Workflow question:

Im trying to clone a gene. While amplifying it, i had some problems. I then realized that its gene model changes across genome versions meaning that i have the 5' region in the CDS that displays some indels. I have multiple transcripts in both genome versions and i realized i dont know anymore what transcript im working with because of this problem. So what workflow do you suggest? i was thinking to simply remap all reads i have from several RNAseq studies against both genome versions with some mapping tools like Bowtie or STAR and then analyse the coverage in that specific region. Ideally i could also extract the mapping reads a perform a denovo assembly, correct?

What else do you suggest OR what would you prefer?

thanks in advance