GENCODE reference annotation for the human and mouse genomes

TLDR

Accurate identification and description of genes in the human and mouse genomes is essential for high‑quality genomic analysis, and over the past 15 years the GENCODE consortium has produced reference‑quality annotations by combining experimental and computational biology groups. GENCODE generates primary data, develops bioinformatics tools, and provides analysis to support manual gene annotators and automated pipelines, integrating publicly available data and literature to identify and characterize gene loci to the highest standard. GENCODE gene annotations are available through Ensembl and UCSC Genome Browsers, Ensembl FTP, Biomart, Perl and REST APIs, and the GENCODE website.

Abstract

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.