{PDOC00030}
{PS50102; RRM}
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* Eukaryotic RNA recognition motif profile *
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Many eukaryotic proteins  that are known or  supposed  to bind single-stranded
RNA contain one or more  copies of a putative  RNA-binding  domain of about 90
amino acids [1,2]. This domain is known as the RNA recognition motif (RRM).

This region has been found in the following proteins:

   ** Heterogeneous nuclear ribonucleoproteins **
 - hnRNP A1 (helix destabilizing protein) (twice).
 - hnRNP A2/B1 (twice).
 - hnRNP C (C1/C2) (once).
 - hnRNP E (UP2) (at least once).
 - hnRNP G (once).

   ** Small nuclear ribonucleoproteins **
 - U1 snRNP 70 Kd (once).
 - U1 snRNP A  (once).
 - U2 snRNP B'' (once).

   ** Pre-RNA and mRNA associated proteins **
 - Protein synthesis initiation factor  4B (eIF-4B) [3], a  protein  essential
   for the binding of mRNA to ribosomes (once).
 - Nucleolin (4 times).
 - Yeast single-stranded nucleic acid-binding protein (gene SSB1) (once).
 - Yeast protein NSR1 (twice). NSR1  is  involved  in  pre-rRNA processing; it
   specifically binds nuclear localization sequences.
 - Poly(A) binding protein (PABP) (4 times).

   ** Others **
 - Drosophila sex determination protein Sex-lethal (Sxl) (twice).
 - Drosophila sex determination protein Transformer-2 (Tra-2) (once).
 - Drosophila 'elav' protein (3 times), which is  probably involved in the RNA
   metabolism of neurons.
 - Human paraneoplastic encephalomyelitis antigen HuD (3 times) [4],  which is
   highly similar to  elav  and  which  may play a role in neuron-specific RNA
   processing.
 - Drosophila 'bicoid' protein (once) [5], a segment-polarity homeobox protein
   that may also bind to specific mRNAs.
 - La antigen (once), a protein which  may play a role in the transcription of
   RNA polymerase III.
 - The 60 Kd Ro protein (once), a putative RNP complex protein.
 - A maize protein induced by abscisic acid in response to water stress, which
   seems to be a RNA-binding protein.
 - Three  tobacco  proteins,  located  in  the  chloroplast  [6], which may be
   involved in splicing and/or processing of chloroplast RNAs (twice).
 - X16 [7], a mammalian protein  which  may  be involved in RNA processing  in
   relation with cellular proliferation and/or maturation.
 - Insulin-induced growth response protein Cl-4 from rat (twice).
 - Nucleolysins  TIA-1  and  TIAR  (3  times)  [8] which possesses nucleolytic
   activity against  cytotoxic  lymphocyte  target  cells.  may be involved in
   apoptosis.
 - Yeast RNA15 protein, which plays a role in mRNA stability  and/or  poly-(A)
   tail length [9].

Inside the RRM there are two regions which are highly conserved. The first one
is a  hydrophobic  segment  of six residues (which is called the RNP-2 motif),
the second  one is an octapeptide motif (which is called RNP-1 or RNP-CS). The
position of  both  motifs  in  the  domain is shown in the following schematic
representation:

  xxxxxxx######xxxxxxxxxxxxxxxxxxxxxxxxxxxxx########xxxxxxxxxxxxxxxxxxxxxxxxx
         RNP-2                              RNP-1

We have developed a profile that spans the RRM domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: August 2004 / Text revised; pattern deleted.

[ 1] Bandziulis R.J., Swanson M.S., Dreyfuss G.
     "RNA-binding proteins as developmental regulators."
     Genes Dev. 3:431-437(1989).
     PubMed=2470643
[ 2] Dreyfuss G., Swanson M.S., Pinol-Roma S.
     "Heterogeneous nuclear ribonucleoprotein particles and the pathway of
     mRNA formation."
     Trends Biochem. Sci. 13:86-91(1988).
     PubMed=3072706
[ 3] Milburn S.C., Hershey J.W.B., Davies M.V., Kelleher K., Kaufman R.J.
     "Cloning and expression of eukaryotic initiation factor 4B cDNA:
     sequence determination identifies a common RNA recognition motif."
     EMBO J. 9:2783-2790(1990).
     PubMed=2390971
[ 4] Szabo A., Dalmau J., Manley G., Rosenfeld M., Wong E., Henson J.,
     Posner J.B., Furneaux H.M.
     "HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding
     domains and is homologous to Elav and Sex-lethal."
     Cell 67:325-333(1991).
     PubMed=1655278
[ 5] Rebagliati M.
     "An RNA recognition motif in the bicoid protein."
     Cell 58:231-232(1989).
     PubMed=2752425
[ 6] Li Y.Q., Sugiura M.
     "Three distinct ribonucleoproteins from tobacco chloroplasts: each
     contains a unique amino terminal acidic domain and two
     ribonucleoprotein consensus motifs."
     EMBO J. 9:3059-3066(1990).
     PubMed=1698606
[ 7] Ayane M., Preuss U., Koehler G., Nielsen P.J.
     "A differentially expressed murine RNA encoding a protein with
     similarities to two types of nucleic acid binding motifs."
     Nucleic Acids Res. 19:1273-1278(1991).
     PubMed=2030943
[ 8] Kawakami A., Tian Q., Duan X., Streuli M., Schlossman S.F., Anderson P.
     "Identification and functional characterization of a TIA-1-related
     nucleolysin."
     Proc. Natl. Acad. Sci. U.S.A. 89:8681-8685(1992).
     PubMed=1326761
[ 9] Minvielle-Sebastia L., Winsor B., Bonneaud N., Lacroute F.
     Mol. Cell. Biol. 11:3075-3087(1991).

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