Question about mm10 GTF annotation used in AlphaGenome

Help & Support
1

Hi AlphaGenome team,

I’m using AlphaGenome with the mm10 reference and noticed that the Akap11 coordinates differ from those shown in UCSC Genome Browser.

Could you clarify which mm10 gene annotation (GTF/GFF) is used internally (e.g., Ensembl and which release, GENCODE, or UCSC)?

Thanks!!

Zuwen

2

Hi,

Based on the supplementary methods:

Gene and transcript annotations used for model evaluations were based on the GTF V46 annotations ( GENCODE - Human Release 46 ), unless otherwise specified.

Best,

Ray