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

Castellano S, Gladyshev VN, Guigó R, Berry MJ - Nucleic Acids Res. (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii, USA. castellanos@janelia.hhmi.org

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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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).
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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).

Mentions: All search methods produce a list of matching Feature Reports links (Gene, Transcript, Protein and others) ordered by species, family and subfamily (Figure 2). Feature IDs are color coded: (i) selenoproteins in red; (ii) Cys-containing homologs in green; (iii) homologs bearing any other amino acid in the homologous Sec site in yellow and (iv) selenium machinery proteins or trans-acting proteins involved in the translational recodification of Sec residues in brown. The color code is maintained across all search results and Feature Reports, whenever a Feature ID is displayed.Figure 2.


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

Castellano S, Gladyshev VN, Guigó R, Berry MJ - Nucleic Acids Res. (2008)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238826&req=5

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).
Mentions: All search methods produce a list of matching Feature Reports links (Gene, Transcript, Protein and others) ordered by species, family and subfamily (Figure 2). Feature IDs are color coded: (i) selenoproteins in red; (ii) Cys-containing homologs in green; (iii) homologs bearing any other amino acid in the homologous Sec site in yellow and (iv) selenium machinery proteins or trans-acting proteins involved in the translational recodification of Sec residues in brown. The color code is maintained across all search results and Feature Reports, whenever a Feature ID is displayed.Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii, USA. castellanos@janelia.hhmi.org

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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