Hello everyone,
How can i find the specific promoter region of a gene in my crop, as it is not identified yet? However is reported in Arabidopsis genome.
What could be the strategy?
Hi Hamza,
I’m guessing you don‘t have access to the genome sequence of your specific crop? If you do, you can simply BLAST the coding sequence of the gene from Arabidopsis into your crop genome sequence and find the best match.
But if you don’t have the crop genome sequence, then you can try pCR amplifying the promoter in your crop using several reverse primers designed to anneal to the coding sequence of the gene of interest, and several nonspecific forward primers. In this way, you may obtain parts of the promoter sequence.
if you want to be more certain or obtain longer promoter sequences, consider doing whole genome sequencing and assembly of your crop first.
Andika Gunadi Thank you so much dear, No i have access to genome of my crop, my crop is cucumber but as you know its not very developed yet so we don,t know the promoters yet in cucumber
You just download the genome sequence from the public database and take the target promoter sequences from Arabidopsis and BLAST them to the target genome. Alternatively you can use HMM technique by using the promoter sequences, it will give the all possible location of the target promoter in your target genome.
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