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. 2021 Jan 8;49(D1):D916-D923.
doi: 10.1093/nar/gkaa1087.

GENCODE 2021

Adam Frankish  1 , Mark Diekhans  2 , Irwin Jungreis  3   4 , Julien Lagarde  5 , Jane E Loveland  1 , Jonathan M Mudge  1 , Cristina Sisu  6   7 , James C Wright  8 , Joel Armstrong  2 , If Barnes  1 , Andrew Berry  1 , Alexandra Bignell  1 , Carles Boix  3   4   9 , Silvia Carbonell Sala  5 , Fiona Cunningham  1 , Tomás Di Domenico  10 , Sarah Donaldson  1 , Ian T Fiddes  2 , Carlos García Girón  1 , Jose Manuel Gonzalez  1 , Tiago Grego  1 , Matthew Hardy  1 , Thibaut Hourlier  1 , Kevin L Howe  1 , Toby Hunt  1 , Osagie G Izuogu  1 , Rory Johnson  11   12 , Fergal J Martin  1 , Laura Martínez  10 , Shamika Mohanan  1 , Paul Muir  13   14 , Fabio C P Navarro  6 , Anne Parker  1 , Baikang Pei  6 , Fernando Pozo  10 , Ferriol Calvet Riera  1 , Magali Ruffier  1 , Bianca M Schmitt  1 , Eloise Stapleton  1 , Marie-Marthe Suner  1 , Irina Sycheva  1 , Barbara Uszczynska-Ratajczak  15 , Maxim Y Wolf  16 , Jinuri Xu  6 , Yucheng T Yang  6   17 , Andrew Yates  1 , Daniel Zerbino  1 , Yan Zhang  6   18 , Jyoti S Choudhary  8 , Mark Gerstein  6   17   19 , Roderic Guigó  5   20 , Tim J P Hubbard  21 , Manolis Kellis  3   4 , Benedict Paten  2 , Michael L Tress  10 , Paul Flicek  1
Affiliations

GENCODE 2021

Adam Frankish et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
Schematic of the TAGENE workflow to add long transcriptomic data to GENCODE annotation. Points in the workflow where manual review is applied are indicated.
Figure 2.
Figure 2.
Screenshot from the Ensembl genome browser of the transcript view page for the gene LDHB, which contains a transcript (ENST00000673047, LDHB-211) with an annotated stop-codon readthrough event. The location of the annotation attribute flagging the stop-codon readthrough is highlighted by the red box.
Figure 3.
Figure 3.
A screenshot from the Ensembl genome browser of the location view for the CTSS gene. The Comprehensive annotation from GENCODE 35 is shown in the upper panel and the updated annotation in the COVID-19 genes trackhub is shown in the lower panel. Transcript models that are unchanged with respect to release Ensembl 101 are coloured blue, whereas new models or pre-existing models that have been modified are shown in orange.
See this image and copyright information in PMC

References

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