I am designing primers for gen in nuclear protein-coding region of a toxic protein rhodostomin in the Calloselasma rhodostoma snake. However, there is no whole genome or full-length record on NCBI, only a cDNA sequence. How can I design primers for my DNA sequence based on the cDNA sequence?
Have you tried a BLAST search to see if there are homologs in related species?
Download those, do an alignment, and see if there are conserved regions that flank the cDNA to pick some primers. Design a few pairs, make sure the 3' end of the primers have several bases of perfect matches and see if they work.
Or a really old method is to "chromosome walk" if you have a library of cloned gDNA (like BACs). Start with primers from the cDNA & sequence your way out in both directions on the BAC.
Good luck!
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