For 3` terminal region of potyvirus we can use poly A tail but for 5`the terminal internal sequence is required. Before sequencing we can`t know about the 5` terminal, so my question is, how can we design primer for 5` RACE?
Wan-Chin Yeap
An adapter (provided by RACE kit) is usually added to the 5' region of the transcript and the kit will provide the universal primer, complement to the 5' adapter for PCR. However, you will still need the gene specific primer for 5' RACE for your case is potyvirus gene. As long as you have any known sequence from your target gene, then you can design the gene specific primer according to that and use for 5' and 3' RACE.
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