Downloadable File With Gene Locations

Question

[anuragm]

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 ?

[Ido Tamir]

start here: https://main.g2.bx.psu.edu/ import data from ucsc as GTF, filter for your gene names, do the statistics (?)

[Neilfws]

The Downloads link is right there on the main UCSC page, left-hand column.

Answer 1

[PoGibas]

1. Go to UCSC Genome Browser
2. Select Tables
3. Select clade and genome of interest (for example: vertebrate & X. tropicalis)
4. Under group select "Genes and gene prediction tracks"
5. Under track select whatever annotation you like (for example: RefSeq genes, Ensebml genes)
6. 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).

[anuragm]

Thanks a lot!

lets say I want to know the distance in bp between NM_001078816 and NM_001016199 on GL172637 (the first two genes in the RefSeq track for the Xenopus genome). I would be grateful if you show me how to go about it in awk. Thanks again!

[jon.klonowski]

but this is transcripts, how can you get genes? I.E. one gene one interval