how to define promoter region - (Nov/02/2007 )
I am searching for promoter region of a gene. I found the 5'-flanking region before the first exon in emsembl. But I am quite confused as how far should I go before the first exon. 1kb? 500 bp? or 100bp.
Say, If I can find a trancription-factor binding box within 1kb but not within 500 bp upstream from the first exon, can we say that the promoter of this gene contains the trancription-factor binding box ?
For my gene i went up to -5000bp. My transcription factor has binding sites even at -4000bp. So in ur case u can definetely say that the promoter contains the transcription factor binding box.
most genes have CpG islands in this region,
How do you check these CpG islands?
I have a flat definition 2kb above the ATG is my promoter, unless its invading into the previous gene. If it is invading in the previous gene and the gene as opposite orientation than that of my gene then I don't care but if it has the same orientation then I make sure that I avoid first 2 exons and introns.
The promoter size of each gene varies from gene to gene. You really need to dig up the original paper or subsequent ones that have characterised the promoter to get an idea on where the promoter lies for your gene. If the papers have not been done, you really can't make too many assumptions. If you can find a TATA box in your promoter I suppose that helps but characterisation of the promoter is what you really need.
Good luck, Rob
hello!I want to find the promoter of an unknown gene .How i can get it and how long i will choose?Thank you very much!
you should consider the fact it's a polymerase I II or III gene.
For pol III, 500bp are sufficent, as well for pol I.
for pol II genes at least 1000bp should be first try considering a mRNA coding gene.
Thank you ! Happy new year!