Hi Pitea, If you're just looking for one or two positions, the easiest way is to just look up that position in the genome browser and turn on one of the gene sets, e.g., UCSC genes and visually check to see if it's intergenic or intragenic.
If you have a whole series of positions, I suggest using the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and following these steps: 1.) Create a custom track that contains just intragenic regions (i.e. the region within genes) a.) Select the genome and the gene prediction track of interest (e.g., hg19 / UCSC Genes: knownGenes). b.) Output format: selected fields from primary an related tables - and then "get output" c.) Select (only) chrom, txStart and txEnd, then "get output", highlight and copy this data d.) Go back to the main table browser page and click the "add custom tracks"; paste in data and submit 2.) Create a custom track of the regions you are interested in a.) Back to table browser, and click "manage custom tracks" b.) Paste in your positions using the following (BED) format: browser position chr22:20100000-20100900 track name=YOUR_TRACK_NAME description="Chromosome coordinates list" visibility=2 chr22 20100000 20100100 chr22 20100011 20100200 chr22 20100215 20100400 ... Note: make sure to give it a name, other wise is may overwrite your other custom track 3.) intersect the two custom tracks created in 1 and 2 using the table browser a.) select your first custom track (1) as the table b.) click the "create" button next to intersect c.) select the table (custom track) you created in step 2, representing your positions of interest d.) select: All User Track records that have any overlap with UCSC Genes; submit and get output The output here represents the intragenic regions. To get intergenic regions, go back to the intersect screen and change your selection to "All User Track records that have *no overlap* with UCSC Genes". I hope that helps. Let us know if you have any additional questions: [email protected]. - Greg On 5/30/11 3:09 PM, Pitea Adriana wrote: > Hi everyone, Maybe you could help me. I am trying to find out in what type of > region a certain sequence is situated - whether it's intergenic or > intragenic. I am given the genomic coordinates. How could I use this to see > whether the sequence between the coordinates lies in an intergenic or > intragenic region? > Thank you. > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
