Hi Pini, "Function" is the function determined by dbSNP at NCBI against the RefSeq Genes. The dbSNP function is displayed on the dbSNP item details page and is also in the table.
On the dbSNP item details page, the "UCSC's predicted function relative to selected gene tracks" is the function for the dbSNP item predicted by UCSC with respect to a selected gene prediction track. If you click on the "Go to SNPs (129) track controls" link you can select the tracks for which you want to see UCSC's predicted function. The UCSC function predictions are currently generated on the fly and so, unfortunately, can't be downloaded. Our developers hope to generate tables containing this data at some point in the future but it is very uncertain if or when this will happen. I would like mention that we released the new dbSNP 130 track on hg18 yesterday in case you are interested. Please don't hesitate to contact the mail list if you require further assistance. Katrina Learned UCSC Genome Bioinformatics Group Pini Akiva wrote: > Hi, > > I see differences between the data in the browser and the data in the table > of the dbSNP129 track. > for example: > looking at the Human (hg18) assembly: > rs63750223 predicted functionality is annotated as: > > *UCSC's predicted function relative to selected gene tracks:* UCSC GenesHBB > (uc009yem.1)intron, splice-3 UCSC GenesHBB (uc009yem.1)frameshift UCSC > GenesHBB > (uc001mae.1)intron, splice-3 UCSC GenesHBB (uc001mae.1)frameshift > However the SNP129 table data under "function" is: > "coding-synon,cds-reference". > > What is the reason for the difference? > > Apparently the browser data is correct here.... > > Is there away to download the browser data rather than the table? > > Thanks, > Pini > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
