I have obtained the source sequence of p5cs from NCBI. The title of the genes varies with partial cd, complete cd, mRNA and sometimes only gene. What does this signifies? In case of expression study, do we have to design primer based on cd seq or is it fine if we use the whole gene seq?
In case of expression studies you should design primers against CDS or mRNA or partial mRNA seq. On the other hand avoid using genomic regions which includes introns. In case that you have more than one sequences coding for the same enzyme you should aligned all the mRNAs and design primer specific primers for the gene of interest!!!
if I have more than one sequences coding for the same enzyme then HOW should I align all the mRNAs and design specific primers...
Sometimes one amino acid is coded by different bases in genomic sequences, so download all the sequences and translate them individually using expacy translate tool.
there so many ways to design primer for amplification of any gene concerning expression but the bust one is to design primer using cDNA because when you will convert mRNA to cDNA this will contain only exon which are coding region instead of introns. In case you will design primers form Genomic DNA this will be intron as well in amplified product and it will be a problem in expression...
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