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PR01738

Identifier
RNABINDINGM8  [View Relations]  [View Alignment]  
Accession
PR01738
No. of Motifs
4
Creation Date
13-JUN-2002
Title
RNA binding motif protein 8 family signature
Database References
Literature References
1. BIRNEY, E., KUMAR, S. AND KRAINER, A.R.
Analysis of the RNA-recognition motif and RS and RGG domains: conservation
in metazoan pre-mRNA splicing factors.
NUCLEIC ACIDS RES. 21 5803-5816 (1993).
 
2. SALICIONI, A.M., XI, M., VANDERVEER, L.A., BALSARA, B., TESTA, J.R.,
DUNBRACK, R.L.JR. AND GODWIN, A.K.
Identification and structural analysis of human RBM8A and RBM8B: two highly
conserved RNA-binding motif proteins that interact with OVCA1, a candidate
tumor suppressor.
GENOMICS 69 54-62 (2000).
 
3. ZHAO, X.F., NOWAK, N.J., SHOWS, T.B. AND APLAN, P.D.
MAGOH interacts with a novel RNA-binding protein.
GENOMICS 63 145-148 (2000).
 
4. MOHR, S.E., DILLON, S.T. AND BOSWELL, R.E.
The RNA-binding protein Tsunagi interacts with Mago Nashi to establish
polarity and localize oskar mRNA during Drosophila oogenesis.
GENES DEV. 15 2886-2899 (2001).
 
5. ROBBINS, J., DILWORTH, S.M., LASKEY, R.A. AND DINGWALL, C.
Two interdependent basic domains in nucleoplasmin nuclear targeting
sequence: identification of a class of bipartite nuclear targeting sequence.
CELL 64 615-623 (1991).

Documentation
RNA-binding motif protein 8 (RBM8) contains a putative RNA-binding domain 
known as an RNA recognition motif (RRM). The RRM motif is found in numerous
RNA-binding proteins, including heterogenous nuclear ribonucleoproteins
(hnRNPs), and proteins implicated in regulation of alternative splicing. The
RRM is a 90-residue domain that binds single-stranded RNA; the structure
consists of four beta-stands and two alpha-helices arranged in an alpha/beta 
sandwich, with a third helix present in some cases during RNA binding [1].
Three-dimensional modelling of the RBM8 RRM domain indicates that the
sequences fold into an RNA-binding domain, forming a hydrophobic core
between a beta-sheet and two helices.
 
The human RBM8A protein is ubiquitously expressed; the protein is localised
predominantly in the cell nucleus and diffused throughout the cytoplasm
[2]. It preferentially associates with mRNAs produced by splicing, including
both nuclear mRNAs and newly exported cytoplasmic mRNAs. Evidence suggests
the protein remains associated with spliced mRNAs as a tag to indicate the
position of spliced introns. Human RBM8A protein specicially binds to MAGOH,
the human homologue of Drosophila mago nashi, a protein required for normal
germ plasm development in the Drosophila embryo [3]; a similar association
occurs with the Drosophila RBM8 protein, Tsunagi [4].
 
The RBM8A and RBM8B protein sequences contain a putative bipartate nuclear
localisation signal [5] at the N-terminus, as well a stretch of glycine
residues. In addition, the RRM contained within RBM8A and RBM8B contains 
one set of the two consensus nucleic acid-binding motifs, RNP-1 and RNP-2,
charactersitic of heterogeneous nuclear ribonucleoprotein (hnRNP). 
 
RNABINDINGM8 is a 4-element fingerprint that provides a signature for the
RNA-binding motif 8 protein family. The fingerprint was derived from an
initial alignment of 7 sequences: the motifs were drawn from conserved
regions spanning the full alignment length - motifs 2-4 span the RRM. Two
iterations SPTR40_20f were required to reach convergence, at which point a
true set comprising 10 sequences was identified.
Summary Information
10 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
410101010
30000
20000
1234
True Positives
Q21832        Q95X08        Q9C8K3        Q9CWZ3        
Q9D6U5 Q9DF42 Q9GZX8 Q9NZI4
Q9V535 RBM8_HUMAN
Sequence Titles
Q21832      R07E5.14 PROTEIN - Caenorhabditis elegans.    
Q95X08 TSUNAGI - Drosophila melanogaster (Fruit fly).
Q9C8K3 RNA-BINDING PROTEIN, PUTATIVE - Arabidopsis thaliana (Mouse-ear cress).
Q9CWZ3 2310057C03RIK PROTEIN (RNA BINDING MOTIF PROTEIN 8A) - Mus musculus (Mouse).
Q9D6U5 2310057C03RIK PROTEIN - Mus musculus (Mouse).
Q9DF42 RNA-BINDING PROTEIN Y14 - Xenopus laevis (African clawed frog).
Q9GZX8 RNA BINDING MOTIF PROTEIN 8B (MDS014) - Homo sapiens (Human).
Q9NZI4 RNA BINDING MOTIF PROTEIN 8 (RNA BINDING MOTIF PROTEIN 8A) - Homo sapiens (Human).
Q9V535 CG8781 PROTEIN - Drosophila melanogaster (Fruit fly).
RBM8_HUMAN RNA-binding protein 8 (RNA binding motif protein 8) (Ribonucleoprotein RBM8) (RNA-binding protein Y14) - Homo sapiens (Human).
Scan History
SPTR40_20f 2  160  NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
KEKAKKRKGRGFG RBM8_HUMAN 29 29 -
KEKAKKRKGRGFG Q9NZI4 29 29 -
KEKAKKRKGRGFG Q9D6U5 29 29 -
KEKAKKRKGRGFG Q9DF42 29 29 -
KEKAKHRKGRGFG Q95X08 27 27 -
GESAKKTKGRGFR Q9C8K3 49 49 -
VANAERSRGRGLA Q21832 12 12 -

Motif 2 width=15
Element Seqn Id St Int Rpt
PGPQRSVEGWILFVT RBM8_HUMAN 64 22 -
PGPQRSVEGWILFVT Q9NZI4 63 21 -
PGPQRSVEGWILFVT Q9D6U5 63 21 -
PGPQRSVEGWILFVT Q9DF42 64 22 -
PGPQRSVEGWILFVT Q95X08 64 24 -
PGPQRSVEGWIILVS Q9C8K3 86 24 -
GAPQRSVEGWIVFVT Q21832 46 21 -

Motif 3 width=17
Element Seqn Id St Int Rpt
EYETYKEAQAAMEGLNG RBM8_HUMAN 120 41 -
EYETYKEAQAAMEGLNG Q9NZI4 119 41 -
EYETYKEAQAAMEGLNG Q9D6U5 119 41 -
EYETYKEALAAMEGLNG Q9DF42 120 41 -
EYETHKQALAAKEALRG Q95X08 120 41 -
EYEKKEEAQSAISAMNG Q9C8K3 142 41 -
EYETQKEANEAIDQSND Q21832 102 41 -

Motif 4 width=13
Element Seqn Id St Int Rpt
DLMGQPISVDWCF RBM8_HUMAN 138 1 -
DLMGQPISVDWCF Q9NZI4 137 1 -
DLMGQPISVDWCF Q9D6U5 137 1 -
DLMGQPVSVDWGF Q9DF42 138 1 -
EIMGQTIQVDWCF Q95X08 138 1 -
ELLTQNVSVDWAF Q9C8K3 160 1 -
DLLGQNVKVDWCF Q21832 120 1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
KEKAKKRKGRGFG Q9CWZ3 29 29 -
KEKAKKRKGRGFG RBM8_HUMAN 29 29 -
KEKAKKRKGRGFG Q9NZI4 29 29 -
KEKAKKRKGRGFG Q9GZX8 13 13 -
KEKAKKRKGRGFG Q9D6U5 29 29 -
KEKAKKRKGRGFG Q9DF42 29 29 -
KEKAKHRKGRGFG Q9V535 27 27 -
KEKAKHRKGRGFG Q95X08 27 27 -
GESAKKTKGRGFR Q9C8K3 49 49 -
VANAERSRGRGLA Q21832 12 12 -

Motif 2 width=15
Element Seqn Id St Int Rpt
PGPQRSVEGWILFVT Q9CWZ3 63 21 -
PGPQRSVEGWILFVT RBM8_HUMAN 64 22 -
PGPQRSVEGWILFVT Q9NZI4 63 21 -
PGPQRSVEGWILFVT Q9GZX8 48 22 -
PGPQRSVEGWILFVT Q9D6U5 63 21 -
PGPQRSVEGWILFVT Q9DF42 64 22 -
PGPQRSVEGWILFVT Q9V535 64 24 -
PGPQRSVEGWILFVT Q95X08 64 24 -
PGPQRSVEGWIILVS Q9C8K3 86 24 -
GAPQRSVEGWIVFVT Q21832 46 21 -

Motif 3 width=17
Element Seqn Id St Int Rpt
EYETYKEAQAAMEGLNG Q9CWZ3 119 41 -
EYETYKEAQAAMEGLNG RBM8_HUMAN 120 41 -
EYETYKEAQAAMEGLNG Q9NZI4 119 41 -
EYETYKEAQAAMEGLNG Q9GZX8 104 41 -
EYETYKEAQAAMEGLNG Q9D6U5 119 41 -
EYETYKEALAAMEGLNG Q9DF42 120 41 -
EYETHKQALAAKEALNG Q9V535 120 41 -
EYETHKQALAAKEALRG Q95X08 120 41 -
EYEKKEEAQSAISAMNG Q9C8K3 142 41 -
EYETQKEANEAIDQSND Q21832 102 41 -

Motif 4 width=13
Element Seqn Id St Int Rpt
DLMGQPISVDWCF Q9CWZ3 137 1 -
DLMGQPISVDWCF RBM8_HUMAN 138 1 -
DLMGQPISVDWCF Q9NZI4 137 1 -
DLMGQPISVDWCF Q9GZX8 122 1 -
DLMGQPISVDWCF Q9D6U5 137 1 -
DLMGQPVSVDWGF Q9DF42 138 1 -
EIMGQTIQVDWCF Q9V535 138 1 -
EIMGQTIQVDWCF Q95X08 138 1 -
ELLTQNVSVDWAF Q9C8K3 160 1 -
DLLGQNVKVDWCF Q21832 120 1 -