{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:16:39Z","timestamp":1778058999834,"version":"3.51.4"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T00:00:00Z","timestamp":1606953600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U41HG007234"],"award-info":[{"award-number":["U41HG007234"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT108749\/Z\/15\/Z"],"award-info":[{"award-number":["WT108749\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT200990\/Z\/16\/Z"],"award-info":[{"award-number":["WT200990\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009068","name":"University of Bern","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009068","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https:\/\/www.gencodegenes.org.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1087","type":"journal-article","created":{"date-parts":[[2020,10,25]],"date-time":"2020-10-25T04:07:42Z","timestamp":1603598862000},"page":"D916-D923","source":"Crossref","is-referenced-by-count":1273,"title":["GENCODE 2021"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4333-628X","authenticated-orcid":false,"given":"Adam","family":"Frankish","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0430-0989","authenticated-orcid":false,"given":"Mark","family":"Diekhans","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3197-5367","authenticated-orcid":false,"given":"Irwin","family":"Jungreis","sequence":"additional","affiliation":[{"name":"MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA"},{"name":"Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA"}]},{"given":"Julien","family":"Lagarde","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7669-2934","authenticated-orcid":false,"given":"Jane\u00a0E","family":"Loveland","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Jonathan M","family":"Mudge","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Cristina","family":"Sisu","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"},{"name":"Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK"}]},{"given":"James C","family":"Wright","sequence":"additional","affiliation":[{"name":"Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK"}]},{"given":"Joel","family":"Armstrong","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA"}]},{"given":"If","family":"Barnes","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, 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Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7445-2419","authenticated-orcid":false,"given":"Fiona","family":"Cunningham","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Tom\u00e1s","family":"Di\u00a0Domenico","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"given":"Sarah","family":"Donaldson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Ian\u00a0T","family":"Fiddes","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, 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