Im working on rice mutant. After mapping and sequencing the gene, I found that there is a 6 base deletion occurred in the gene. But when I tried to PCR amplify using cDNA, the amplicon size is same as that of wild type.
No, the deletion region is not the part of intron. In the cDNA sequencing result of Wild Type plant deletion region is present (and also in cDNA of mutant, which is actually a matter of concern), which means that it is a part of exon. In Gramene database also shows that it is a part of exon.
Yes, I have done the blast search at genome database and it shows there are no multiple copies of the gene. For additional information, there are two spliced variants of the gene and in both deletion region is present. So you mean I should TA clone my cDNA PCR products or DNA PCR products?
Yes, I have done TA cloning with genomic DNA PCR product and waiting for the sequencing results. With regard to phenotypic variation, yes the mutant shows different phenotype than wild type. qRT-PCR result shows significant decrease in the expression of gene compared to wild type. As there is a deletion occurred in the coding region (based on genomic DNA sequencing result), then there should be change in the amino acid sequence. But cDNA sequencing result show the presence of deletion region which means no change in the amino acid sequence (at this moment).
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