GENCODE: reference annotation for the human and mouse genomes in 2023

Area of Science:

• Genomics
• Transcriptomics
• Bioinformatics

Background:

• GENCODE provides comprehensive gene and transcript annotation for human and mouse genomes.
• Annotation is crucial for genome biology and clinical genomics applications.
• The GENCODE consortium integrates experimental data and bioinformatic analyses.

Purpose of the Study:

• To present an update on GENCODE annotation for human and mouse genes.
• To highlight advancements in annotation tools, data, and analytical methods.
• To report on key collaborations and their impact on annotation quality and scope.

Main Methods:

• Generation of targeted experimental data.
• Development and application of bioinformatic tools for transcript identification and annotation.
• Integration of external data and collaborative efforts with RefSeq and UniProt.
• Analysis of long transcriptomic data for model building (LRGASP).

Main Results:

• Identification and annotation of non-canonical open reading frames (ORFs).
• Increased convergence in human and mouse protein-coding gene annotation through collaborations.
• Expansion of GENCODE annotation across the human pan-genome.
• Development of new tools for regulatory feature annotation.

Conclusions:

• GENCODE annotation is a continuously improving reference standard for genomic research.
• Collaborations and technological advancements enhance the accuracy and breadth of gene annotation.
• The updated GENCODE release supports diverse applications in basic and clinical genomics.