Hi all,
I searched my genes against pseudogene database (http://www.pseudogene.org/) and found some of them are considered as pseudogenes. However, according the the annotation database, most of these genes have full length cDNA support and can be translated into relatively long proteins. I was wondering is there a way to determine these genes are real pseudogenes.
Chen
It is possible that pseudogenes are transcribed. Usually a functional protein is not formed (otherwise it wouldn't be classified as a pseudogene). I found an interesting article (please see the attachment). I also recommend the Wikipedia entry on pseudogenes, it is written very well and contains a lot of valuable information.
Regards, Christian
Article Transcribed processed pseudogenes in the human genome: An in...
Absence of function is hard thing to prove. Basically absence of proof is not proof of absence.
Having said that there are couple of accepted features that mark a gene as a pseudogene. Shorter/interrupted ORF, lack of introns, similarity to functional gene, lack of negative evolutionary pressure (drifting). None of these is of course infallible and on top of that it is thought pseudogenes can regain functional state. This is also described in the Wikipedia page, which I agree is very well written.
If you have good evidence your genes may retain their function I would suggest to test it further experimentally. For example- is there mass spec evidence for protein level expression (you can search PIR for example: http://research.bioinformatics.udel.edu/peptidematch/index.jsp)? Is there selection pressure in the genomic region (this can be found in ensembl or UCSC browser tracks)? Can you perhaps express the protein you predict in some expression system? Can you delete the gene and establish a phenotype that you can reliably track to the deletion?
- Badges
- Science topic
- Similar topics
- Philosophy
- Moral Philosophy
- Free Will