During Sanger Sequencing by forward primer, I realised that I have palindrome sequencing, my gene of interest is on the 5' side located in the promotor region while not targeted gene is on the 3' side located in the intron region. could you please give me some advice and information to make sure i don't have any problem?
As long as your primer doesn't anneal to the palindrome regions, you should have any problems. Not sure how big the region is that you want to sequence, but a quality Sanger read should get you 800-1000 bp. Just get good overlap if you need multiple reads to span the entire region.
Good luck!
Do you have the target regions in the middle of the Amplicons amplified in the PCR product?
Have you designed the primers based on region specific?
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