I have a gene which is having 10 transcript variants. However, only 4 transcripts are protein coding ORFs. I need to find out the level of expression of only one transcript out of 4 protein coding transcripts. I used NCBI Primer blast tool to design qPCR primers. however, designed primers not only detect expected transcript but also detect other transcripts variants. during primer designing with Primer BLAST i used these parameters. expected product length 70-200bp, from the Exon/intron selection I selected exon -exon junction.all the other parameters set as default.
I am happy if someone can help me to find out ONLY one transcript variant-specific primer for qPCR out of several other transcripts from the same gene.