Good Afternoon Kevin: Can you give an example ID of a UCSC gene in the first 3,000,000 bases of chr19 ? I see the first UCSC gene uc008fvx.1 on chr19 at chr19:3065710-3197714
You can directly select the sequence for the genes from the table browser. Use the "output format" menu to select "sequence" with options in the next output screens to select different types of exons, introns, or both. --Hiram Clancy, Kevin wrote: > Dear Sirs > I would like to get a copy of all the known genes for a particular > chromosome, extract all the exons and then use this data for another > application. I decided to use the UCSC genes as they are a nice > conservative set of gene predictions for this project. > > So using the Table browser, I selected genome: Mouse, assembly: July > 2007, groups: Genes and Gene Prediction tracks, track: UCSC genes, > table: known genes, which appeared to have all the information I was > looking for. I then selected region, highlighted position and typed in > chr19. I selected to save the output to a file and I used the ftp site > to select the mouse chromosome sequences. The intention was to get a > copy of all UCSC genes that are annotated as being on Mouse chromosome > 19. > > When I examined the output from Table browser, I found a number of genes > near the start of the chromosome, however when I looked at this data for > the same build in the Genome Browser, no such genes were shown in the > UCSC genes track. So for example, there are 267 rows of genes from the > Table Browse that are not displayed in the Genome browser. Extracting a > number of these from the corresponding chromosome files, I find the > sequences are primarily Ns, so that does not seem correct. > > My questions are is this the best strategy to go about extracting this > information? Why are there apparently genes located in the first 3 > million bases of mouse chromosome 19 with Table Browser but not shown > with Genome Browser? Am I misunderstanding something in setting up the > query? > > Thanks > kevin > > Kevin Clancy, PhD > Senior Scientist, Informatic Sciences > Invitrogen Corp > Carlsbad, CA 92008 > Phone: (768) 268 8356 > Email: [email protected] _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
