Whole-exon multiple sequence alignment

[thejustpark]

Hello guys,

Always appreciate your active contributions to this website.
I wish I get to a place where I can help others through this web site, too.

The dataset I am interested in is a multiple sequence alignments of exons for some number of mammalians.
The closest thing I can get from UCSC web site is alignments of CDS sequences over 29 mammalians (in alignment folder on Downloads page of the site).
But what I want to have is the alignments that not only contain CDS sequences, but they also should contain UTRs, both 5-end and 3-end.

I checked on the other directory on the same path (maf folder), but they maintain the whole-genome sequence alignment with only a small subset of species, and the involved species are changing by region. So this is not the data set I am looking for.

Do you know where I can obtain this kind of data set in UCSC Genome browser, and if there's not, do you know why?
I mean, in the alignment folder, they maintain a nicely composed alignments of CDS sequences over 29 mammalians (it is 29 mammalians all the time, unlike the case of maf folder). If they can do this, I cannot see any reason there shouldn't be exon alignments for the species.

[Richard Finney]

Check if xenoRefGene is what you're after.. It's called Other RefSeq under the Group "Genes and Gene Prediction Tracks". This other other species genes aligned to the selected species.

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=289824627&c=chr12&g=xenoRefGene

schema: http://genome.ucsc.edu/cgi-bin/hgTab...e+table+schema

duped at: https://cgwb.nci.nih.gov/cgi-bin/hgT...e+table+schema

[thejustpark]

Maybe I was not clear.
I want multiple sequence alignments of EXONS including human, not those only of CDS sequences.
In other words, I want to have 5' and 3' UTR alignments with the CDS sequences for the same species set (including human).

Anyway, thank you for the reply.