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Many proteins are assembled from multiple exons with the introns between adjacent exons being spliced out. But are there any proteins that have unrelated to them exons in the middle of their sequence?

I think the equivalent question would be: are there any protein-coding genes (in any species) that are broken in two or more parts by another protein-coding gene(s)?

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I think that you are talking about trans-splicing. This does indeed happen. It is fairly common in protist organisms, though in humans it is quite rare. For more information about how this process works, including mechanisms in vertebrate organisms, see this paper.

Here is one model from that last paper for how it works: enter image description here

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  • $\begingroup$ Yes, this is what I was thinking about. Thank you! $\endgroup$
    – guzey
    Commented May 22, 2020 at 16:42

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