Home | Contact

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.

August 2004 / Text revised; pattern deleted.

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

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

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE

• Domain architecture view of Swiss-Prot proteins matching PS50102 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50102 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50102 • Scan Swiss-Prot/TrEMBL entries against PS50102 • view ligand binding statistics

Matching PDB structures: 1A9N 1AUD 1B7F 1BNY ... [ALL]

1	Authors	Bandziulis R.J., Swanson M.S., Dreyfuss G.
	Title	RNA-binding proteins as developmental regulators.
	Source	Genes Dev. 3:431-437(1989).
	PubMed ID	2470643

2	Authors	Dreyfuss G., Swanson M.S., Pinol-Roma S.
	Title	Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation.
	Source	Trends Biochem. Sci. 13:86-91(1988).
	PubMed ID	3072706

3	Authors	Milburn S.C., Hershey J.W.B., Davies M.V., Kelleher K., Kaufman R.J.
	Title	Cloning and expression of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif.
	Source	EMBO J. 9:2783-2790(1990).
	PubMed ID	2390971

4	Authors	Szabo A., Dalmau J., Manley G., Rosenfeld M., Wong E., Henson J., Posner J.B., Furneaux H.M.
	Title	HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and Sex-lethal.
	Source	Cell 67:325-333(1991).
	PubMed ID	1655278

5	Authors	Rebagliati M.
	Title	An RNA recognition motif in the bicoid protein.
	Source	Cell 58:231-232(1989).
	PubMed ID	2752425

6	Authors	Li Y.Q., Sugiura M.
	Title	Three distinct ribonucleoproteins from tobacco chloroplasts: each contains a unique amino terminal acidic domain and two ribonucleoprotein consensus motifs.
	Source	EMBO J. 9:3059-3066(1990).
	PubMed ID	1698606

7	Authors	Ayane M., Preuss U., Koehler G., Nielsen P.J.
	Title	A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs.
	Source	Nucleic Acids Res. 19:1273-1278(1991).
	PubMed ID	2030943

8	Authors	Kawakami A., Tian Q., Duan X., Streuli M., Schlossman S.F., Anderson P.
	Title	Identification and functional characterization of a TIA-1-related nucleolysin.
	Source	Proc. Natl. Acad. Sci. U.S.A. 89:8681-8685(1992).
	PubMed ID	1326761

9	Authors	Minvielle-Sebastia L., Winsor B., Bonneaud N., Lacroute F.
	Source	Mol. Cell. Biol. 11:3075-3087(1991).

PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to

Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)

SIB Swiss Institute of Bioinformatics | Disclaimer