Hello Rodney, I am unable to find the same results are you describe. The dbSNP entry rs7873546 has been annotated as intronic for several dbSNP releases, including the most current, 130.
Here is a link (below) to a saved Session of the data as am viewing it in hg18 (the result in hg19 is similar). The SNP is in the intron region, does not overlap with any exons, is color coded black, and is noted "Function: intron" by dbSNP. http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Jen&hgS_otherUserSessionName=rs7873546 Please examine and correct me if this is not the region you were also examining. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/12/10 10:47 AM, Rodney Perry, Ph.D. wrote: > I need some help with interpretation of location of SNP. The SNP is > rs7873546 at chr9:86,672,037 on BLD 36. It is in the gene, NTRK2. This > gene has 3 major isoforms and these can be seen on the browser. The > 2nd isoform on the browser is a shortened version of the full length. > The 3' UTR of this shortened isoform is located around 86,678,039. You > will notice there is an exon proximal to the 3'UTR, located around > 86,671,977. It is in almost all isoforms. Indeed, there is a SNP > located at this junction of the exon and intron, rs66564170, that is red > in color and is describeb as a frameshift SNP. Yet, the browser lists > rs7873546 as being in an intron even though the SNP is also red, > indicating a splice site SNP. Isn't it in an exon? > > > > This isoform is also shown on model maker of NCBI and is AF410901.1 or > NM001018065.2. It calls this an exon (#28). > > > > Can you please explain why this SNP is not listed as an exonic SNP on > UCSC or NCBI? > > > > Thanks for the assistance. > > > > R. Perry > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
