GENCODE 2021

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.

Cited by papers we hold 18

• ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data · 2024
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• Systematic assessment of long-read RNA-seq methods for transcript identification and quantification · 2024
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• Improving prime editing with an endogenous small RNA-binding protein · 2024
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• Global detection of human variants and isoforms by deep proteome sequencing · 2023
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• COSMIC: a curated database of somatic variants and clinical data for cancer · 2023
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• Accurate isoform discovery with IsoQuant using long reads · 2023
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• Identification of constrained sequence elements across 239 primate genomes · 2023
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• A draft human pangenome reference · 2023
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• INX-315, a Selective CDK2 Inhibitor, Induces Cell Cycle Arrest and Senescence in Solid Tumors · 2023
  Corrected
• A pangenome reference of 36 Chinese populations · 2023
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• GENCODE: reference annotation for the human and mouse genomes in 2023 · 2022
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• CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data · 2022
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• The UCSC Genome Browser database: 2023 update · 2022
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• Ensembl 2023 · 2022
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• rGREAT : an R/bioconductor package for functional enrichment on genomic regions · 2022
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• A joint NCBI and EMBL-EBI transcript set for clinical genomics and research · 2022
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• The Functions and Unique Features of LncRNAs in Cancer Development and Tumorigenesis · 2021
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• Ensembl 2022 · 2021
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