Hi,
I have used de novo methods (Cufflinks, isoSCM) to assemble new transcripts for some badly annotated genes.
I have now a large gene family (mice olfactory receptors) with fully annotated transcripts, which often have exons and introns in both CDS and UTRs. There were already quite a few studies of the CDSs, but the UTRs have never been looked into.

1. I would like to align them and try to some serious phylogeny work. How do I take into account the fact that there are large natural occurring gaps due to introns? Should I only consider spliced transcripts and consider that introns are much less conserved?
2. Is it relevant to focus on statistics such as the length of the UTRs and the number of introns? Should I consider the variability of the CDS vs that of the UTRs?
3. If I resort to the MEME suite to look for patterns (such as RNA binding ones), should I focus only on the UTRs or also the CDS?
4. Can I study SNPs? I have too few RNA Seq samples of my own, so I would have to look into databases. I can expect a rather high level of variation...