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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.
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:
|
|
NESbase version 1.0, a database of Nuclear Export Signals.
1
Center for Biological Sequence Analysis, Technical University of Denmark,
DK-2800 Lyngby, 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].
Tanja la Cour2,1, Ramneek Gupta1,
Kristoffer Rapacki1,
Karen Skriver2, Flemming M. Poulsen2
and Søren Brunak1.
2
Department of Protein Chemistry, Institute of Molecular Biology,
University of Copenhagen, DK-1353 Copenhagen, Denmark
Download database
NESbase-1.0.db.html
Correspondance: Ramneek Gupta