GENCODE 2025: reference gene annotation for human and mouse

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species' genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.

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Publication Details

Journal
Nucleic Acids Research
Published
2024-11-20
DOI
https://doi.org/10.1093/nar/gkae1078
Citations
260
Primary Topic
RNA and protein synthesis mechanisms
Type
article
Field-Weighted Citation Impact
60.79

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article

GENCODE 2025: reference gene annotation for human and mouse

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260 citations
Nucleic Acids Research
RNA and protein synthesis mechanisms
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GENCODE 2025: reference gene annotation for human and mouse

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article en
260 citations

Abstract

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species' genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.

Nucleic Acids ResearchVol. 53(D1)
University College Dublin (IE), Broad Institute (US), Vassar College (US), Guy's Hospital (GB), European Bioinformatics Institute (GB), Harvard University (US), Universitat Pompeu Fabra (ES), King's College London (GB), University of California, Santa Cruz (US), Fudan University (CN), University Hospital of Bern (CH), Yale University (US), Shanghai Institute for Science of Science (CN), Spanish National Cancer Research Centre (ES), Centre for Genomic Regulation (ES), Institute of Bioorganic Chemistry, Polish Academy of Sciences (PL), Elixir Medical (United States) (US), Shanghai Center for Brain Science and Brain-Inspired Technology (CN), Institute of Science and Technology, Brunel University of London (GB), Massachusetts Institute of Technology (US), Stanford University (US)
Wellcome Trust, European Molecular Biology Laboratory, National Institutes of Health, National Human Genome Research Institute
Openalex Percentile: Top 0%
RNA and protein synthesis mechanisms
60.79
DOIOpen Access PDFOpenAlex
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