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I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro boundaries). I've tried performing several database searches with the sequences, but each search produces a set of different unrelated hits. How would one go about using this info to confirm the exon shuffling hypothesis? Any tips are appreciated. Thanks!

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It's not clear what is 'several database searches with the sequences'. The most obvious solution is blasting your sequence so you can see which part can't be aligned and then blasting the rest. You can choose different implementations (megablast of blastn) and play with algorithm parameters because it may not work for you as-is. But it will work as-is if you'll blast exons separately. This way you can identify origin genes.

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