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GENCODE 2021

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Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos García Girón, Jose Manuel Gonzalez & 36 more Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C.P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinuri Xu, Yucheng T. Yang, Andrew Yates, Daniel Zerbino, Yan Zhang, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigó, Tim J.P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek

Original languageEnglish
Pages (from-to)D916-D923
JournalNucleic Acids Research
Volume49
Issue numberD1
DOIs
Published8 Jan 2021

Bibliographical note

Funding Information: National Human Genome Research Institute of the National Institutes of Health [U41HG007234]; the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health; Wellcome Trust [WT108749/Z/15/Z, WT200990/Z/16/Z]; European Molecular Biology Laboratory; Swiss National Science Foundation through the National Center of Competence in Research 'RNA & Disease' (to R.J.); Medical Faculty of the University of Bern (to R.J). Funding for open access charge: National Institutes of Health. Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

King's Authors

Abstract

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.

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