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Help: how to identify the promoter region of an arabidopsis gene.

Nobody nobody at hgmp.mrc.ac.uk
Fri Dec 20 15:14:21 EST 2002


Hi,
     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:
5=EDUTR-StartCodon =F1UpstreamGene(introns,exons)-StopCodon-3=EDUTR-
SequenceBetweenTwoGenes-
5=EDUTR-StartCodon-GeneOfInterest(introns,exons)-StopCodon-3=EDUTR-
      The intergenic sequence is between the stop codon of the 
upstream gene and the start codon of  the gene we are interested in.
Promoter region:
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
     Thanks.
Li Ling



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