQNKTIKV 75
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 30.2 bits (68), Expect = 0.15
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
+GT V + L TV E L F+ +G + + FVEF + DA A +MN
Sbjct: 1 QGTLV-IFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMN 59
Query: 68 DQDLMGSKLRVE 79
+++ G + +E
Sbjct: 60 GKEISGKPVVIE 71
>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 = 30.4 bits (68), Expect = 0.15
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEAAC 63
G +++ L + DL F FG + S V + F FV + N A+AA
Sbjct: 4 GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63
Query: 64 DSMNDQDLMGSKLRVE 79
+MN + +L+V+
Sbjct: 64 QAMNGFQIGTKRLKVQ 79
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 30.7 bits (70), Expect = 0.15
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 24 EDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
+D+ EFEKFG++ V N G +V++ ++ +A AA N + G +L E
Sbjct: 43 DDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCE 102
Query: 80 ISR 82
S
Sbjct: 103 FSP 105
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup
corresponds to the RRM1 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Its
cellular function remains unknown currently, however,
PSPC1 forms a novel heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 30.3 bits (68), Expect = 0.15
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R++VG L + +ED + FEK+G+ + V++ + GF F+ ++ AE A ++
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-RGFGFIRLESRTLAEIAKAELDGTI 61
Query: 71 LMGSKLRV 78
L LR+
Sbjct: 62 LKNRPLRI 69
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 30.3 bits (68), Expect = 0.17
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 12 VYVGGLTETVKKEDLELE----FEKFGKLNSVWVAFNP---PGFAFVEFSNQIDAEAACD 64
+Y+ L E VKKE+L+ F +FG++ + VA G AFV F + A A
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDI-VALKTLKMRGQAFVVFKDISSATNALR 60
Query: 65 SMNDQDLMGSKLRVEISR 82
SM +R+ S+
Sbjct: 61 SMQGFPFYDKPMRIAYSK 78
>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 = 30.1 bits (68), Expect = 0.17
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEA 61
++GGL+ E L F KFG++ V +P GF FV FS+ +
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDK 55
>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 = 30.1 bits (68), Expect = 0.17
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDSM 66
++VG L+ +++L F + G++ V + GFAFV+F + E A +++
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE---EIEFATNAL 57
Query: 67 NDQDLMGSKLRVEI 80
+ L G LRVE
Sbjct: 58 KGKHLNGRALRVEY 71
>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 = 30.0 bits (68), Expect = 0.17
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
++++GGL+ + L+ F ++G++ V +P GF FV F++ + +AA
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57
>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 = 30.2 bits (68), Expect = 0.19
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAA 62
ER +++VG L++ + D+ + F FG + V + G AFV F+++ A A
Sbjct: 1 ER--KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNA 58
Query: 63 CDSMNDQDLM 72
+M+ M
Sbjct: 59 IKAMHHSQTM 68
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 29.9 bits (68), Expect = 0.19
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 43 FNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG 83
FAFV F ++ + + A + ++ G L +++
Sbjct: 39 LKRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). SLT11 can facilitate the cooperative formation
of U2/U6 helix II in association with stem II in the
yeast spliceosome by utilizing its RNA-annealing and
-binding activities. .
Length = 86
Score = 30.1 bits (68), Expect = 0.20
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM 72
++ G+ + + + + FE+FGK SV V + FV F + AE ++++ L
Sbjct: 6 FLFGVEDDLPEYKIRDYFEQFGKSKSVIVN-HRAKCGFVRFETREAAEKFAAAISENGLN 64
Query: 73 GSKLR 77
R
Sbjct: 65 AGLSR 69
>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 = 29.9 bits (67), Expect = 0.20
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
+++VGGL V + DL F +FG + V + GF FV F N A+ A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM1 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 29.8 bits (67), Expect = 0.20
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA----FNPPGFAFVEFSNQIDAEAACDSMN 67
+YVG L V ++ L+ F+ G + +V + + FVE+ DAE A ++N
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 68 DQDLMGSKLRV 78
+ + +++RV
Sbjct: 61 GRQIENNEIRV 71
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 32.0 bits (72), Expect = 0.21
Identities = 19/64 (29%), Positives = 24/64 (37%), Gaps = 13/64 (20%)
Query: 80 ISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRG 139
++ R RGR GG +S G G G GG G G+G G R
Sbjct: 382 VANARLRGRPSSSIGGNANSSTGGNGAAGAGGA-------------GAAGKGGGSAAARA 428
Query: 140 SRGG 143
+ GG
Sbjct: 429 TVGG 432
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A
or U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding
protein associated with the U1 snRNP, a small
RNA-protein complex involved in pre-mRNA splicing. U1A
binds with high affinity and specificity to stem-loop
II (SLII) of U1 snRNA. It is predominantly a nuclear
protein that shuttles between the nucleus and the
cytoplasm independently of interactions with U1 snRNA.
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins, including polypyrimidine tract binding
protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and it may be free for binding other proteins.
U1A also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 30.1 bits (67), Expect = 0.21
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
+++ L E + L + F +F V + AFVEF N++ A AA +++
Sbjct: 8 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAREAL 62
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 29.7 bits (67), Expect = 0.22
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP------PGFAFVEFSNQIDAEAACDSM 66
Y+G L V +ED++ EF + ++SV + P GF + EF ++ A S+
Sbjct: 5 YLGNLPYDVTEEDIK-EFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL-SL 62
Query: 67 NDQDLMGSKLRVEIS 81
ND+ L ++RV+I+
Sbjct: 63 NDESLKNRRIRVDIA 77
>gnl|CDD|190398 pfam02714, DUF221, Domain of unknown function DUF221. This
family consists of hypothetical transmembrane proteins
none of which have any function, the aligned region is
at 538 residues at maximum length.
Length = 325
Score = 31.7 bits (73), Expect = 0.22
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 49 AFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
AFV F +Q A+ A ++ Q K +
Sbjct: 1 AFVTFKSQAAAQMAAQAL--QHHNPLKWPTYL 30
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 30.0 bits (67), Expect = 0.24
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMND 68
V L+ V E LE F +FG + V + P G FVEF+ + A A + D
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALERCAD 62
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 29.6 bits (67), Expect = 0.24
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMND 68
V L+ V E LE F +FG++ V + G VEFS + A+AA ++
Sbjct: 4 VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCSE 62
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM4 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 29.7 bits (67), Expect = 0.25
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
VY+G + +++ +E L +F ++G++ SV AFV F+N +A A D +
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESV-NYLREKNCAFVNFTNISNAIKAIDGV 59
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 29.6 bits (66), Expect = 0.26
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF----AFVEFSNQIDAEAACDSM 66
++++G +++ + D+ + F FG++ + P G AFV F+ + A+ A +M
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 62
Query: 67 NDQDLM 72
+ M
Sbjct: 63 HQAQTM 68
>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 = 29.6 bits (66), Expect = 0.27
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
++++GGL+ E L FE++G L V +P GF FV +S+ + +AA ++
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63
>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 = 29.4 bits (66), Expect = 0.27
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
V+VG + +E L+ F + G + S + ++ P G+ F E+ +Q A +A ++
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 67 NDQDLMGSKLRVE 79
N +L G +LRV+
Sbjct: 61 NGYELNGRQLRVD 73
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 31.1 bits (71), Expect = 0.29
Identities = 20/64 (31%), Positives = 22/64 (34%), Gaps = 11/64 (17%)
Query: 122 GDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNG 181
G R GGG R GG G GGG+ GF P + G
Sbjct: 5 GGRIGGGSFRAPSRSSSSPRSSSPGGGG----YYGSPGGGF-------GFPFLIPFFGFG 53
Query: 182 GGGG 185
GGGG
Sbjct: 54 GGGG 57
Score = 31.1 bits (71), Expect = 0.31
Identities = 18/56 (32%), Positives = 18/56 (32%), Gaps = 4/56 (7%)
Query: 86 RGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRF----GGGGRGRGDGGF 137
G GG R SR GG G G GG F G G G G F
Sbjct: 4 SGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGGLF 59
Score = 28.8 bits (65), Expect = 1.9
Identities = 18/54 (33%), Positives = 19/54 (35%), Gaps = 2/54 (3%)
Query: 138 RGSR-GGGGYRGGRDEYGGGRGGGGYRGG-RDSRGFDGGKPDYYNGGGGGRGGG 189
G R GGG +R R GG S G G P G G GGG
Sbjct: 4 SGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGG 57
Score = 28.8 bits (65), Expect = 2.0
Identities = 24/87 (27%), Positives = 28/87 (32%), Gaps = 7/87 (8%)
Query: 73 GSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFG----GG 128
G R G GG + S GG G+ +G GG GG FG
Sbjct: 10 GGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGG---GGGLFGLLILMA 66
Query: 129 GRGRGDGGFRGSRGGGGYRGGRDEYGG 155
G FR + GGGG G
Sbjct: 67 IAGVLVNAFRSAGGGGGGLSSAGRSNG 93
Score = 28.4 bits (64), Expect = 2.3
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 154 GGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRF 192
GG GGG +R SR + GGG GG F
Sbjct: 5 GGRIGGGSFRA--PSRSSSSPRSSSPGGGGYYGSPGGGF 41
Score = 26.5 bits (59), Expect = 8.9
Identities = 29/95 (30%), Positives = 29/95 (30%), Gaps = 10/95 (10%)
Query: 88 RGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYR 147
GG GG R GGGGY GGG F G GGGG
Sbjct: 3 ASGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSP---GGGFGFPFLIPFFGFGGGGGLF 59
Query: 148 G-------GRDEYGGGRGGGGYRGGRDSRGFDGGK 175
G R GG GG S G GK
Sbjct: 60 GLLILMAIAGVLVNAFRSAGGGGGGLSSAGRSNGK 94
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
family also includes polypyrimidine tract binding
protein homolog 3 (PTBPH3) found in plant. Although its
biological roles remain unclear, PTBPH3 shows
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 29.5 bits (67), Expect = 0.29
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 44 NPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
+ PG A V+ + AE A + +N L G KL V
Sbjct: 35 SKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEV 69
>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 = 29.6 bits (66), Expect = 0.31
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQ 56
+++VGG+ E ++ L FE++GK+ + + + GFAFV F +
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 52
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads and is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 83
Score = 29.7 bits (66), Expect = 0.31
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAACD 64
T + V L + + +E+L+ F G++ S + G+ FV + + DAE A +
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64
Query: 65 SMNDQDLMGSKLRVEISR 82
++N L ++V +R
Sbjct: 65 TLNGLRLQTKTIKVSYAR 82
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form
of the carboxy-terminal domain (CTD) of the largest
subunit of RNA polymerase II (pol II). The pol II CTD
plays a role in coupling transcription and pre-mRNA
processing. SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 29.6 bits (66), Expect = 0.31
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
T ++VG + + ++DL FE+FG++ S+ + P G A+V ++ DA A ++
Sbjct: 3 TTLWVGQVDKKATQQDLTNLFEEFGQIESINM-IPPRGCAYVCMVHRQDAYRALQKLSSG 61
Query: 70 DL-MGSKL 76
+GSK+
Sbjct: 62 SYKIGSKV 69
>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 = 29.4 bits (66), Expect = 0.32
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR 82
GF FV F + A+AA +M+ L G L V+ S
Sbjct: 48 GFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 31.3 bits (71), Expect = 0.32
Identities = 25/64 (39%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 96 RFDSRGGRG-GYRGGGGGYGGGG------YRDGGDRFGGGGRGRGD-GGFRGSRGGGGYR 147
R+D G G G GGGG+ G G + GD FGG G G G GGF G
Sbjct: 66 RYDQFGHAGVGGAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGGFGGFGGFGGGGSQQRVF 125
Query: 148 GGRD 151
G D
Sbjct: 126 RGSD 129
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing
Sarcoma Protein (EWS). This subgroup corresponds to
the RRM of EWS, also termed Ewing sarcoma breakpoint
region 1 protein, a member of the FET (previously TET)
(FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding
proteins whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the
FET family, EWS contains an N-terminal Ser, Gly, Gln
and Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U
RNA. It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor
gene. .
Length = 84
Score = 29.5 bits (66), Expect = 0.33
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 12 VYVGGLTETVKKEDLELEFEKFG--KLN--------SVWV---AFNPPGFAFVEFSNQID 58
+YV GL + V E+L F+ G K+N +++ P G A V + +
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 59 AEAACDSMNDQDLMGSKLRVEI 80
A+AA + + +D GSKL+V +
Sbjct: 63 AKAAVEWFDGKDFQGSKLKVSL 84
>gnl|CDD|221518 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 30.5 bits (69), Expect = 0.34
Identities = 26/78 (33%), Positives = 28/78 (35%), Gaps = 3/78 (3%)
Query: 89 GGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRG--RGDGGFRGSRGGGGY 146
GG GG R G G GGG+ D D G G + D G G GGGG
Sbjct: 39 DGGNDGGAGPKPKPRPQPDPGNPGGDGGGFSDS-DLADVAGDGGYKPDKGKGGGGGGGGG 97
Query: 147 RGGRDEYGGGRGGGGYRG 164
G GG G G
Sbjct: 98 GGTDGGPEGGAETGTIAG 115
Score = 27.1 bits (60), Expect = 5.5
Identities = 21/57 (36%), Positives = 22/57 (38%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRG 139
G G GGG G GGY+ G GGGG GG GG G G G
Sbjct: 59 GNPGGDGGGFSDSDLADVAGDGGYKPDKGKGGGGGGGGGGGTDGGPEGGAETGTIAG 115
>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 = 29.2 bits (66), Expect = 0.34
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAA 62
V+V L +V +++L F K G++ V + N G+A+VEF N+ + A
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA 56
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding
protein 12 (RBM12) and similar proteins. This
subfamily corresponds to the RRM3 of RBM12. RBM12, also
termed SH3/WW domain anchor protein in the nucleus
(SWAN), is ubiquitously expressed. It contains five
distinct RNA binding motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. The biological role of
RBM12 remains unclear. .
Length = 101
Score = 29.9 bits (67), Expect = 0.35
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 11/64 (17%)
Query: 7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLN----SVWVAFNPPGFA----FVEFSNQID 58
E G VY+ GL + + + + F KL+ S+++A+ P G A FVEF N+ D
Sbjct: 7 ELGFCVYLKGLPYEAENKHV---IDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 63
Query: 59 AEAA 62
+AA
Sbjct: 64 YKAA 67
>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 = 29.3 bits (66), Expect = 0.38
Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
+++VGGL+ +E + F KFG + + + + GF F+ F ++ + ++
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
>gnl|CDD|185087 PRK15133, PRK15133, microcin C ABC transporter permease YejB;
Provisional.
Length = 364
Score = 30.9 bits (70), Expect = 0.40
Identities = 12/36 (33%), Positives = 13/36 (36%), Gaps = 1/36 (2%)
Query: 108 GGGGGYGGGGYRDGGDRFGGGGRGR-GDGGFRGSRG 142
G GG G G G G D +RG RG
Sbjct: 45 GQAGGLPGAGGEGVRASHAQTGVGNISDSNYRGGRG 80
Score = 27.4 bits (61), Expect = 5.2
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 133 GDGGFRGSRGGGGYRGGRDEYGGGR-GGGGYRGGR 166
G G GG G R + G G YRGGR
Sbjct: 45 GQAGGLPGAGGEGVRASHAQTGVGNISDSNYRGGR 79
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 28.7 bits (65), Expect = 0.43
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 49 AFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
AF F N+ A A ++ ++G +L VE
Sbjct: 41 AFATFDNEQAASQALSRLHQLKILGKRLVVE 71
>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 = 29.2 bits (65), Expect = 0.43
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
+++VGGL +E + F +FG++ ++ + +P GF F+ F +
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEE 56
>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 = 28.9 bits (65), Expect = 0.44
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
+++VGGL V +E+ + F +FGK+ + + GF FV F ++ E S
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVF-S 59
Query: 66 MNDQDLMGSKLRV 78
+L G ++ V
Sbjct: 60 AGMLELGGKQVEV 72
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 29.6 bits (67), Expect = 0.44
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 24 EDLELEFE-KFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
ED+ +E E K+G++ + V N G +V+F + DAE A + +N++ G +
Sbjct: 41 EDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQPIYA 100
Query: 79 EISR 82
E+S
Sbjct: 101 ELSP 104
>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 = 28.7 bits (65), Expect = 0.44
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
++GGL+ +E L F K+G++ + +P GF FV F++ + +
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59
>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 = 28.9 bits (64), Expect = 0.45
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
++++GGL+ + L FEK+G L V +P GF FV +S + +AA
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60
>gnl|CDD|221509 pfam12287, Caprin-1_C, Cytoplasmic
activation/proliferation-associated protein-1 C term.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 343 and 708 amino
acids in length. This family is the C terminal region of
caprin-1. Caprin-1 is a protein involved in regulating
cellular proliferation. In mutated phenotypes, the G1
phase of the cell cycle is greatly lengthened, impairing
normal proliferation. The C terminal region of caprin-1
contains RGG motifs which are characteristic of RNA
binding domains. It is possible that caprin-1 functions
through an RNA binding mechanism.
Length = 319
Score = 30.7 bits (69), Expect = 0.46
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 90 GGGRGGRFDSRGGRGGYRGGGGGYGGG--GYR 119
G RGG + RG GYRG G+ GG GYR
Sbjct: 243 GMSRGGPRNPRGMINGYRGPSNGFRGGYDGYR 274
Score = 27.6 bits (61), Expect = 4.6
Identities = 15/33 (45%), Positives = 16/33 (48%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGY 113
SRG RG RG RG G+RGG GY
Sbjct: 241 SRGMSRGGPRNPRGMINGYRGPSNGFRGGYDGY 273
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct 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. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 98
Score = 29.5 bits (66), Expect = 0.46
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
GFA VE+ AE +M+ + GS++++
Sbjct: 45 GFAVVEYETAEQAEEVQLAMDGTTIKGSRIQL 76
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 31.0 bits (70), Expect = 0.49
Identities = 16/42 (38%), Positives = 17/42 (40%)
Query: 96 RFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGF 137
GGGG GGGG+ G GGGG G G F
Sbjct: 65 NGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWRF 106
Score = 30.2 bits (68), Expect = 0.76
Identities = 19/63 (30%), Positives = 25/63 (39%)
Query: 53 FSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGG 112
A A+ + + + + V + GGGG GG F GG GG GGGGG
Sbjct: 43 IKCSASASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGG 102
Query: 113 YGG 115
Sbjct: 103 GWR 105
Score = 28.7 bits (64), Expect = 2.7
Identities = 19/37 (51%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 89 GGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRF 125
GG GG GG+ GGGGG GGGG GG RF
Sbjct: 73 ASAISGGGGGGGGGFGGFGGGGGGGGGGG---GGWRF 106
Score = 27.9 bits (62), Expect = 5.1
Identities = 21/43 (48%), Positives = 21/43 (48%), Gaps = 10/43 (23%)
Query: 154 GGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRS 196
GGG GGGG GG G GGGGG GGG RF R
Sbjct: 78 GGGGGGGGGFGGFGGGG----------GGGGGGGGGWRFWLRL 110
Score = 27.1 bits (60), Expect = 9.0
Identities = 20/39 (51%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 125 FGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYR 163
GG G G GGF G GGGG GGG GGGG+R
Sbjct: 75 AISGGGGGGGGGFGGFGGGGG--------GGGGGGGGWR 105
>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 = 28.8 bits (64), Expect = 0.49
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMND 68
V GL+ + DL F ++G L V V ++ GFAFV F D++ A + N
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63
Query: 69 QDLMGSKLRVEIS 81
+L G ++RV+ S
Sbjct: 64 MELDGRRIRVDYS 76
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 31.0 bits (71), Expect = 0.51
Identities = 11/53 (20%), Positives = 22/53 (41%)
Query: 118 YRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRG 170
+RD ++F + +G +G G + G + G +GG+ +G
Sbjct: 608 FRDLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQG 660
Score = 27.9 bits (63), Expect = 4.9
Identities = 18/84 (21%), Positives = 23/84 (27%), Gaps = 5/84 (5%)
Query: 91 GGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRG--SRGGGGYRG 148
+ G + G+GG G G G + G G GG R
Sbjct: 616 NAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQ---QGQQGQGGQGGQGSLAERQQALRDE 672
Query: 149 GRDEYGGGRGGGGYRGGRDSRGFD 172
+ GG G GG G
Sbjct: 673 LGRQRGGLPGMGGEAGEAARDALG 696
Score = 27.6 bits (62), Expect = 6.3
Identities = 29/147 (19%), Positives = 40/147 (27%), Gaps = 26/147 (17%)
Query: 81 SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGG--------GGRGR 132
+G+ G G + G+G +G G G GG +R G
Sbjct: 622 QQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQALRDELGRQRGGLP 681
Query: 133 GDGGFRGSRGGGGYRGGRDEYGG-----GRGGGGYRGGRDSRGFDG-------------G 174
G GG G GG G+G R R +
Sbjct: 682 GMGGEAGEAARDALGRAGRAMGGAEEALGQGDLAEAVDRQGRALEALREGARALGEAMAQ 741
Query: 175 KPDYYNGGGGGRGGGGRFRSRSPVQRR 201
+ GG G + G R P+ R
Sbjct: 742 QQGQQQGGQGQQQGRQGGNGRDPLGRP 768
Score = 26.8 bits (60), Expect = 9.5
Identities = 9/46 (19%), Positives = 19/46 (41%)
Query: 146 YRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
+R ++++ RG + G+ +G G G +G G+
Sbjct: 608 FRDLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQ 653
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 30.7 bits (69), Expect = 0.51
Identities = 17/67 (25%), Positives = 22/67 (32%), Gaps = 7/67 (10%)
Query: 65 SMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDR 124
D +++ R R + R GGGGG+ GGG
Sbjct: 534 KALDMEIIKDSYSPIFHNNYSRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGG------- 586
Query: 125 FGGGGRG 131
GGGG G
Sbjct: 587 SGGGGGG 593
Score = 29.1 bits (65), Expect = 1.9
Identities = 15/24 (62%), Positives = 16/24 (66%)
Query: 96 RFDSRGGRGGYRGGGGGYGGGGYR 119
R S GG GG+ GGG G GGGG R
Sbjct: 572 RSSSSGGGGGFSGGGSGGGGGGAR 595
Score = 27.2 bits (60), Expect = 7.8
Identities = 15/44 (34%), Positives = 15/44 (34%), Gaps = 2/44 (4%)
Query: 123 DRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGR 166
R R SR GG GGG GGGG G R
Sbjct: 554 SRSFNN-LNRAYSAIASSRRSSSSGGGGGFSGGGSGGGG-GGAR 595
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 28.7 bits (65), Expect = 0.54
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKL-NSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
V + GL + +ED+ F + + + ++ P G A+VEF++ DA A
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRAL-RK 60
Query: 67 NDQDLMGSKLRV 78
++ + G + V
Sbjct: 61 HNNKMGGRYIEV 72
>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 = 28.9 bits (65), Expect = 0.56
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG 85
GF FV++ + DA+ A ++N L +++V +R G
Sbjct: 43 GFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPGG 81
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 28.7 bits (65), Expect = 0.56
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACD 64
G V+VG + + +++L FEK G + + + + G+AFV ++N+ A+ A
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVK 60
Query: 65 SMNDQDLMGSK-LRVEIS 81
+++ ++ K L V IS
Sbjct: 61 QLHNYEIRPGKRLGVCIS 78
>gnl|CDD|240716 cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate
methenyltetrahydrofolate synthetase domain-containing
proteins. This subfamily corresponds to
methenyltetrahydrofolate synthetase domain (MTHFSD), a
putative RNA-binding protein found in various
vertebrate species. It contains an N-terminal
5-formyltetrahydrofolate cyclo-ligase domain and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The biological role of MTHFSD remains unclear. .
Length = 74
Score = 28.5 bits (64), Expect = 0.58
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFG--KLNSVWVAFNPPGFAFVEFSN--QIDAEAACDSMN 67
V VG ++ ++ DL+ + G L W G AF+ F + DA++A S+
Sbjct: 2 VKVGNISRNLRVSDLKSALRERGVKPLRITWQGAR--GKAFLHFPDKDAADADSALASLQ 59
Query: 68 DQDLMGSKLRVE 79
+ G+ L VE
Sbjct: 60 QLSIGGNTLTVE 71
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 75
Score = 28.6 bits (64), Expect = 0.59
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 7/67 (10%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV----AFNPPGFAFVEFSNQIDAEAACDS-- 65
++VG L E V++E + F+++G++ SV + + AFV+F + A+ A ++
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61
Query: 66 -MNDQDL 71
M D+DL
Sbjct: 62 KMGDRDL 68
>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 = 28.7 bits (64), Expect = 0.61
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
T +YV L + +++L FE +G + + + P G AFV + + +A+AA
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 65 SMN 67
S+N
Sbjct: 61 SLN 63
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 28.4 bits (63), Expect = 0.61
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
VY GG+ + ++ + F FG++ + V F G++F+ FS A A S+N +
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRV-FPEKGYSFIRFSTHESAAHAIVSVNGTTI 61
Query: 72 MG 73
G
Sbjct: 62 EG 63
>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 = 28.4 bits (63), Expect = 0.62
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQ 56
++++GGL+ +E L F +FG++ V +P GF FV F +Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 29.8 bits (67), Expect = 0.63
Identities = 16/39 (41%), Positives = 17/39 (43%)
Query: 98 DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
D RG GG GGG GGG + G GG GG
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGG 153
Score = 27.1 bits (60), Expect = 5.1
Identities = 18/46 (39%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 87 GRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
GRG GG GG GG G + G GG G GGG R
Sbjct: 116 GRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSG---GGGNFSR 158
>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 = 28.4 bits (64), Expect = 0.66
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-------NPPGFAFVEFSNQIDAEAACD 64
+YVG LT EDLE + G ++ + F GFA+VEF+++ A A +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 65 SMNDQDLMGSKLRV 78
+ ++ G K V
Sbjct: 61 KLEGREFNGKKCVV 74
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 77
Score = 28.4 bits (64), Expect = 0.66
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
V++ GL E+V ++ L F ++G + V + G A V F A+AA + M + L
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQR-GQALVFFDKVEAAQAAVNEMKGRKL 68
Query: 72 MGSKLRV 78
G KL+V
Sbjct: 69 GGRKLQV 75
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 28.4 bits (63), Expect = 0.78
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFG--KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
++Y+G L+ V EDL + FG KL G+AFV++ +Q A A ++++
Sbjct: 3 KLYIGNLSPAVTAEDLR---QLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSG 59
Query: 69 Q-DLMGSKLRVEIS 81
+ +L G + V+ S
Sbjct: 60 KVELHGKVMEVDYS 73
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a major
component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 29.8 bits (67), Expect = 0.79
Identities = 23/65 (35%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 87 GRGGGGRGGRFDSRGGRGG--YRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGG 144
G G G R+ +G GG Y GGG+G G GGG GG+ GGG
Sbjct: 7 GGGWNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGG 66
Query: 145 GYRGG 149
+GG
Sbjct: 67 WGQGG 71
Score = 28.7 bits (64), Expect = 1.8
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 104 GGYRGGGGGYGGGGYRDGGDRF---GGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGG 160
GG+ GG Y G G GG+R+ GGG GG+ GGG + +G GGG
Sbjct: 8 GGWNTGGSRYPGQG-SPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGG 66
Query: 161 GYRGG 165
+GG
Sbjct: 67 WGQGG 71
Score = 27.9 bits (62), Expect = 3.1
Identities = 31/95 (32%), Positives = 40/95 (42%), Gaps = 14/95 (14%)
Query: 110 GGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSR 169
GGG+ GG R G GG R GG G GGG+ G GGG
Sbjct: 7 GGGWNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGG-------- 58
Query: 170 GFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYNV 204
G+P +GGG G+GGG + P + + N+
Sbjct: 59 ---WGQP---HGGGWGQGGGTHNQWNKPSKPKTNM 87
>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 = 28.2 bits (63), Expect = 0.81
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAE 60
R++VGG+ + DL F ++G + V + + G+ FV F Q DA+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQ 57
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 30.0 bits (67), Expect = 0.82
Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 7/117 (5%)
Query: 8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
+ T +YV L T+ + L+ F K+G++ + + P G AFV F+ + +A+ A
Sbjct: 192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251
Query: 63 CDSMNDQDLMGSK--LRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGG 117
++N+ G L V ++ G+ + G G+ G G G
Sbjct: 252 ISALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAGGSGM 308
>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 = 28.1 bits (62), Expect = 0.83
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSN 55
++++GGL+ + L F KFG++ V +P GF FV F++
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD 50
>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 = 0.85
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAA- 62
GT V+VG + + +++L FEK G + + + +P G+AF+ F + A+ A
Sbjct: 1 GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
Query: 63 --CDS 65
CD+
Sbjct: 61 KLCDN 65
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 28.2 bits (63), Expect = 0.93
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG---FAFVEFSNQIDAEAACDSMND 68
VYV + + V +E L F G++ V +P FAF+EF+++ A AA S++
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAAL-SLSG 63
Query: 69 QDLMGSKLRVEISR 82
L +RV S+
Sbjct: 64 TMLGFYPVRVLPSK 77
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and
2 (NRF-1 and NRF-2), CREB (cAMP-response
element-binding protein), and estrogen-related receptor
alpha (ERRalpha). It interacts indirectly with the
NRF-2beta subunit through host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. Furthermore, like
PGC-1alpha and PGC-1beta, PRC can transactivate a
number of NRF-dependent nuclear genes required for
mitochondrial respiratory function, including those
encoding cytochrome c, 5-aminolevulinate synthase,
Tfam, and TFB1M, and TFB2M. Further research indicates
that PRC may also act as a sensor of metabolic stress
that orchestrates a redox-sensitive program of
inflammatory gene expression. PRC is a multi-domain
protein containing an N-terminal activation domain, an
LXXLL coactivator signature, a central proline-rich
region, a tetrapeptide motif (DHDY) responsible for HCF
binding, a C-terminal arginine/serine-rich (SR) domain,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 91
Score = 28.3 bits (63), Expect = 0.94
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQ 69
VY+G + + + +L+ F FG++ + F G + FV + +A AA ++
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFVTYRYTEEAFAAIEN---- 60
Query: 70 DLMGSKLR 77
G KLR
Sbjct: 61 ---GHKLR 65
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 29.8 bits (67), Expect = 0.96
Identities = 34/87 (39%), Positives = 36/87 (41%), Gaps = 2/87 (2%)
Query: 104 GGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYR 163
GG GGGG +R G GGGGR G GG GS GG GG G Y
Sbjct: 153 GGGGGGGGASLKNSWRGNGVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYG 212
Query: 164 GGRDSRGFDGGKPDYYNGGGGGRGGGG 190
GG + G G GG G GGG
Sbjct: 213 GG--NGGNVGAAGGRAWGGNGYEYGGG 237
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 29.7 bits (67), Expect = 1.0
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 96 RFDSRGGRGGYRGGGGGYGG-------GGYRD-GGDRFGGGGRGR 132
++ + G GG+ GG GG+GG GG+ D FGGGG R
Sbjct: 67 QYGAAGANGGFGGGAGGFGGFDGSGGFGGFEDIFSSFFGGGGARR 111
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La)
family. It is expressed predominantly in neurons and
muscle in vertebrates. LARP6 functions as a key
regulatory protein that may play a role in mediating a
variety of developmental and homeostatic processes in
animals, including myogenesis, neurogenesis and
possibly metastasis. LARP6 binds to
Ca2+/calmodulin-dependent serine protein kinase (CASK),
and forms a complex with inhibitor of differentiation
transcription factors. It is structurally related to
the La autoantigen and contains a La motif (LAM),
nuclear localization and export (NLS and NES) signals,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 93
Score = 28.4 bits (64), Expect = 1.0
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
A VEF A A + ++ +D ++V
Sbjct: 59 CAVVEFEKLEAARKAVEELSARDDWRDGIKV 89
>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 = 27.6 bits (61), Expect = 1.1
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSN 55
+++VGGL+ K+DL+ F KFG++ + +P GF F+ F +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKD 50
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 83
Score = 27.9 bits (62), Expect = 1.2
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 22 KKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLR 77
K L+ F ++GK+ + GFAFV + +AE A ++ N ++ G +
Sbjct: 14 KPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVA 73
Query: 78 VE 79
V+
Sbjct: 74 VD 75
>gnl|CDD|218666 pfam05633, DUF793, Protein of unknown function (DUF793). This
family consists of several plant proteins of unknown
function.
Length = 389
Score = 29.4 bits (66), Expect = 1.2
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 151 DEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRS 196
DE G GGG+R R + + G G G GG RS S
Sbjct: 169 DEKDSGGSGGGHRNRSFGRSWSFHH---RSIGSSGGGTGGHLRSLS 211
Score = 27.1 bits (60), Expect = 8.2
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 87 GRGGGGRGGRFDSRGGRGGYR-GGGGGYGGGGY 118
G GGG R R +R G G G GG+
Sbjct: 174 GGSGGGHRNRSFGRSWSFHHRSIGSSGGGTGGH 206
>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 = 28.0 bits (63), Expect = 1.3
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
+Y+GGL + + D+ F ++G++ + + + GFAF+ + +Q A D++
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 67 NDQDLMGSKLRVE 79
N L+G +RV+
Sbjct: 72 NGIKLLGRTIRVD 84
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in
Saccharomyces cerevisiae protein Nrd1,
Schizosaccharomyces pombe Rpb7-binding protein seb1 and
similar proteins. This subfamily corresponds to the
RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous
nuclear ribonucleoprotein (hnRNP)-like RNA-binding
protein encoded by gene NRD1 (for nuclear pre-mRNA
down-regulation) from yeast S. cerevisiae. It is
implicated in 3' end formation of small nucleolar and
small nuclear RNAs transcribed by polymerase II, and
plays a critical role in pre-mRNA metabolism. Nrd1
contains an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a short arginine-, serine-, and glutamate-rich
segment similar to the regions rich in RE and RS
dipeptides (RE/RS domains) in many metazoan splicing
factors, and a proline- and glutamine-rich C-terminal
domain (P+Q domain) similar to domains found in several
yeast hnRNPs. Disruption of NRD1 gene is lethal to
yeast cells. Its N-terminal domain is sufficient for
viability, which may facilitate interactions with RNA
polymerase II where Nrd1 may function as an auxiliary
factor. By contrast, the RRM, RE/RS domains, and P+Q
domain are dispensable. Seb1 is an RNA-binding protein
encoded by gene seb1 (for seven binding) from fission
yeast S. pombe. It is essential for cell viability and
bound directly to Rpb7 subunit of RNA polymerase II.
Seb1 is involved in processing of polymerase II
transcripts. It also contains one RRM motif and a
region rich in arginine-serine dipeptides (RS domain).
Length = 79
Score = 27.5 bits (61), Expect = 1.3
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
++ GG+T + + DL F +FG++ S + N AFV+ N+ DAE A ++M
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSCILN-NDKRHAFVKMYNRRDAENAREAMEQYKS 64
Query: 72 MGSKLRVEISRGRG 85
+LR G G
Sbjct: 65 GDMQLRTRWGVGFG 78
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 27.6 bits (62), Expect = 1.4
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
R++VG L V E L F K+ V + G+ FV FS+ D A
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 66 MN 67
MN
Sbjct: 68 MN 69
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an
N-terminal C4C4 type RING finger motif, followed by a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RING fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 27.9 bits (63), Expect = 1.4
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 13/78 (16%)
Query: 12 VYVGGLTETVKKEDLELE----FEKFGKLNSVWV-------AFNPPGF-AFVEFSNQIDA 59
VYV GL + E++ L+ F ++GK+ + + P A+V +S + DA
Sbjct: 8 VYVVGLPPRLADEEV-LKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDA 66
Query: 60 EAACDSMNDQDLMGSKLR 77
+++ L G L+
Sbjct: 67 LRCIQAVDGFYLDGRLLK 84
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 28.0 bits (63), Expect = 1.4
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 24 EDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
ED+ LE +FG++ + V N G +V+F + DAEAA ++N + G L E
Sbjct: 40 EDVFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99
Query: 80 IS 81
+S
Sbjct: 100 LS 101
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 29.1 bits (66), Expect = 1.4
Identities = 36/90 (40%), Positives = 38/90 (42%), Gaps = 10/90 (11%)
Query: 89 GGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGG--------GRGRGDGGFRGS 140
GGGG G GG GG GGGG G GG + GG G G G
Sbjct: 113 GGGGSGNYNGGSGGFGGGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGG 172
Query: 141 RGGGGYRGG--RDEYGGGRGGGGYRGGRDS 168
GGGGY GG GGG GG Y G+D
Sbjct: 173 GGGGGYFGGGGGHYAGGGGGGSSYISGKDG 202
Score = 27.9 bits (63), Expect = 3.1
Identities = 33/82 (40%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 109 GGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDS 168
GGGG G G GG G G S GG GG GG GG GY G +
Sbjct: 112 GGGGGSGNYNGGSGGFGGGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNG 171
Query: 169 RGFDGGKPDYYNGGGGGRGGGG 190
G GG Y+ GGGG GGG
Sbjct: 172 GGGGGG---YFGGGGGHYAGGG 190
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and is essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 27.3 bits (61), Expect = 1.4
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R+ V L+ V +DL+ K G++ P VEF+ D + A + ++ +
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPNEGVVEFATYSDMKRAIEKLDGTE 61
Query: 71 LMGSKLRV 78
L G K+++
Sbjct: 62 LNGRKIKL 69
>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 = 27.5 bits (61), Expect = 1.5
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 48 FAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
F FV F N A+AA +MN + +L+V+
Sbjct: 48 FGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ 79
>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 = 27.3 bits (61), Expect = 1.5
Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 7/74 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLN-----SVWVAFNPPGFAFVEFSNQIDAEAACDS 65
V V GL ETV + LEL FE + + + G A V F++ AE
Sbjct: 2 CVLVAGLPETVSDDKLELYFEN-KRRSGGGDVTRVQYLREKGSALVTFADFKVAERVVK- 59
Query: 66 MNDQDLMGSKLRVE 79
L G++L V
Sbjct: 60 QKKHPLNGTQLSVR 73
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 28.1 bits (62), Expect = 1.5
Identities = 15/64 (23%), Positives = 31/64 (48%)
Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
E V + L F +G + V + +N A ++ ++ ++ A +N Q + G +RV
Sbjct: 24 EMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRV 83
Query: 79 EISR 82
+S+
Sbjct: 84 TLSK 87
>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 = 27.5 bits (61), Expect = 1.6
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDS 65
V+VGG+ + + ++ F K+G + V + + G+ FV F + +D + +S
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVES 65
>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 = 27.3 bits (61), Expect = 1.7
Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 6/73 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQIDAEAACDSM 66
++VG L EDL F+ G SV + G AFVEF A +
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KL 61
Query: 67 NDQDLMGSKLRVE 79
+ L G K+ VE
Sbjct: 62 HHTLLKGRKINVE 74
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 28.0 bits (62), Expect = 1.7
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
++V L +E L F KFG + + G FV F +Q A
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 29.1 bits (65), Expect = 1.7
Identities = 9/45 (20%), Positives = 15/45 (33%)
Query: 104 GGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRG 148
G G GGG ++ + G + G G + G +
Sbjct: 267 GLSSGKNAPKTGGGAKNASSQGSGAAKNSGASGADIDQYAGQIKS 311
>gnl|CDD|241143 cd12699, RRM3_hnRNPL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM3 of hnRNP-L, a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 27.3 bits (60), Expect = 1.8
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 33 FGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR 82
+G + V + PG A VE ++ + A +N+ + G KL V +S+
Sbjct: 24 YGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKLNVCVSK 73
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 28.9 bits (65), Expect = 1.9
Identities = 14/30 (46%), Positives = 14/30 (46%)
Query: 82 RGRGRGRGGGGRGGRFDSRGGRGGYRGGGG 111
G GRG G GRGGR RG G G
Sbjct: 6 GGEGRGFGRRGRGGRGRGRGRGRGGEGEEK 35
>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 = 27.1 bits (60), Expect = 2.0
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACD 64
++VGGL+ K+DL+ F KFG++ + +P GF FV F + E D
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58
>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 = 27.3 bits (60), Expect = 2.0
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEF 53
+++GGL+ K+DL+ F KFG++ + +P GF FV F
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 47
>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 = 27.6 bits (62), Expect = 2.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 47 GFAFVEFSNQIDAEAACDSMN 67
G+ FVEF+N A A ++N
Sbjct: 58 GYGFVEFTNHEHALKALRALN 78
>gnl|CDD|241144 cd12700, RRM3_hnRPLL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM3 of
hnRNP-LL which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 71
Score = 26.9 bits (59), Expect = 2.3
Identities = 14/46 (30%), Positives = 21/46 (45%)
Query: 33 FGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
+G + V PG A VE ++ E A +N+ L G +L V
Sbjct: 24 YGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 69
>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 = 26.8 bits (60), Expect = 2.4
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
V+V L+ V++ DL F K GK+ V + + G A+VEF ++ A +
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60
Query: 67 NDQDLMGSKLRV 78
Q L+G + V
Sbjct: 61 TGQRLLGQPIMV 72
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 26.9 bits (59), Expect = 2.5
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMND 68
V L + V E LE F FG++ V + P G VEF+ + A A D +D
Sbjct: 4 VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDRCSD 62
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 27.4 bits (61), Expect = 2.6
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 90 GGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRG 131
G G G + + G GG+ GGGG+G GG+ +GG + G G
Sbjct: 74 GNGGGRGWGNGGSGGGWVNGGGGWGNGGWVNGG-GWRNGYGG 114
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic
translation initiation factor 4H (eIF-4H) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4H, also termed Williams-Beuren syndrome
chromosomal region 1 protein, which, together with
elf-4B/eIF-4G, serves as the accessory protein of RNA
helicase eIF-4A. eIF-4H contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It
stimulates protein synthesis by enhancing the helicase
activity of eIF-4A in the initiation step of mRNA
translation. .
Length = 76
Score = 26.5 bits (59), Expect = 2.8
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
GF +VEF + + A + + LRV+I+
Sbjct: 43 GFCYVEFEDVESLKEALE-YDGALFDDRSLRVDIA 76
>gnl|CDD|226642 COG4174, COG4174, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 364
Score = 28.5 bits (64), Expect = 2.8
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 117 GYRDGGDRFGGGGRGRGDGGF-RGSRGGGGYRGGR 150
G + G DR GGGG G G+ YRG +
Sbjct: 44 GGQSGLDRLGGGGVDASGAGGGVGNISDSQYRGAQ 78
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 26.9 bits (59), Expect = 2.8
Identities = 14/64 (21%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQIDAEAACDS 65
+++VG + T+ ++++ FE+ G + V + + G FV++S + +A+ A +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60
Query: 66 MNDQ 69
+++Q
Sbjct: 61 LHNQ 64
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in
yeast. Yra2p belongs to the evolutionarily conserved
REF (RNA and export factor binding proteins) family of
hnRNP-like proteins. It is a major component of
endogenous Yra1p complexes. It interacts with Yra1p and
functions as a negative regulator of Yra1p. Yra2p
consists of two highly conserved N- and C-terminal
boxes and a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 26.6 bits (59), Expect = 2.8
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 49 AFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
A EF + E + N ++L G+K+ VEI
Sbjct: 41 AVFEFEDPSILEKVVEKYNGKELNGAKIEVEI 72
>gnl|CDD|112890 pfam04094, DUF390, Protein of unknown function (DUF390). This is a
family of long proteins currently only found in the rice
genome. They have no known function. However they may be
some kind of transposable element.
Length = 843
Score = 28.6 bits (63), Expect = 2.8
Identities = 32/82 (39%), Positives = 34/82 (41%), Gaps = 10/82 (12%)
Query: 102 GRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRG--DGGFRGSRGGGGYRGGRDEYGG---- 155
G R G G GG R G GGGR G DGG GSR RG R + G
Sbjct: 58 GASEERALKGHDGAGGSRRGEQSTPGGGRASGPRDGGPGGSRPADA-RGKRKQEGTPPPS 116
Query: 156 -GRGGGGYRGGRDSRGFDGGKP 176
RGGG R SR +G P
Sbjct: 117 PPRGGGAVRA--SSRRPEGAAP 136
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 28.5 bits (63), Expect = 2.9
Identities = 20/45 (44%), Positives = 21/45 (46%)
Query: 145 GYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGG 189
G RGG G GRGG G R R DGG+ GG R GG
Sbjct: 801 GNRGGHAHSGSGRGGDGGRSIDGGRSIDGGRSIDGGEGGDERDGG 845
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 28.5 bits (63), Expect = 2.9
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 101 GGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
G GY G G G G+ +G + G G G+G G++
Sbjct: 7 GTGNGYSNGNGYTNGNGHTNGNGNYNGNGHVNGNGKANGAK 47
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 26.6 bits (59), Expect = 3.0
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 38 SVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
SV + +N P G A V F +A AA +N + + K+++
Sbjct: 30 SVSLLYNDNGAPTGEATVAFDTHREAMAAVRELNGRPIGTRKVKL 74
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit
4 (THOC4) and similar proteins. This subgroup
corresponds to the RRM of THOC4, also termed
transcriptional coactivator Aly/REF, or ally of AML-1
and LEF-1, or bZIP-enhancing factor BEF, an mRNA
transporter protein with a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It is
involved in RNA transportation from the nucleus. THOC4
was initially identified as a transcription coactivator
of LEF-1 and AML-1 for the TCRalpha enhancer function.
In addition, THOC4 specifically binds to rhesus (RH)
promoter in erythroid. It might be a novel
transcription cofactor for erythroid-specific genes. .
Length = 75
Score = 26.4 bits (59), Expect = 3.0
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDS 65
T++ V L V +D++ F +FG L V ++ G A V F + DA A
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
Query: 66 MNDQDLMGSKLRVEI 80
N L G +++++
Sbjct: 61 YNGVPLDGRPMKIQL 75
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 26.6 bits (59), Expect = 3.1
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI 80
G V+F + I+A A N Q L +RV++
Sbjct: 40 GMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVKM 73
>gnl|CDD|217596 pfam03515, Cloacin, Colicin-like bacteriocin tRNase domain. The
C-terminal region of colicin-like bacteriocins is either
a pore-forming or an endonuclease-like domain. Cloacin
and Pyocins have similar structures and activities to
the colicins from E coli and the klebicins from
Klebsiella spp. Colicins E5 and D cleave the anticodon
loops of distinct tRNAs of Escherichia coli both in vivo
and in vitro. The full-length molecule has an N-terminal
translocation domain and a middle, double alpha-helical
region which is receptor-binding.
Length = 279
Score = 27.9 bits (62), Expect = 3.3
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 98 DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
D G G+ G +G GG GGD GGG G G G
Sbjct: 3 DIPGDGIGWGSEGTPWGPGGGSPGGDYNPGGGSGVGGSG 41
Score = 27.9 bits (62), Expect = 4.3
Identities = 18/45 (40%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 151 DEYGGGRG----GGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
D G G G G + G G GG DY GGG G GG G
Sbjct: 3 DIPGDGIGWGSEGTPWGPGG---GSPGG--DYNPGGGSGVGGSGN 42
>gnl|CDD|241001 cd12557, RRM3_RBM15, RNA recognition motif 3 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM3 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possesses mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RBM15 belongs to the Spen (split end)
protein family, which contains three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralogue and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 73
Score = 26.5 bits (58), Expect = 3.4
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
R++VGGL V L EF++FG + ++ +A++++ + A+AAC M
Sbjct: 1 RLWVGGLGPWVPLAALAREFDRFGTIRTIDYR-KGDSWAYIQYESLDAAQAACTHMRGFP 59
Query: 71 LMGSKLRVEI 80
L G R+ +
Sbjct: 60 LGGPDRRLRV 69
>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 = 26.5 bits (58), Expect = 3.5
Identities = 13/51 (25%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
+V+VGGL+ +E ++ F FG++ ++ + + GF FV ++++
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDE 51
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.4 bits (63), Expect = 3.6
Identities = 22/117 (18%), Positives = 32/117 (27%), Gaps = 13/117 (11%)
Query: 85 GRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGG 144
G G G + + G G +G + G G +GD G G
Sbjct: 745 GEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHE 804
Query: 145 GYRGGRDEYGGGRGGGGYRGGRDSRGFDG-----------GKPDY--YNGGGGGRGG 188
G ++ + + G K D +GGGG GG
Sbjct: 805 GETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGG 861
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells, as well as the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 26.6 bits (58), Expect = 3.8
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAACD 64
T + V L + + +E+ F G++ S + G+ FV + + DAE A +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 65 SMNDQDLMGSKLRVEISR 82
++N L ++V +R
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 84
Score = 26.6 bits (58), Expect = 3.8
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR 82
G+ FV + + DA+ A +++N L ++V +R
Sbjct: 46 GYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 81
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 26.2 bits (58), Expect = 3.8
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP--PGFAFVEFSNQIDAEAACDSMNDQD 70
++G L +T DL FE+FG++ + + P +AF++++ D + +M D
Sbjct: 6 FIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYA---DIASVVKAMRKMD 62
>gnl|CDD|218797 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This
family consists of several Eukaryotic rRNA processing
protein EBP2 sequences. Ebp2p is required for the
maturation of 25S rRNA and 60S subunit assembly. Ebp2p
may be one of the target proteins of Rrs1p for executing
the signal to regulate ribosome biogenesis. This family
also plays a role in chromosome segregation.
Length = 270
Score = 27.7 bits (62), Expect = 4.0
Identities = 21/74 (28%), Positives = 27/74 (36%), Gaps = 2/74 (2%)
Query: 122 GDRFGGGGRGRGDGGFRGSRGGGGYRGGRDE-YG-GGRGGGGYRGGRDSRGFDGGKPDYY 179
D GG + +G G R +D +G GG+ G +S G
Sbjct: 191 DDAAKGGSKKKGRKGGAARGKPNAKRKAKDAKFGFGGKKRGSKSNTAESSNDLSGFSVKK 250
Query: 180 NGGGGGRGGGGRFR 193
GGGG G GG R
Sbjct: 251 MKGGGGAGKGGNKR 264
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 26.6 bits (59), Expect = 4.2
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 24 EDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
ED+ E KFG++ ++ V N G +V+F ++ A AA ++ + G + VE
Sbjct: 41 EDIFEELSKFGEVEALNVCDNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVE 100
Query: 80 IS 81
S
Sbjct: 101 FS 102
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing (RBP-MS).
This subfamily corresponds to the RRM of RBP-MS, also
termed heart and RRM expressed sequence (hermes), an
RNA-binding proteins found in various vertebrate
species. It contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). RBP-MS physically interacts
with Smad2, Smad3 and Smad4 and plays a role in
regulation of Smad-mediated transcriptional activity.
In addition, RBP-MS may be involved in regulation of
mRNA translation and localization during Xenopus laevis
development. .
Length = 76
Score = 26.2 bits (57), Expect = 4.3
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKF-GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
++V GL +K +L L F F G S+ + FV F ++ +AEAA +++N
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALN 60
>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 = 26.2 bits (58), Expect = 4.6
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
V+V G +E L F FG + +V + + +A VEF ++ + S L
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVL-SEPQHTL 63
Query: 72 MGSKLRV 78
G +LRV
Sbjct: 64 NGHRLRV 70
>gnl|CDD|219796 pfam08325, WLM, WLM domain. This is a predicted metallopeptidase
domain called WLM (Wss1p-like metalloproteases). These
are linked to the Ub-system by virtue of fusions with
the UB-binding PUG (PUB), Ub-like, and Little Finger
domains. More specifically, genetic evidence implicates
the WLM family in de-SUMOylation.
Length = 183
Score = 27.3 bits (61), Expect = 5.2
Identities = 19/48 (39%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 85 GRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
GR GGRG S G GG G GGG R GGD G
Sbjct: 127 SSGRRLGGRG----SYNSAEGRELGGNGLSGGGERLGGDSLSRSGESA 170
>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 = 25.9 bits (57), Expect = 5.3
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 12 VYVGGLTETVKKEDLELEFE-KFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
++VG L+ V + DL F+ +F S + +P G+ FV FS++ D + A
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 66 MNDQDLMGSKLRV 78
M G +R+
Sbjct: 64 MQGVYCGGRPMRI 76
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 27.6 bits (62), Expect = 5.3
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 154 GGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQ---RRYNVD 205
GGG GGGG G D F D + GG GG GR R P + RY+++
Sbjct: 71 GGGGGGGGGFNGFDIGFFGDFG-DIFGDFFGGGGGSGRRRRSGPRRGEDLRYDLE 124
Score = 27.2 bits (61), Expect = 6.0
Identities = 21/57 (36%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 123 DRFG-------GGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFD 172
D+FG GGG G G GF G D +GGG G G R RG D
Sbjct: 62 DQFGHAGFNGGGGGGGGGFNGFDIGFFGDFGDIFGDFFGGGGGSGRRRRSGPRRGED 118
Score = 26.8 bits (60), Expect = 7.9
Identities = 22/58 (37%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 96 RFDSRGGRGGYRGGGGGYGGGGYRDGGD------RFGGGGRGRGDGGFRGSRGGGGYR 147
+F G GG GGGGG+ G GD F GGG G G G R G R
Sbjct: 63 QFGHAGFNGGGGGGGGGFNGFDIGFFGDFGDIFGDFFGGGGGSGRRRRSGPRRGEDLR 120
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 92
Score = 26.0 bits (57), Expect = 5.8
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 47 GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
GFA +E+ + AE + L GS +RV
Sbjct: 45 GFAVLEYESAEMAEMVQQQADGLSLAGSHIRV 76
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 25.9 bits (57), Expect = 5.9
Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-GFAFVEFSNQIDAEAACDSMND 68
T VYVG + + DL F+ FG + + P GFAFV+ A A +
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYI--LEFRHQPDRGFAFVKLDTHEQAAMAIVQLQG 58
Query: 69 QDLMGSKLR 77
+ G LR
Sbjct: 59 FPVHGRPLR 67
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding
protein 19 (RBM19) and similar proteins. This
subfamily corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 25.4 bits (56), Expect = 7.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 44 NPPGFAFVEFSNQIDAEAA 62
GFAFV+ ++ D + A
Sbjct: 38 RKTGFAFVDLKSEEDLKKA 56
>gnl|CDD|226450 COG3941, COG3941, Mu-like prophage protein [General function
prediction only].
Length = 633
Score = 27.2 bits (60), Expect = 7.2
Identities = 14/49 (28%), Positives = 16/49 (32%)
Query: 80 ISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGG 128
I RG GR G + RG RG GG + G G
Sbjct: 391 IDVLRGAGRLGRRVTPAVVTLIPRGAGRGSGGSETQRVFVTGRPVPKGT 439
>gnl|CDD|226728 COG4278, COG4278, Uncharacterized conserved protein [Function
unknown].
Length = 269
Score = 26.8 bits (59), Expect = 7.5
Identities = 16/51 (31%), Positives = 16/51 (31%), Gaps = 2/51 (3%)
Query: 97 FDSRGGRGGYRGGGGGYGGGGYRDGGDRFGG--GGRGRGDGGFRGSRGGGG 145
G G Y G G G GG GG G GG G GG
Sbjct: 215 KKWMSGCGSYGGKNFGSPSGVGDMYFHGCGGHTGGDGSFCGGGCGGFGGDP 265
Score = 26.8 bits (59), Expect = 9.1
Identities = 19/62 (30%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 104 GGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYR 163
+ G G YGG + G G GD F G G G G G G GG
Sbjct: 215 KKWMSGCGSYGGKNF--------GSPSGVGDMYFHGCGGHTGGDGSFCGGGCGGFGGDPL 266
Query: 164 GG 165
G
Sbjct: 267 GE 268
>gnl|CDD|221759 pfam12764, Gly-rich_Ago1, Glycine-rich region of argonaut. This
domain is often found at the very N-terminal of
argonaut-like proteins.
Length = 102
Score = 26.1 bits (57), Expect = 7.8
Identities = 15/31 (48%), Positives = 15/31 (48%)
Query: 89 GGGGRGGRFDSRGGRGGYRGGGGGYGGGGYR 119
G GRGG G GG G GGG GG R
Sbjct: 7 QGRGRGGPPQQGGRGGGGGGRGGGSTGGPPR 37
>gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional.
Length = 386
Score = 27.1 bits (60), Expect = 8.3
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 109 GGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYR 147
G GG+G GG+ GG F GG G G G G R
Sbjct: 81 GQGGFGQGGFGGGGFDFDFGGFGDIFEDIFGDFFGTGRR 119
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 27.0 bits (60), Expect = 8.4
Identities = 21/71 (29%), Positives = 25/71 (35%), Gaps = 13/71 (18%)
Query: 107 RGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYG--------GGRG 158
RG GGYG D +G G + G GG G GG R G D R
Sbjct: 618 RGSAGGYG-----DAHAEWGVGPKILGKGGKLGLGVKGGGRAGIDWSDSDGHSASSSSRS 672
Query: 159 GGGYRGGRDSR 169
R D++
Sbjct: 673 SHDARHDIDAQ 683
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate
their translation. CPEB proteins are well conserved in
both, vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The
second subfamily includes CPEB-2, CPEB-3, CPEB-4, and
related protiens. Due to high sequence similarity,
members in this subfamily may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. CPEB-2 impedes target RNA translation
at elongation; it directly interacts with the
elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a Zn-finger motif. CPEB-2, -3, and -4 have
conserved nuclear export signals that are not present
in CPEB-1. .
Length = 112
Score = 26.1 bits (57), Expect = 8.4
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVW 40
+V+VGGL + + D+ F +FG L W
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGSLQVDW 31
>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 = 25.4 bits (55), Expect = 8.9
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
+++VGGL+ +E + F FG++ S+ + + GF F+ F +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>gnl|CDD|240701 cd12255, RRM1_LKAP, RNA recognition motif 1 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to
the RRM1 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D
member 3, known previously as PMP-70) and/or PXF
(peroxisomal farnesylated protein, known previously as
PEX19). It associates with LIM kinase 2 (LIMK2) and may
serve as a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. LKAP contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). However, whether
those RRMs are bona fide RNA binding sites remains
unclear. Moreover, there is no evidence of LAKP
localization in the nucleus. Therefore, if the RRMs are
functional, their interaction with RNA species would be
restricted to the cytoplasm and peroxisomes. .
Length = 73
Score = 24.9 bits (55), Expect = 9.4
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 46 PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
G A + F NQ A A MN +D+ G K+ V
Sbjct: 39 GGTAIIRFPNQDSARRALKRMNGEDVFGRKISVS 72
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 26.9 bits (59), Expect = 9.5
Identities = 20/83 (24%), Positives = 20/83 (24%), Gaps = 4/83 (4%)
Query: 83 GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRG 142
G G G G GG G GG G G G G G
Sbjct: 699 GALSGGGSASTGAGSVFHFAAGGVYGSGGLPEYAGGVVSSPTVFTKAAGLGLMGEAGPEA 758
Query: 143 ----GGGYRGGRDEYGGGRGGGG 161
G G G GGG
Sbjct: 759 ILPLDRGSDGKLGVAAGMGGGGA 781
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 25.3 bits (55), Expect = 9.7
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACD 64
G V+VG + V +++L FE G++ + + + G+AFV ++ + +A+ A
Sbjct: 1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVR 60
Query: 65 SMNDQDLMGSKL 76
+N+ ++ +L
Sbjct: 61 ELNNYEIRPGRL 72
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 26.7 bits (59), Expect = 9.8
Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 7/61 (11%)
Query: 100 RGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRG-----SRGGGGYRGGRDEYG 154
R G+GG R G GG R R + R SR G + ++G
Sbjct: 31 RTGKGGGRPSGKSRADGGRRP--ARDDRNSQSRDRKWEDSPWRTVSRAPGDETPEKADHG 88
Query: 155 G 155
G
Sbjct: 89 G 89
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
0.317 0.149 0.468
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,045,108
Number of extensions: 1285463
Number of successful extensions: 4714
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2745
Number of HSP's successfully gapped: 831
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.9 bits)