Question: How to search for conserved Pseudogenes in nematodes?
gravatar for virg4l
5.1 years ago by
United States
virg4l0 wrote:

I'm looking into a list of pseudogenes that are being expressed in C. elegans.  I'm curious if these annotated pseudogenes are in any way functional, and I'd like to figure out if they're conserved in other Caenorhabditis species.

When I search BioMart and ParaSITE for orthologs of these pseudogenes, I only get a few protein coding genes from other species.  However, I can't figure out if these tools are even querying other organisms' pseudogenes.

I have lists of the annotated pseudogenes' gene IDs in C. elegans, C. japonica, C. briggsae, and C. brenneri.  Is there a better/different way to go about this search, or is the output from BioMart (no conservation) accurate and sufficient?

homology biomart pseudogenes • 1.1k views
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