Source Of Drosophila (Dm3) Canonical Transcripts?

Question

[Ian]

Background:

I have been using the UCSC gene knownCanonical transcript lists available for mammalian genomes, such as human and mouse, to get one TSS coordinate per gene, for the purpose of plotting NGS reads in sequence bins either side of TSSs.

Question:

However, canonical transcripts do not appear to be available for lower organisms. I am particularly interested in getting canonical TSSs Drosophila melanogaster (DM3) genes.

Does anyone know of such a resource?

[Casey Bergman]

Lower organisms, how dare you! Can you fly and get your entire body in a beer bottle?

Answer 1

[Steve Lianoglou]

Wouldn't the Ensembl, RefSeq or FlyBase annotations do just as well for your purpose?

[Ian]

You know i think you have a point there! I am so UCSC centric these days i forgot to look.

[Steve Lianoglou]

@Ian: FYI, you can download those annotations from UCSC table browser as well -- perhaps that will be easier for you?

[Ian]

If they have a refined set of gene models based on one representative transcript per gene, then that will be fine. I will check. Thanks.

Answer 2

[Mary]

I would look into the ModENCODE data too. Use their ModMine tool.

http://modencode.org/