I need to known a DNA sequence for a gene in the plant(V.faba) in order to design primer for PCR for DNA methylation purpose analysis.However I only had the mRNA seq and AA seq for the gene in this plant. What should I do
You may need to do BLAST your mRNA sequence to the public database in NCBI against DNA or genome to detect the DNA sequence expressed that mRNA. The best hits (from DNA of V.faba or other closely related plants) in which should have long size, may contain your mRNA sequence and introns as well as the promoter sequence. With DNA sequence you can predict CpG site and make the strategy in PCR as well as primer design and sequencing for assessing the methylation pattern.
I have blast it on NCBi and i do get lots of hit from closely related seq but they are all mRNA. Also because V.faba is not fully sequence genome i dont hace the DNA sew for that gene