GENCODE 2021

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ID: 296857
2020
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Abstract
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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Authors Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles A. Boix, Sílvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos García Girón, José M. González, Tiago Grego, Matthew P. Hardy, Thibaut Hourlier, Kevin Howe, Toby Hunt, Osagie Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez Gómez, Shamika Mohanan, Paul Muir, Fábio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Campo del Pozo, Ferriol Calvet, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie‐Marthe Suner, Irina Sycheva, Barbara Uszczyńska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng Yang, Andrew Yates, Daniel R. Zerbino, Yan Zhang, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigó, Tim Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek
Journal Nucleic Acids Research
Year 2020
DOI
10.1093/nar/gkaa1087
URL
https://academic.oup.com/nar/article-pdf/49/D1/D916/35363795/gkaa1087.pdf
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