Genes From Ucsc Genome Browser

Question

[anuragm]

Is there a way to visualize individual genes in the ucsc genome browser and its conservation value across multiple taxa ? For eg, if I want to visualise the region corresponding to RAG-1 gene of Xenopus tropicalis in the Xenopus conservation alignment.

Answer 1

[Giovanni M Dall'Olio]

To visualize the conservation:

1. go to the genome browser
2. select Vertebrates->X. tropicalis as species
3. search for the RAG1 gene
4. make sure that the Comparative Genomics -> Conservation track is set to full

To get the scores:

1. go to the "Tables" page of the Genome Browser
2. select the track Comparative Genomics->Conservation
3. make sure that you are getting only the position correspondant to RAG1, and not the whole genome
4. select the "data points" output format, and click on "get output"