Is there a way to determine the conservation of any genomic regions?

[emanlee]

We identified a long intergenic non-coding RNA in chicken, for example, located:
exon1, chr1, 200000,201000,+
exon2, chr1, 203000,204000,+
Is there a way to determine conservation levels across species? Thanks!

[GenoMax]

You can find pre-computed pair-wise alignments and multiple alignments for the chicken genome here: http://hgdownload.soe.ucsc.edu/downloads.html#chicken

Resources at Ensembl: http://www.ensembl.org/info/genome/compara/index.html

[biocomputer]

On the UCSC Genome Browser, version WUGSC 2.1/galGal3 of the chicken genome has several conservation and comparative genomics tracks but this version is from 2006. The newer version ICGSC Gallus_gallus-4.0/galGal4 doesn't seem to have that many related tracks. I think these tracks are basically showing the data that GenoMax linked to but they're already in genome browser form.

[emanlee]

Thanks. For the well-studied organisms, there are multiple alignments. We can get phastcons and take them as conservation levels. For others, such as Alpaca genome, there are only pairwise alignments and no pre-computed phastcons, how to get conservation levels? Thanks again!
Can we indirectly get the phastcons? For example, what we want is to get the conservation levels of 'Alpaca, chr1, +, 2000,000--2000,006'.
First, we get the corresponding positions/regions on human genome, say 'Human, chr1, +, 2100,000--2100,006', according to the pairwise alignment Alpaca/Human. (http://hgdownload.soe.ucsc.edu/golde...icPac2/vsHg19/)
Then, we get the phastcons of 'Human, chr1, +, 2100,000--2100,006' according to human 100-way multiple alignment (http://hgdownload.soe.ucsc.edu/golde.../multiz100way/).