[ensembl-dev] Ugt1a locus in rat

[Podtelezhnikov, Alexei]

Dear developers,

The tox community looks forward to the mRatBN7.2 assembly that should come in Ensembl 105. My benchmark is Ugt1a locus (ENSRNOG00000018740) which is historically very problematic for Ensembl. Mouse and Human get it right with multiple genes having distant first exons (and promoters) but sharing the trailing exons. Rat was never correct when using transcript variants of a single gene. What is even more confusing that the rat gene name is randomly changing: Ugt1a3 in Rapid, Ugt1a6 in 104, Ugt1a3 in 96, Ugt1a5 in 90, and so on.

In general the Rapid with mRatBN7.2 is much improved with fewer gene duplications and less gene entanglement in large families. It is just Ugt1a family which continues to be a problem. I suggest that this family be aligned with NCBI and with mouse and human. I think there should be reasonable alignment between three mammalian genomes selected for GRC.

Please consider this improvement for the future release. Thank you for your time and help.

Alexei

Alexei A Podtelezhnikov, PhD
Principal Scientist
Genome & Biomarker Sciences
Merck & Co., Inc.

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