How To Design Primer Against Partial Gene Sequences

Question

[Raghav]

dear all , I have a partial gene sequences of interest, I want to design primer against my desire gene, for that I need complete gene sequences (start codon and ed codon) with flanking regions. problem I don't have genomic sequences of my organism. I have only transcriptome data of my organism.

your suggestions are most welcome.

[Devon Ryan]

What is the organism and for what reason do you need the genomic clone? Do you know the sequence for the UTRs and, if so, do your primers need to flank them or can the primers be contained within them?

Answer 1

[Damian Kao]

You are just going to have to RACE it. You can spend a lot of effort trying to find your transcript in a close related species or something and use their UTRs, but that's ultimately going to waste more time trying different primers sets. Do you have an idea of how long the transcript should be and how much of it you are missing? The only thing annoying about RACEing it would be primer walking if you are missing a bunch of it.