Say for example the gene size is 2 kb. In general 300-500 bp length antisense gives best result in plants. So if we have to select 300-400 bases then how to find that which specific portion of this gene will be the best for it's silencing? Does any software/tool available for it? Or any other option?
You can try dsCheck (http://dscheck.rnai.jp/) in order to identify an efficient off-target minimised 300-500 bp region in a given sequence.
Any part of the coding region can be used, as antisense technology works on a phenomenon where its makes the coding part unavailable to enzyme for further action.
Thanks Rebijith and Waseem.
In dscheck, input sequences are checked against limited model sequence database. But it is useful. Thanks.
Sir,
You can do domain identification in NCBI and then see the off target effect of that domain and function of the domain to select the coding region of the gene.
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