title: SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans.
abstract: SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. In addition, we annotate the homologous genes containing cysteine (Cys) instead of Sec. Finally, we have surveyed genetic variation in the annotated genes in humans. We use exon capture and resequencing approaches to identify single-nucleotide polymorphisms in more than 50 human populations around the world. We thus present a detailed view of the genetic divergence of Sec- and Cys-containing genes in animals and their diversity in humans. The addition of these datasets into the second release of the database provides a valuable resource for addressing medical and evolutionary questions in selenium biology.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Romagné
authors.forename: Didac
authors.initials: D
authors.lastname: Santesmasses
authors.forename: Louise
authors.initials: L
authors.lastname: White
authors.forename: Gaurab K
authors.initials: GK
authors.lastname: Sarangi
authors.forename: Marco
authors.initials: M
authors.lastname: Mariotti
authors.forename: Ron
authors.initials: R
authors.lastname: Hübler
authors.forename: Antje
authors.initials: A
authors.lastname: Weihmann
authors.forename: Genís
authors.initials: G
authors.lastname: Parra
authors.forename: Vadim N
authors.initials: VN
authors.lastname: Gladyshev
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Sergi
authors.initials: S
authors.lastname: Castellano
mesh_terms: D000818:Animals; D030562:Databases, Protein; D005796:Genes; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D051140:Selenoproteins / Q000145:classification / Q000235:genetics*
chemical_list: D051140:Selenoproteins