New isoform found in mouse, can we use RNAseq to find it in humans?

[sindrle]

Hi!

I got a request about looking for a new isoform found in mouse, only now in human material. That means it does not exist in Ensembl Human release 74.

Im starting by running Cufflinks without a reference genome (the whole Cufflinks->cuff merge-> cuffdiff pipeline), but does anyone have some good tips along the way?

Thanks!

[Dario1984]

Isn't it simpler to use UCSC Genome Browser to BLAT the novel mouse transcript to the human genome ? Then, just look for RNA-seq reads present in that region in your human transcriptome data, mapped to the human genome.

[sindrle]

Thats a good ide, even though I don't know how I can "see" the novel isoform? Its supposed to have another promotor and is truncated (50 AA less).
In other words its the same as the longest isoform, but shorter start. Wont this be masked? How can I visually separate these two isoforms?

[sindrle]

Another thing, the Ensembl ensGene table includes 8 transcripts from this gene (I checked today). In the iGenome genes.gtf, which is from UCSC hg19, its only 2 transcripts (newest update march 2013).

But none of the 8 is the one Im looking for, but I guess it will be difficult to visually separate 9 isoforms..