On Wednesday, December 26, 2012 9:21:51 AM UTC-8, Mega wrote:
But there is a very big question:
The pre-czn-peptide is based on this
http://www.bio.davidson.edu/courses/molbio/restricted/ 02gfpseq/GFPseqfig2.GIF
Nucleotide 736-739 (in frame!) is TAA so the jellyfish polymerase will stop and fall of the mRNA. Then it goes on with ATG TCC ..... That is junk DNA? I would expect it to be an apo-protein or something alike. But jellyfish machinery doesn't support operons, so this wouldn't be expresssed.
No time to look it up (my wife says "no work on vacation!" and this is starting to look too much like work ;-), but make sure you're using the right genetic code - jellyfish may well use something nonstandard - and take any introns into account.
The GFP sequences we use every day have typically been recoded for E. coli, so they won't have any nonstandard codons or introns.
Patrik
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