In most explanations, the sections of RNA removed during splicing are called introns, and the remaining segments that are stitched together are called exons. That is, introns and exons are defined in terms of the splicing process.

But I've come across several counter-examples. For instance:

From A simple answer for a splicing conundrum:

Exons without these elements [exonic splicing enhancers (ESEs)] are generally not recognized and tend to be excluded from the mature mRNA.

And from Wikipedia on alternative splicing:

Intron retention: A sequence may be spliced out as an intron or simply retained...

In what sense is an exon still an exon (and not an intron) if it tends to be excluded from the mRNA? In what sense is an intron an intron if it included in an alternatively spliced mRNA?

  • 2
    $\begingroup$ Try searching for “alternative splicing”. It’s not a question of nomenclature. $\endgroup$ – David May 11 '20 at 19:17

You must know that:

  • Introns are non-coding regions of an RNA transcript, or the DNA encoding it, that are eliminated by splicing before translation.

  • An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing.

Now, about the exceptions, alternative splicing: Here,

particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. There are numerous modes of alternative splicing observed, of which the most common is exon skipping. In this mode, a particular exon may be included in mRNAs under some conditions or in particular tissues, and omitted from the mRNA in others.

Apparently, this greatly increases the biodiversity of proteins (since there are differences in their amino acid sequence and, often, in their biological functions) which might explain why it is so common.

So in this case, it becomes easier to understand if you use 'coding' and non-coding' as the difference instead of 'spliced' and 'not-spliced'.

EDIT- The coding region of a gene:

In DNA, the coding region is flanked by the promoter sequence on the 5' end of the template strand and the termination sequence on the 3' end. Although this term is also sometimes used interchangeably with exon, it is not the exact same thing: the exon is composed of the coding region as well as the 3' and 5' untranslated regions of the RNA, and so therefore, an exon would be partially made up of coding regions. The 3' and 5' untranslated regions of the RNA, which do not code for protein, are termed non-coding regions.

I had previously forgotten about the UTR's, so I have included that. Now, if there is a definite sequence where coding regions are found, it points out to the fact that coding regions must be intrinsic. Another point in favour:

The evidence suggests that there is a general interdependence between base composition patterns and coding region availability.The coding region is thought to contain a higher GC-content than non-coding regions. There is further research that discovered that the longer the coding strand, the higher the GC-content. Short coding strands are comparatively still GC-poor, similar to the low GC-content of the base composition translational stop codons like TAG, TAA, and TGA.

  • $\begingroup$ Thanks. I am still not 100% clear. Given your comment, I think it boils down to this: Is whether a region is coding or non-coding, a property that exists regardless of whether it is included or not in the mRNA? In other words: Are regions inherently coding or non-coding, and the splicing process selects for that? Or, does the result of the splicing process itself determine whether a region is encoding or non-encoding? If it is the former, then what exactly is it that gives a region its coding property? If it is the latter then the questions I asked above remain. $\endgroup$ – zenna May 12 '20 at 17:40
  • $\begingroup$ A biologist (but not geneticist) friend suggested that: "An exon is any region that is included in at least one of the alternative splices, and an intron is a region that is included in none of them." Regarding intron retention, he hadn't heard of it, but on further inspection said: "It's looks looks like an aberrant case and shouldn't detract from the main definition" Would you agree with this? $\endgroup$ – zenna May 12 '20 at 17:41
  • $\begingroup$ RNA splicing ultimately determines what part of the sequence becomes translated and expressed. So, exons (since they code) should, usually, be included in mRNA. Your friend's statement seems alright to me, though I still suggest exons to be defined on the basis of coding regions. $\endgroup$ – Bipasha May 13 '20 at 2:43

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