SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans

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 releas...

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Autores: Romagné, Frédéric, Santesmasses Ruiz, Didac, 1978-, White, Louise, Sarangi, Gaurab K., Mariotti, Marco, 1984-, Hübler, Ron, Weihmann, Antje, Parra Farré, Genís, Gladyshev, Vadim N., Guigó Serra, Roderic, Castellano Hereza, Sergi
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23102
Acceso en línea:http://hdl.handle.net/10230/23102
http://dx.doi.org/10.1093/nar/gkt1045
Access Level:acceso abierto
Palabra clave:Porteïnes
Genètica
Selenoproteïnes
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spelling SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humansRomagné, FrédéricSantesmasses Ruiz, Didac, 1978-White, LouiseSarangi, Gaurab K.Mariotti, Marco, 1984-Hübler, RonWeihmann, AntjeParra Farré, GenísGladyshev, Vadim N.Guigó Serra, RodericCastellano Hereza, SergiPorteïnesGenèticaSelenoproteïnesSelenoDB (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.This work was supported by the Plan Nacional and the Instituto Nacional de BIoinformatica (Spain)Oxford University Press201520152014info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23102http://dx.doi.org/10.1093/nar/gkt1045reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNucleic Acids Research. 2014;42(1):D437-43© 2014 Frédéric Romagné et al. Published by Oxford University Press. This is an Open Access article distributed under the terms a Creative Commons Attribution License which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly citedhttp://creativecommons.org/licenses/by/3.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/231022026-06-12T07:21:37Z
dc.title.none.fl_str_mv SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
title SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
spellingShingle SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
Romagné, Frédéric
Porteïnes
Genètica
Selenoproteïnes
title_short SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
title_full SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
title_fullStr SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
title_full_unstemmed SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
title_sort SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
dc.creator.none.fl_str_mv Romagné, Frédéric
Santesmasses Ruiz, Didac, 1978-
White, Louise
Sarangi, Gaurab K.
Mariotti, Marco, 1984-
Hübler, Ron
Weihmann, Antje
Parra Farré, Genís
Gladyshev, Vadim N.
Guigó Serra, Roderic
Castellano Hereza, Sergi
author Romagné, Frédéric
author_facet Romagné, Frédéric
Santesmasses Ruiz, Didac, 1978-
White, Louise
Sarangi, Gaurab K.
Mariotti, Marco, 1984-
Hübler, Ron
Weihmann, Antje
Parra Farré, Genís
Gladyshev, Vadim N.
Guigó Serra, Roderic
Castellano Hereza, Sergi
author_role author
author2 Santesmasses Ruiz, Didac, 1978-
White, Louise
Sarangi, Gaurab K.
Mariotti, Marco, 1984-
Hübler, Ron
Weihmann, Antje
Parra Farré, Genís
Gladyshev, Vadim N.
Guigó Serra, Roderic
Castellano Hereza, Sergi
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Porteïnes
Genètica
Selenoproteïnes
topic Porteïnes
Genètica
Selenoproteïnes
description 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.
publishDate 2014
dc.date.none.fl_str_mv 2014
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23102
http://dx.doi.org/10.1093/nar/gkt1045
url http://hdl.handle.net/10230/23102
http://dx.doi.org/10.1093/nar/gkt1045
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research. 2014;42(1):D437-43
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/3.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/3.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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