Hello Francisco, The data for both strands is displayed by default. However, when zoomed in, the genomic's three frame AA translation (if this track option is displayed) and the actual AA translation of the coding region (protein, if displayed) will always be with respect to the transcription strand. Click on the little "-->" or "<--" at the very top left corner of the Assembly browser to flip between strand. Direction of transcription is also indicated by arrows for each transcript.
Some help about this and associated topics: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 http://genome.ucsc.edu/FAQ/FAQtracks#tracks17 http://genome.ucsc.edu/FAQ/FAQtracks#tracks15 http://genome.ucsc.edu/FAQ/FAQdownloads#download20 http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Good test cases are easy to create. Pick out a representative gene from the UCSC Genes or RefSeq Genes track (or perhaps two, one for each strand). Make sure the genes are as complete as possible (many exons, 5' + 3' UTR, defined coding region). Then open the same genes in the browser and zoom in. Follow along with the file data versus the browser for the two genes (turn on codon display in the track controls). Now try a few genbank alignments (pick EST/mRna, perhaps each with a few exons, maybe one for each strand). Just these two simple exercises can help significantly when first trying to understand the data display. It can also help later if/when you begin to build up your own custom track data. We hope this helps, Jennifer Jackson UCSC Genome Bioinformatics Group Francisco J. Sanchez-Rivera wrote: > Hi: > > My name is Francisco, a graduate student from MIT. > > I was wondering... > > If I have a gene that is transcribed from the minus strand (i.e. in > the UCSC database, it appears w/ arrows to the left (<---) indicating > direction of transcription)... does the UCSC database shows the > sequence of the 5' --> 3' plus strand or does it show the actual 5'-- > >3' minus strand that encodes my gene of interest? > > I would really appreciate it if anyone could answer me this question. > > Thanks, > > Francisco > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
