As long as you don't want to commercialize your final construct/product of that construct, I wouldn't bother much with patent protection of GFP. In most countries patent infringement in academic and non-for profit research is either tolerated or even explicitly made possible by the law. Even if you do plan to comemrcialize it eventually, the eGFP variant might expire by then so its kind of OK to use it. Most generic companies work on patented drugs years before the original patent expires, so that they can market the generic version the day patent actually expires.
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