I have designed a pair of primers for my target gene to determine its expression by Syber-green kit. Both primers are spanning two across exons. However, when I BLAST primer pair in NCBI, one primer showed 100% complementary with the long non-coding transcript variant 3 of my target gene (other primer has 80% complimentary sequence). I tried to design different primer pairs, but every time was getting either one or both primers showing 100% complementary with the long non-coding transcript variant.
As I am using syber-green for qPCR and only one primer is having 100% complementarity, my question is, would it effect on the qPCR results of target gene expression?
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