SelenoDB 1.0 : A Database of Selenoprotein Genes, Proteins and SECIS Elements

Authors

Sergi Castellano, University of Hawaii at Manoa
Vadim N. Gladyshev, University of Nebraska-LincolnFollow
Roderic Guigo, Grup de Recerca en Informa` tica Biome` dica, Institut Municipal d’Investigacio´ Me` dica, Barcelona, Spain
Marla J. Berry, University of Hawaii at Manoa

Date of this Version

2008

Comments

Published in Nucleic Acids Research, 2008, Vol. 36, Database issue. Copyright © 2007 The Author(s). Used by permission.

Abstract

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.