GENCODE: reference annotation for the human and mouse genomes in 2023

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  • dc.contributor.author Frankish, Adam
  • dc.contributor.author Carbonell Sala, Silvia
  • dc.contributor.author Arnan Ros, Carme
  • dc.contributor.author Calvet, Ferriol
  • dc.contributor.author Lagarde, Julien
  • dc.contributor.author Guigó Serra, Roderic
  • dc.contributor.author Flicek, Paul
  • dc.date.accessioned 2023-02-21T07:25:19Z
  • dc.date.available 2023-02-21T07:25:19Z
  • dc.date.issued 2023
  • dc.description.abstract GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-49. DOI: 10.1093/nar/gkac1071
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkac1071
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/55835
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Nucleic Acids Res. 2023 Jan 6;51(D1):D942-49
  • dc.rights © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri https://creativecommons.org/licenses/by/4.0/
  • dc.title GENCODE: reference annotation for the human and mouse genomes in 2023
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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Articles (Departament de Medicina i Ciències de la Vida)
Articles (Center for Genomic Regulation (CRG))