PROSITE documentation PDOC00030

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
   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.