Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or alternative splicing.
Answer
I don't have any literature to back this up but I doubt that it occurs (at least frequently).
For example, imagine a simple three exon gene. Upon splicing exon 1 to exon 3, exon 2 would be excised as part of the intron lariat and subsequently degraded. So in order for exon 2 to be spliced to exon three you would need to either have splicing between exon 3 and exon 2 in the lariat or another copy of the pre-mRNA. This is typically called trans-splicing but it only occurs in specialized systems such as spliced-leader sequences in C. elegans.
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