I am trying to identify splice variants in a specific gene. Am I able to design primers to the UTR regions in order to capture the internal variation ignoring splice variation at the UTR regions? How else might I be able to identify variants and isolate them?
The simplest way you can identify them is by designing primers on each of the exon-exon junction to check if any of them are missing. For an example, if you design a primer for 6-7 exon-exon junction and you do not find amplification, but when you use your 7-8 exon-exon junction primers and find amplification, you can assume there might be a splice variant at exon 6. However, you have to incorporate other techniques to confirm your finding.
In my own lab we have used a combination of exon to exon PCR: not only with known adjacent junctional sequences but also across multiple exons - together with RACE to identify 5' ends using alternate promoters. Beware that asking PCR to span very large sequences (>2kb) will be less efficient than shorter PCR, though.
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