Finding Conservation Scores Of Human Pseudogene

Question

[Stephanhart]

I have identified a pseudogene in my human RNA-seq data. I would like to know how well this gene is conserved in (i) other primates and (ii) other mammals. Is the best course of action to put the gene ID through UCSC (i.e., Multiz, Phylop, Phastcons)? Or should I do a multiple alignment myself and then analyze it? I would, of course, eventually like to identify which regions specifically are conserved/derived. Your advice is appreciated.

Thanks Stephan

[Farhat]

I thought pseudogenes aren't transcribed. So how would they show up in RNA-seq?

Answer 1

[Gareth Palidwor]

Have you checked the predicted pseudogenes available from the Gerstein lab at pseudogene.org? If your putative pseudogene is predicted by them you could use their score...

[Stephanhart]

Thank you. Unfortunately, I couldn't find it there.

[Gareth Palidwor]

I'd recommend doing a multiple alignment yourself then. You could have a look at the UCSC conservation data as you say, though it's probably best to do your own alignment. Characterizing it (if possible) as a processed or unprocessed pseudogene may help your analysis as it can guide how you do the alignment.