This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Finding Conservation Scores Of Human Pseudogene

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

comparative ucsc
• 3,688 views • link
updated by Gareth Palidwor Gareth Palidwor • written by Stephanhart • Stephanhart

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

• 0 views • link
written by Farhat Farhat

1 answer

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...

• 1 views • link
written by Gareth Palidwor Gareth Palidwor

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

• 0 views • link
written by Stephanhart • Stephanhart

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.

• 0 views • link
written by Gareth Palidwor Gareth Palidwor

Log in to answer this question.

More posts like this