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Nucleic Acids Research Advance Access originally published online on January 3, 2008
Nucleic Acids Research 2008 36(Database issue):D332-D338; doi:10.1093/nar/gkm731
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Nucleic Acids Research, 2008, Vol. 36, Database issue D332-D338
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Sergi Castellano1,*, Vadim N. Gladyshev2, Roderic Guigó3,4 and Marla J. Berry1

1Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii, 2Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA, 3Centre de Regulació Genòmica and 4Grup de Recerca en Informàtica Biomèdica, Institut Municipal d’Investigació Mèdica, Barcelona, Spain

*To whom correspondence should be addressed. Tel: +1 571 209 4000 ext. 7160; Fax: +1 571 209 4095; Email: castellanos{at}janelia.hhmi.org

Received August 14, 2007. Accepted September 3, 2007.

Selenoproteins are a diverse group of proteins usually misidentified and misannotated in sequence databases. The presence of an in-frame UGA (stop) codon in the coding sequence of selenoprotein genes precludes their identification and correct annotation. The in-frame UGA codons are recoded to cotranslationally incorporate selenocysteine, a rare selenium-containing amino acid. The development of ad hoc experimental and, more recently, computational approaches have allowed the efficient identification and characterization of the selenoproteomes of a growing number of species. Today, dozens of selenoprotein families have been described and more are being discovered in recently sequenced species, but the correct genomic annotation is not available for the majority of these genes. SelenoDB is a long-term project that aims to provide, through the collaborative effort of experimental and computational researchers, automatic and manually curated annotations of selenoprotein genes, proteins and SECIS elements. Version 1.0 of the database includes an initial set of eukaryotic genomic annotations, with special emphasis on the human selenoproteome, for immediate inspection by selenium researchers or incorporation into more general databases. SelenoDB is freely available at http://www.selenodb.org.


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L. Latreche, O. Jean-Jean, D. M. Driscoll, and L. Chavatte
Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine
Nucleic Acids Res., September 1, 2009; 37(17): 5868 - 5880.
[Abstract] [Full Text] [PDF]


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