Where Can I Find The Genomic Co-Ordinates Of Known Pathogenic Loci In Both Mouse (Mm9) And Human (Hg19)

Question

[biorepine]

I would like to download the genomic co-ordinates of mouse and human pathogenic loci in BED format. Any suggestions ?

Ex: Beckwith-Wiedemann syndrome locus, INK4b/ARF/INK4alpha locus and X inactivation locus.

Thanx in advance!

Answer 1

[Sean Davis]

You might check OMIM for human.

Answer 2

[abhay.krishna]

As suggested by Sean Davis, I think OMIM is the source for such loci, for other animals it is OMIA.

For automating it In UCSC there is a track of OMIM loci, so you could be able to get BED genomic coordinates using table browser

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=omimGene2

I am unaware of any available OMIA track.

oops.....Sorry .....OMIA does not collate mouse loci

For Mouse I think Jacksons Mouse genome informatics tracks on mm9

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=317470363&g=jaxPhenotype

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=317470363&g=jaxQtl

[biorepine]

I flagged your both responses as answers. However many known loci are missing in the referred databases (OMIM & UCSC) especially the given examples in my question.

[Sean Davis]

It is quite possible that no single database contains all the information you need. Note that the loci in OMIM are phenotypic, by-and-large. You mention INK4a/INK4b as an example--these are genomic loci and can be located using "normal" genomic tools like Entrez Gene.