Description

This track shows the Ensembl gene, version 86, annotations on the 26 Apr 2016 Mus musculus castaneus (southeastern Asian house mouse)/GCA_001624445.1_CAST_EiJ_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: 102,138; Bases covered: 1,149,782,902

Credits

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

References

König S, Romoth LW, Gerischer L, Stanke M. Simultaneous gene finding in multiple genomes. Bioinformatics. 2016 Nov 15;32(22):3388-3395. PMID: 27466621

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