PROSITE documentation PDOC00030 [for PROSITE entry PS50102]
Eukaryotic RNA recognition motif profile


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
 - 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
 - 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:

         RNP-2                              RNP-1

We have developed a profile that spans the RRM domain.

Last update:

August 2004 / Text revised; pattern deleted.


Technical section

PROSITE method (with tools and information) covered by this documentation:

RRM, PS50102; Eukaryotic RNA Recognition Motif (RRM) profile  (MATRIX)


1AuthorsBandziulis R.J. Swanson M.S. Dreyfuss G.
TitleRNA-binding proteins as developmental regulators.
SourceGenes Dev. 3:431-437(1989).
PubMed ID2470643

2AuthorsDreyfuss G. Swanson M.S. Pinol-Roma S.
TitleHeterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation.
SourceTrends Biochem. Sci. 13:86-91(1988).
PubMed ID3072706

3AuthorsMilburn S.C. Hershey J.W.B. Davies M.V. Kelleher K. Kaufman R.J.
TitleCloning and expression of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif.
SourceEMBO J. 9:2783-2790(1990).
PubMed ID2390971

4AuthorsSzabo A. Dalmau J. Manley G. Rosenfeld M. Wong E. Henson J. Posner J.B. Furneaux H.M.
TitleHuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and Sex-lethal.
SourceCell 67:325-333(1991).
PubMed ID1655278

5AuthorsRebagliati M.
TitleAn RNA recognition motif in the bicoid protein.
SourceCell 58:231-232(1989).
PubMed ID2752425

6AuthorsLi Y.Q. Sugiura M.
TitleThree distinct ribonucleoproteins from tobacco chloroplasts: each contains a unique amino terminal acidic domain and two ribonucleoprotein consensus motifs.
SourceEMBO J. 9:3059-3066(1990).
PubMed ID1698606

7AuthorsAyane M. Preuss U. Koehler G. Nielsen P.J.
TitleA differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs.
SourceNucleic Acids Res. 19:1273-1278(1991).
PubMed ID2030943

8AuthorsKawakami A. Tian Q. Duan X. Streuli M. Schlossman S.F. Anderson P.
TitleIdentification and functional characterization of a TIA-1-related nucleolysin.
SourceProc. Natl. Acad. Sci. U.S.A. 89:8681-8685(1992).
PubMed ID1326761

9AuthorsMinvielle-Sebastia L. Winsor B. Bonneaud N. Lacroute F.
SourceMol. Cell. Biol. 11:3075-3087(1991).

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