Hi,
I am blat-ing sequences using the UCSC Genome Browser to see if the neighboring genes of certain sequences are conserved in different species. There is one track that confuses me: Non-human Refseq Genes (or non-chimp refseq genes, etc).
If I am looking at chimp, for example: I blat the sequence to see if it has the same neighbors as in human; I find that the only track listing the expected neighboring gene is the non-chimp refseq gene track.
What am I to make of this track? Do these genes exist in the species of interest? Are they expressed? Can I say, in the above example, that the neighbor gene is conserved in human and chimp?
I've found nothing in the UCSC FAQ section. I'm grateful for any information.
Thanks, eric
@Gjain I appreciate the response, but it does not help. I'm still unsure whether I can say, because a non-species-of-interest refseq gene has been (partially) aligned to that region, that the neighboring gene region in the species-of-interest is conserved.
I agree ... if you want to see that ... Mizbee is good. MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. http://www.cs.utah.edu/~miriah/mizbee/Overview.html