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NESbase 1.0

NESbase is a database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature.

NESbase 1.0 format description

The database is in HTML; it is downloadable as text without any loss of information other than the hyperlinks to Swiss-Prot and Medline. It is organized in entries, one per protein. Each entry has the following fields:
NES-accession	NESbase accession code e.g. NES-0001
Date	Dates for creation and updates of entry.
Protein	Protein description.
Organism	Species name e.g. Homo sapiens
DB_reference	Sequence Cross-reference to Swiss-Prot, PIR or Genbank.
Necessity	Experimental evidence (if any), indicating that the signal is necessary for export. Usually shown by deletion of or mutations in the signal that greatly impairs or abrogates export.
Sufficiency	Experimental evidence (if any), indicating that the signal is nsufficient for export. Usually shown by a peptide bearing the NES-signalp mediating export of a reporter protein.
Pathway	LMB-sensitivity and/or CRM1-dependency if described.
Location	Nucleocytoplasmic shuttling proteins are often predominantly localised to either nucleus or cytoplasm at steady state. When available, information of steady state localisation is given in this field.
Regulation	Export can be regulated, for instance, by a change in phosphorylation state of the protein or by protein-protein interaction masking the NES signal. When available, information of regulation is given in this field.
Comments	Other relevant information.
References	Literature references and Medline links.
Sequence	Sequence followed by an assignment field. The assignment field reflects the experimental data described in the necessity and sufficiency fields: Point-mutations that greatly impair export either alone or together are designated "M"; Sequence segments shown to mediate export of either truncations of the protein being tested or of a reporter protein are designated "a".

Article abstract

NESbase version 1.0, a database of Nuclear Export Signals.
Tanja la Cour^2,1, Ramneek Gupta¹, Kristoffer Rapacki¹,
Karen Skriver², Flemming M. Poulsen² and Søren Brunak¹.
Nucleic Acids Res., 31(1):393-6, 2003.

¹ Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark
² Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, DK-1353 Copenhagen, Denmark

Protein export from the nucleus is often mediated by a Leucine-rich nuclear export signal. NESbase is a database of experimentally validated Leucine-rich Nuclear Export Signals (NES) curated from literature. These signals are not annotated in databases such as SWISS-PROT, PIR or PROSITE. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Surprisingly, only 36% of the sequences used for the logo fit the widely accepted NES consensus L-x(2,3)-[LIVFM]-x(2,3)-L-x-[LI].

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NESbase-1.0.db.html

Correspondance: Ramneek Gupta