Home | Contact

The uptake of protein by the nucleus is extremely selective and nuclear proteins must therefore contain within their final structure a signal that specifies selective accumulation in the nucleus [1,2]. Studies on some nuclear proteins, such as the large T antigen of SV40, have indicated which part of the sequence is required for nuclear translocation. The known nuclear targeting sequences are generally basic, but there seems to be no clear common denominator between all the known sequences. Although some consensus sequence patterns have been proposed (see for example [3]), the current best strategy to detect a nuclear targeting sequence is based [4] on the following definition of what is called a 'bipartite nuclear localization signal':

  (1) Two adjacent basic amino acids (Arg or Lys).
  (2) A spacer region of any 10 residues.
  (3) At least three basic residues (Arg or Lys) in the five positions
      after the spacer region.

The profile we developed covers the entire bipartite nuclear localization signal.

This profile replace an obsolete rule. All the information in the rule has been encoded in the profile format.

October 2006 / Text revised; profiles added; rule deleted.

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

NLS_BP, PS50079; Bipartite nuclear localization signal profile  (MATRIX with a high probability of occurrence!)

Sequences known to belong to this class detected by the profile: 56% of known nuclear proteins according to [4] Other sequence(s) detected in Swiss-Prot: about 4.2% of non-nuclear proteins according to [4].

• Scan Swiss-Prot/TrEMBL entries against PS50079 • view ligand binding statistics

1	Authors	Dingwall C., Laskey R.A.
	Title	Protein import into the cell nucleus.
	Source	Annu. Rev. Cell Biol. 2:367-390(1986).
	PubMed ID	3548772
	DOI	10.1146/annurev.cb.02.110186.002055

2	Authors	Garcia-Bustos J.F., Heitman J., Hall M.N.
	Source	Biochim. Biophys. Acta 1071:83-101(1991).

3	Authors	Gomez-Marquez J., Segade F.
	Source	FEBS Lett. 226:217-219(1988).

4	Authors	Dingwall C., Laskey R.A.
	Title	Nuclear targeting sequences -- a consensus?
	Source	Trends Biochem. Sci. 16:478-481(1991).
	PubMed ID	1664152

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