Limits...
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.

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

License
getmorefigures.php?uid=PMC2238826&req=5

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.

Mentions: Annotation section. In all Feature Reports, this section provides the annotation method (note the possibility to report annotation errors), orientation of the annotated Feature and displays the exonic structure of the annotated gene (Figure 3). In Gene Reports, a list of links to the corresponding Transcript, Promoter, Exon, Intron, Protein and SECIS Report is given. In all other Feature Reports, the Annotation section provides the sequence of the Feature of interest, e.g. the sequence of a particular exon in an Exon Report, the SECIS sequence in a SECIS Report or the transcript sequence in a Transcript Report (Figure 3). Both the gene structure plot and the displayed sequence in each Feature Report is color coded by feature type: (a) promoters in gray (note that promoter elements in the promoter regions are not yet provided due to the low quality of current computational prediction methods); (b) coding and non-coding exon regions (UTRs) in dark and light blue, respectively; (c) introns in black; (d) SECIS in brown and (e) Sec, Cys and other homologous residues in red, green and yellow, respectively. See Figure 3 for an example.


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

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

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

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

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.
Mentions: Annotation section. In all Feature Reports, this section provides the annotation method (note the possibility to report annotation errors), orientation of the annotated Feature and displays the exonic structure of the annotated gene (Figure 3). In Gene Reports, a list of links to the corresponding Transcript, Promoter, Exon, Intron, Protein and SECIS Report is given. In all other Feature Reports, the Annotation section provides the sequence of the Feature of interest, e.g. the sequence of a particular exon in an Exon Report, the SECIS sequence in a SECIS Report or the transcript sequence in a Transcript Report (Figure 3). Both the gene structure plot and the displayed sequence in each Feature Report is color coded by feature type: (a) promoters in gray (note that promoter elements in the promoter regions are not yet provided due to the low quality of current computational prediction methods); (b) coding and non-coding exon regions (UTRs) in dark and light blue, respectively; (c) introns in black; (d) SECIS in brown and (e) Sec, Cys and other homologous residues in red, green and yellow, respectively. See Figure 3 for an example.

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.

Show MeSH