Hi Manuel, You example gene SOX10 does have several alternatively spliced transcripts in many of the tracks from the browser's "Gene and Gene Prediction Tracks" grouping. Comparing between these results in the main Browser display window demonstrates the variability between multiple human and non-human versions of the gene. For any particular gene, the transcript with the most 5' may be different from the transcript with the most 3' UTR.
For SOX10 , the longest transcript reported is RefSeq NM_006941. However, we chose the transcript RefSeq NM_006941 as our "representative" transcript in the UCSC Genes and CCDS Gene tracks. (Please see these track's descriptions for details about how the data was compiled by clicking the track names in the main browser display page). To obtain a file with a set of non-redundant transcripts, based on our "representative" transcripts, use the knownCanonical table as a base and add on additional data points from linked tables as desired. Using SOX10 as an example, the following steps give a single line of data for the gene in the most recent human database included in the UCSC Genes track. Table browser settings: clade=mammal genome=human assembly=Mar.2006 group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownCanonical region: genome identifiers: paste in SOX10 output format: selected fields from primary and related tables press "get output" select two related tables: kgAlias and knownGene once they are loaded, choose the fields you want to include in the output file Suggested fields (but you can limit/add as needed): all of knownCanonical kgAlias.alias (this is where the original identifier SOX10 will be) all of knownGene press "get output" The fields cannot be re-ordered within the table browser, but you will get one row per identifier. Try this and let us know if you need additional help, Jennifer Jackson UCSC Genome Bioinformatics Group Manuel Rodrigues wrote: > Hi, > > I'm trying to make a custom CGH array with 2500 genes. > I've tried in Table Browser with SOX10 for example and obtain a list of 3 > alternatively spliced transcripts. > > How can I obtain a list of unique genes coordinates for my design starting > where the first transcript starts and ending where the last ends? > > I don't understand.......... > > Manuel RODRIGUES > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
