Hi Vaibhav, It is our convention for gene prediction tracks that the value in the "start" field is always the lowest coordinate and the value in the "end" field is always the highest coordinate, regardless of strand. Thus, you will actually add 5000 to the txEnd for genes on the negative strand.
Actually, the easiest way to get the UTRs, upstream regions, coding exons, etc is to use the table browser. You can obtain the coordinates of these features by choosing the output format "BED - browser extensible data" and then choosing the option you are interested in. If you would like the sequence instead, choose the output format "sequence" and configure as needed. For future reference, the fastest way to download an entire table from our site is to use our download site (http://hgdownload.cse.ucsc.edu/downloads.html). Just click on your organism of interest and then click the "Annotation database" link. This will take you to a folder with text files of all of our tables. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 12/14/10 3:54 AM, vaibhav jain wrote: > Respected sir/madam, > > I have taken the data of Refseq genes of Rat(organism) from the Table > browser and now I want to use txStrt coordinates to find the coordinates for > the region 5000 above the transcription start site. In case of chromosome > with + strand I am subtracting from the given txtStrt coordinate but in case > of chromosome with - strand, how should I go about it, should I subtract > 5000 or should I add 5000, actually I want to focus on the promoter region > usually present upstream from the transcription site. > > > Also how should I get the 5' UTR and 3'UTR using the coordinates of coding > region position and transcription position. > Thanks in advance > > With regards, > Vaibhav Jain > Research Scholar @IGIB > New Delhi, INDIA > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
