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Why am I getting results only for the wild type, not for the expected mTn insertional mutant size when I am performing PCR using gene specific primers 500 bp upstream and downstream of the gene?

The yeast mTn strains are in a diploid parental strain. What may be occurring is that your PCR reaction is successful for the allele that does not contain the mTn insertion. The other PCR product is expected to be very large (the insertion cassette is ~6kb) and because of that the PCR reaction may not be working for this allele.

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