i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this sequence to determine cis regulating element
No, cDNAs are copies of spliced mRNAs, and typically contain a 5'-UTR (untranslated region), an open reading frame, or ORF, and a 3'-UTR. The cis-regulatory information might be revealed by sequencing the genomic DNA upstream of the gene(s). That is where one usually finds the promoter (although there are some rare exceptions, particularly for genes transcribed by RNA polymerase III).
The importance of sequencing
Sequence comparison is important because biologists tend to use prior knowledge to make inferences about the function of unknown entities.
Determing flanking sequences
You can use Genome Walking to isolate flanking regions of known sequences. It's a simple repetitive method. The amount of repeats will depend on how far you want to go upstream or downstream of your gene of interest.
One point is cDNA sequence encoding a specific protei, you will find differences in the coding sequence bewtween plants of different species and, within the same species, difference when you compare the genotypes for promoter analysis you must use the genomic DNA, at leasst 1 kb upstream the ATG, or more (may be there are introns)