Hi Renee, If you only have a few regions you can just input them manually into the browser position/search box. For a long list of coordinates, you can upload the coordinates as a BED format custom track. This will allow you to upload all the coordinates at once, and will also make navigation between the different regions easier by having them all listed and clickable within the custom track.
For more information on how to create a BED file, please see: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED. For more general background on custom tracks, please see this help doc: http://genome.ucsc.edu/goldenPath/help/customTrack.html To determine if the coordinates are within an intron/exon/coding region, you can turn on any of the gene prediction tracks, such as UCSC Genes, RefSeg Genes, Ensembl Genes, etc. to see where your regions map relative to the entries in these tracks. You can turn on any of these gene prediction tracks by scrolling down to "Gene and Gene Prediction Tracks" and selecting a display from the drop down list for the track you would like to use. For miRNAs, these tracks may be of interest you: sno/miRNA (also under "Genes and Gene Prediction Tracks") TS miRNA sites (under "Regulation") I hope this helps. Please contact us again at [email protected] if you have any further questions. Best, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group [email protected] wrote: > L.S, > > is it possible to upload a list with coordinates of 1-10 bp long in > UCSC and to obtain for each given coordinate: > > 1.if a gene/miRNA is located here? > 2.If this given coordinate is in an intron/exon? > 2.If this given coordinate is in the coding sequence? > > regards, > > Renee Beekman > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
