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) , 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) , which is
highly similar to elav and which may play a role in neuron-specific RNA
- Drosophila 'bicoid' protein (once) , 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 , which may be
involved in splicing and/or processing of chloroplast RNAs (twice).
- X16 , 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)  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 .
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
We have developed a profile that spans the RRM domain.
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