How to find promoter region between two closely placed genes - (Jul/12/2007 )
Hi,
Generally for promoter analysis we take ~2000bp upstream of the gene but problem in this case is my gene of interest is in 5'-3' and other gene is upstream 2000bp in 3'-5' direction. How to find out which promoter is of which gene??? If anyone of you have come across this situation than please guide me.
Thanks
-neesheel-
QUOTE (neesheel @ Jul 12 2007, 01:37 PM)
Hi,
Generally for promoter analysis we take ~2000bp upstream of the gene but problem in this case is my gene of interest is in 5'-3' and other gene is upstream 2000bp in 3'-5' direction. How to find out which promoter is of which gene??? If anyone of you have come across this situation than please guide me.
Thanks
Generally for promoter analysis we take ~2000bp upstream of the gene but problem in this case is my gene of interest is in 5'-3' and other gene is upstream 2000bp in 3'-5' direction. How to find out which promoter is of which gene??? If anyone of you have come across this situation than please guide me.
Thanks
hi, i have not come across this situation personally, but I would just assess the region in between the two genes and assume that there are overlapping elements that drive transcription for both but in opposite directions. they may be transcriptionally regulated the same but post-transcriptionally regulated very differently. you could also try to find consensus TATA boxes, CpG islands, and other tell tale markers of promoters and transcriptional start sites. in addition to the upstream region for each gene, i would also check for potential regulatory elements within the beginning introns of each gene.
-mateo-