The GENCODE Genes track (version M39, May 2026 (pre-release)) shows high-quality manual annotations merged with evidence-based automated annotations across the entire mouse genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The M39 annotation was carried out on genome assembly GRCm39 (mm39).
The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release.
GENCODE GFF3 and GTF files are available from the GENCODE release M39 site.
GENCODE version M39 corresponds to Ensembl 116.
See also: The GENCODE Project