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
