Hi Niamh, You can identify the exon/intron boundaries of the AK015100 mouse gene using the Table Browser. First, obtain the position of the gene in the genome browser and then use the position to pull up the appropriate record in the Table Browser. The following instructions will help you do this:
Open the genome browser to the mouse assembly that you are working with. Enter "AK015100" in the position/search field and click "jump." On the results page, click on the link to your gene (under the "UCSC Genes" header). The gene, AK015100, should now span the length of the browser window. Click "Tables" in the blue bar at the top of the page. The Table Browser will open to the assembly & position that were open in the genome browser. Set track to "UCSC Genes" and table to "knownGene." Select the "position" radio button. Set output format to "all fields from selected table" & click "get output." The result is the record for your gene. The exon/intron boundaries can be deduced from the exonStarts and exonEnds fields. If there are many fields in the record that you don't need, you can hit the back button and change the output format to "selected fields from primary and related tables." Click "get output" and select the fields you wish to see in your results, be sure to include exonStarts and exonEnds since these fields contain the data you asked about. Please don't hesitate to contact the mail list again if you require further assistance. Katrina Learned UCSC Genome Bioinformatics Group Niamh Harraghy wrote: > Hi, > > I would like to identify the exon/intron boundaries in the mouse gene > AK015100. I have clicked on Table Schema but this gives data for a > gene on chr 1 (my gene is on chr 13). > > Thanks for your help! > > Niamh > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
