This track shows the Ensembl gene, version 86, annotations on the 26 Apr 2016 Mus musculus (house mouse)/GCA_001624745.1_NZO_HlLtJ_v1 genome assembly.

These gene predictions were generated by Ian Fiddes at UCSC as part of the Mouse Genomes Project. Annotations from GENCODE VM8 were projected through a whole genome alignment on to each strain assembly, and then cleaned up using a special parameterization of the gene-finding tool AUGUSTUS. Ab-initio transcripts were also predicted using another parameterization of AUGUSTUS called Comparative Augustus, or AugustusCGP. These transcript sets were then combined into a final gene set using a consensus finding algorithm, and given unique identifiers. See Mouse Genomes Annotation Pipeline for more details.

Gene count: 103,156; Bases covered: 1,144,203,105


For general questions about these data, please contact Thomas Keane or Ian Fiddes.


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Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656

Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12. PMID: 15215400; PMC: PMC441517