How to analysing isoform thats not yet annotated

[sindrle]

Hi!
I read a paper recently about PPARGC1A. I now want to look at how this isoform is regulated in a RNA seq set I have from human. This is the article, they analyse mouse, but found the ortholog in humans (not using RNAseq):

http://www.cell.com/cell/abstract/S0092-8674(12)01363-3

You can see that all isoforms are annotated for mouse:

http://www.ensembl.org/Mus_musculus/...54249-51567725

But for homo sapiens there is none:

http://www.ensembl.org/Homo_sapiens/...NST00000507380

Question is, can I somehow analyse this isoform in humans using RNAseq? Adding this annotation somehow in the reference genome?

Thank you very much!