PROSITE documentation PDOC00015
Bipartite nuclear localization signal profile


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.

Last update:

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


Technical section

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!)


1AuthorsDingwall C. Laskey R.A.
TitleProtein import into the cell nucleus.
SourceAnnu. Rev. Cell Biol. 2:367-390(1986).
PubMed ID3548772

2AuthorsGarcia-Bustos J.F. Heitman J. Hall M.N.
SourceBiochim. Biophys. Acta 1071:83-101(1991).

3AuthorsGomez-Marquez J. Segade F.
SourceFEBS Lett. 226:217-219(1988).

4AuthorsDingwall C. Laskey R.A.
TitleNuclear targeting sequences -- a consensus?
SourceTrends Biochem. Sci. 16:478-481(1991).
PubMed ID1664152

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