Non-Species Refseq Genes In Ucsc Genome Browser

Question

[Eric]

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

Answer 1

[Gjain]

Hi Eric,

There is some information available on UCSC genome browser on Non-Human RefSeq Genes. In short:

This track shows known protein-coding and non-protein-coding genes for organisms other than human, taken from the NCBI RNA reference sequences collection (RefSeq).

The RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept.

I hope this helps.

[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.

[Gjain]

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