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. 2008 Jan;36(Database issue):D332-8.
doi: 10.1093/nar/gkm731. Epub 2008 Jan 3.

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

Sergi Castellano  1 , Vadim N Gladyshev, Roderic Guigó, Marla J Berry
Affiliations

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

Sergi Castellano et al. Nucleic Acids Res. 2008 Jan.

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.

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Figures

Figure 1.
Figure 1.
Graphical (Chart) search. Note the keyword and species/family search options at the top and bottom of the page, respectively. A click on a species, family or gene box leads to the corresponding query result page.
Figure 2.
Figure 2.
Query results from a keyword search on Gene Reports. Results are ordered by species, family and subfamily. Note the color coded Gene IDs links in the last column (red for selenoprotein and green for Cys-containing homolog).
Figure 3.
Figure 3.
Transcript Report of human SelO. Note the color coded gene structure and the spliced transcript sequence with sequences features colored accordingly. Other sequence views are one click away at links at the end of the sequence ID line.
See this image and copyright information in PMC

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