If the siRNA target sequence is present in both transcript isoforms, you can assume that the siRNA will target both. If you are trying to target one isoform specifically, then you need to select a target site that is unique to that isoform (e.g. a exon-exon junction not present in another isoform).

In general, when you are designing siRNA, you should BLAST your siRNA sequence to make sure it does not target any other gene than your intended.

Hi Ritvik

try to blast your SiRNA sequence in UCSC (http://genome.ucsc.edu) and see in the genome browser of the blast results if it blast under all transcripts.

all the best

fred

I agree with Dr.Fred