Is there a download-able file on UCSC database that gives the information on gene locations (the chromosome ID for the gene, and the base positions) for a given organism ? I want to know the distance (in bp) between certain genes of interest for Xenopus genome. Is there any other way to achieve this in the genome browser ?
- Go to UCSC Genome Browser
- Select Tables
- Select clade and genome of interest (for example: vertebrate & X. tropicalis)
- Under group select "Genes and gene prediction tracks"
- Under track select whatever annotation you like (for example: RefSeq genes, Ensebml genes)
- Press "get ouput"
Wanted gene annotation provides: gene name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts. exonEnds.... and much more.
If you want to know the distance (in bp) between certain genes of interest you can use awk (I need your genes of interest and will provide an example how to compute them).