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Humans have approximately 21000 genes but they probably make more proteins than that. This has been explained by many mechanisms like alternative RNA splicing.

My question is - If what we call as "introns" and "exons" vary so much, then how is the number of introns present in a genome determined ?

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What do you mean? What we call "introns" and "exons" is actually quite well defined. It is the concept of "genes" that causes problems. Counting introns is relatively straightforward (as long as you have an accurate count of genes). It is not a very useful exercise but it is not hard. –  terdon Sep 15 '13 at 16:33
    
@terdon I didn't mean to say that our concept of what we say as intron and exon vary. I meant that for each different protein from the same pre m-RNA , what sequences we call as introns and exons would vary. –  biogirl Sep 16 '13 at 15:30
    
Ah I see, well anything that can make it into a mature mRNA is an exon by definition. Anything that does not is an intron. So yes, the same stretch of genomic nucleotides can actually be both in different mRNAs. –  terdon Sep 16 '13 at 16:02
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up vote 2 down vote accepted

Yes, the individual number of exons/introns will vary in a transcript, but what you can do is just count all possible exons of a gene For example, lets say you have an alternative exon in these two isoforms. The XX's are exons

XX---XX---XX---XX

XX--------XX---XX

We would say this gene has 4 exons and 3 introns, even though one isoform only has 3 exons. Its the transcript that varies in number of exons, the gene remains constant.

Heres a slightly more complex example. Mutually exclusive exons

XX---XX--------XX

XX--------XX---XX

We would still say it has four exons. Pretend that every exon of every isoform is included and thats how you get the number of exons in gene. So for the above example, just pretend both mutually exclusive exons are included

XX---XX---XX---XX

According to this old paper there are 8.8 exons per gene (7.8 introns). Their gene number count is high because its older, but they estimate that there are 207,344 introns in the human genome.

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Introns is not always "exons - 1", you can have spliced UTRs with a leading intron for example, or a trailing one in the 3' UTR. –  terdon Sep 16 '13 at 15:36
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