Where Can I Find The Rat Genome Y Chromosome Sequence?

Question

[User 59]

BioStars,

I'm having a little difficulty finding any sequence information for the rat Y chromosome. I realise that for some mammals (dog and rat included) females were sequenced, but the rat genome paper suggest some sequencing of the Y chromosome was done (but not released in the build).

I've also found references to proposed work at Baylor College of Medicine Human Genome Sequencing Center with regards to sequencing the Y chromosome, the work having moved apparently from Genome Therapeutics to Agencourt. There's also references to a proposed 2008 release, but Ensembl and UCSC only have RGSC v3.4 (2004).

There is an updated build apparently in progress (Rnor4.0) here but the linearised chromosome data doesn't include the Y chromosome.

Any pointers gratefully received - I have some NGS data from a male rat cell line, and the researcher in question is keen to utilise all the data.

Answer 1

[Neilfws]

I think I found all the same links that you did: the BCM information page, the sequencing proposal/discussion (PDF) and the Nature Genetics paper outlining "things to come" in 2008.

The best I can find is a link named finishing status from the BCM page, with accessions for Y chromosome BACs from several species, including Rat. It takes a while to load, then you need to scroll down.