How can we correctly recognize the promoter region for a gene, specially for those genomes which are not well established and annotated?
I have read on many places that its almost 2000 bp before the start codon.
But if i got 900 bp or 1100 bp, will it work for me or not? Thanks to all in advance
Sure about 2 kb pre codon should include most bindung sites for transcription control factors. Thus, I would try to get these 2 kb in your cloning experiments.
While 2kb is probably fine in most cases, please realize that this is only a guess. If it is important that your fragment carries the entire promoter region, then you need to experimentally confirm that it functions as expected, either in an in vitro transcription system or upon transformation.
The only way to know is to test the region empirically. This is going to vary greatly by the organism type. If the genome is sequenced and even partially annotated, you can examine the promotors of other genes to get a better estimate.
Good luck!
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