Hello Nipun, For Human, hg18 has the most data. The track UCSC Genes contains the set of high-quality transcript variants for gene bounds. Used with the track Alt Events, splice variation can be characterized/filtered.
If you are interested in an expanded set of potential variation, then exploring other tracks in the Gene and Gene Prediction group may be helpful (ex: TransMap has cross-species alignments). Tracks in the mRNA and EST Tracks group, in particular the track SIB Alt-Splicing (summarizes splicing for RefSeq and GenBank RNAs and ESTs), would also likely be interesting to you. There may be other tracks that would be useful if quantitative information for splice sites is desired (ex: Expression -> Caltech RNA-seq). The track descriptions will provide the details for each analysis (click on track name in the Assembly browser). Download the data using the Table browser or ftp from the Downloads server. http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 Hopefully this helps to get your analysis started, Jennifer On 3/24/10 4:36 PM, nipun kakkar wrote: > Hi > > I wanted to gather all spice junction variants for an analysis i am doing. > Is there a file somewhere on UCSC i can use for the same. > > Thanks, > Nipun > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
