I want to get the promoter sequence of some genes. Should I get it from upstream of the gene or mRNA? How is gene defined in RSAT plants?
its very simple you just copy the desired gene sequence for which you need promoter. blast it. if you know the species already open genome of the species in NCBI find out at which region your gene is present go to that chromosome and copy the intron region before the start codon. you can get it in ncbi genome project for that particular species
The upstream of mRNA does not contain most of the functional promoter, including enhancers and other regulatory sequences for gene transcription. To capture most of the promoter function, you'll need to take region upstream of the transcription start site (TSS). There are computational tools that can help with finding where the TSS is. Leading introns also often contribute to promoter function/gene expression, so you want to include that as well. My current lab works on this regularly:
Article A Leading Intron of a Soybean elongation Factor 1A Gene Inte...
Article Characterization of 40 soybean (Glycine max) promoters, isol...
If the genomic sequences of this plant species are submitted in NCBI then do what Dr. TSRB Rao suggested. If not then, you either need to prepare Genome Walking Library for the isolation and sequence identification of the regulatory (promoter) region or need to do TAIL-PCR using genomic DNA as template. Second option costs less and is rapid.
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