Question: Finding Conservation Scores Of Human Pseudogene
4
gravatar for Stephanhart
9.3 years ago by
Stephanhart100
Stephanhart100 wrote:

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 • 1.9k views
ADD COMMENTlink written 9.3 years ago by Stephanhart100

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

ADD REPLYlink written 9.3 years ago by Farhat2.9k
1
gravatar for Gareth Palidwor
9.3 years ago by
Gareth Palidwor1.6k
Ottawa
Gareth Palidwor1.6k wrote:

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...

ADD COMMENTlink written 9.3 years ago by Gareth Palidwor1.6k

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

ADD REPLYlink written 9.3 years ago by Stephanhart100

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.

ADD REPLYlink written 9.3 years ago by Gareth Palidwor1.6k
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