I am making promoter-GFP fusions to study the _expression of some
arabidopsis genes. But I am not sure how to identify the promoter
region of an arabidopsis gene.
I think of three choices to get the promoter region that I want.
But each has its own disadvantage.
Here is the figure:
The intergenic sequence is between the stop codon of the
upstream gene and the start codon of the gene we are interested in.
Choice 1 (Exact intergenic sequence without 3=EDUTR of the upstream
gene. But it may be as short as ~150bp)
Choice 2 (Exact intergenic sequence. But it may be as short as ~150bp)
Choice 3 (Upstream up to about 1500 bp. But it may run into 3=EDUTR, or
even introns or exons (codin g sequence), or even worse the start
codon or 5=EDUTR of the upstream gene)
Does anybody have any suggestions? Has anybody systematically
tried extending the promoter region into the different lengths of
the 5' gene when the intergenic region is short (~150 bp)? And how
about the situation that the intergenic sequence is as long as ~6000
bp? What is the longest promoter region? Will it exceed 1500 bp?
Any experience or advice or suggetion will be highly appreciated.
My email address is <mailto:lilingisu at yahoo.com>lilingisu at yahoo.com