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What would be the best protocol to clone a gene about 5kb in size? The genome is not sequenced, but the gene itself very similar to orthologous genes of organisms with known sequences.

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Do you want to clone the gene ( genomic DNA) or a copy of the mRNA (cDNA)? (I imagine it's the latter.) –  Alan Boyd Mar 30 at 16:58
It's a hypothetical problem. If the gene is eukaryotic then the only possible course of action is to use mature mRNA (without introns) and reverse transcriptase to get cDNA, which can then be inserted into a vector. If the gene is of a prokaryotic organism, the only problem would be finding an adequate restriction enzyme? –  sdimitrije Mar 30 at 18:45
How do you know that the gene itself is orthologous? This means that the cDNA sequence is available. So there should be no issue with designing primer for amplifying the cDNA (just that you may not be able to find out other possible targets) –  WYSIWYG Mar 31 at 12:16
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