Exome sequencing can identify causal variants of Mendelian inheritance of desecrate characters (e.g. color).
Hi Charles,
I would think it would be important to have very clean, single bands in the electrophoresis of the PCR product, if you are amplifying the putative gene. Careful design of locus-specific primers should help this, and this will give some level of validation that you are not sequencing a degenerate copy of the locus. Also, if you are Sanger sequencing, you would likely want to look for clean base calls across the length of the locus, or at least a minimum of heterozygosity, again to make sure you are sequencing a single locus.
In the end, if you want to determine whether the putative gene is expressed, likely sequencing of the transcriptome would be a good test.
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