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[kenshire]

Dear everybody
I am a newbie of molecular. There are so many things new for me and I need your helps.
My work now is to digest one gene (I call this gene as A) into 3 UTR of flavivirus (japanese encephalitis virus, JEV). I have several questions, please help me!
1) What is conserverd region ? Can I digest gene A into conserved region of JEV? which is the best region for insertion gene into 3 UTR of JEV (or flavivirus)?
2) I read paper, some researcher did mutation and insert new restriction enzyme into 3 UTR (For example; XhoI and EcoRV with Tick borne encephalitis virus, NotI with West Nile virus). Can you tell me how to choose and make a mutation to insert restriction enzyme to 3 UTR of JEV?
３）In some paper. the author said 3 UTR of flavivirus have predicted secondary structure. Does those secondary structure affect to replicate of recombinant virus?
Thanks for reading and helping me!