Question

I am trying to choose which of two primers is most appropriate to use in qPCR, based on if the primer spans an exon-exon junction or not, where the primer that does span an exon-exon junction is considered the most appropriate.

What exactly is an exon-exon junction?

Answer 1

An exon-exon junction is the boundary between two exons in a gene. A primer that spans an exon-exon junction is the most appropriate for qPCR.

Step-by-step explanation:

An exon-exon junction is a region where two exons (protein-coding sequences) are joined together in a eukaryotic gene. It is the boundary between two exons that are transcribed into RNA and spliced together to create the final messenger RNA (mRNA) molecule. In qPCR, a primer that spans an exon-exon junction is considered more appropriate because it ensures that the target mRNA sequence is amplified accurately.