Thank you, Alex. So far, it appears to me that to use VISTA browser I would need to define first a list of orthologs for every gene (i.e. via Homologene); then I would obtain their MSAs, but I would like to make a compare between genomic contexts, not just the orthologs themselves: maybe this would be achieved adding a large range upstream and downstream to the FASTAs obtained from Homologene, but would the resulting MSAs be good enough? How could I interpretate such results? I also downloaded the alignments, blasting the mouse entries against the human genome to define the location of interest (as they are listed by human chromosome number), and I have now a broad alignment but still I think there should be a better way to start.
I had a look to the VISTA-tracks, they point to a mirror of the UCSC, I visualized the maps but I was not able, until now, to find out how to download the tracks to load them in the Table browser.
LAMHDI lists just three mammal species, mouse included, and it also appears to be focused on disease.
I'd be looking at Ensembl and/or the UCSC database tables to do this, unless there's a reason not to (e.g. lack of species) ?
If I understood well, you mean the tables displayed in the genome browsers; I made a pre-screening with the Ensembl one (see also: http://www.biostars.org/post/show/49097/visualize-gene-descriptions-on-the-maps-of-ensembl-genome-browser/ ). The problems are the lack of species, as you said, and the lack of annotation directly evaluable from the map. I was able to have a general idea, but now I should deepen the analysis.