{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T06:14:04Z","timestamp":1777702444472,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T00:00:00Z","timestamp":1669248000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/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\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG004037"],"award-info":[{"award-number":["R01HG004037"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT222155\/Z\/20\/Z"],"award-info":[{"award-number":["WT222155\/Z\/20\/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"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gkac1071","type":"journal-article","created":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T01:36:14Z","timestamp":1669340174000},"page":"D942-D949","source":"Crossref","is-referenced-by-count":491,"title":["GENCODE: reference annotation for the human and mouse genomes in 2023"],"prefix":"10.1093","volume":"51","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 \u00a0CB10 1SD, UK"}]},{"given":"S\u00edlvia","family":"Carbonell-Sala","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics , Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona \u00a008003, Catalonia, Spain"}]},{"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 ,\u00a0CA\u00a095064, 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 \u00a002139, USA"},{"name":"Broad Institute of MIT and Harvard , 415 Main Street , Cambridge , MA \u00a002142, USA"}]},{"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 \u00a0CB10 1SD, UK"}]},{"given":"Jonathan\u00a0M","family":"Mudge","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, Cambridge \u00a0CB10 1SD, UK"}]},{"given":"Cristina","family":"Sisu","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven , CT\u00a0 06520 , USA"},{"name":"Department of Life Sciences, Brunel University London , Uxbridge \u00a0UB8 3PH, UK"}]},{"given":"James\u00a0C","family":"Wright","sequence":"additional","affiliation":[{"name":"Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research , 237 Fulham Road , London \u00a0SW3 6JB, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7431-2088","authenticated-orcid":false,"given":"Carme","family":"Arnan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics , Centre for Genomic Regulation (CRG) , The 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