I need some help trying to understand how annotations work on plasmids such as the one below. I do not understand the double layers structure, for example the light blue "ORF 2" has a annotation layer on top which is red for the GOI "firefly_Luciferase".
How can there be a ORF where a gene has already been inserted? Or does this mean that the gene can have a site-directed mutagenesis or be replaced by another GOI? Or is it just a double strand...
1 answer
The blue is simply an annotation (probably old or curated by hand) which is showing you the ORF position. The red annotation gives you the actual CDS product. They are depicted side by side because they refer to exactly the same stretch of DNA.
In short, its a bad/redundant annotation.
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