EXon and ATG - where does it start (Oct/23/2007 )

question

when we say exon we mean that the atg position should be at the beginning of exon 1? or the exon 1 can be upstream of the ATG?

thanks

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If you’re talking about codifying sequences, yes, the start of the protein (ATG) should be at the beginning of the exon 1.

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Hmmm. But there are cases of introns in the 5'-UTR, so what do you call the exon upstream of the UTR intron? Exon zero? If it comes out of the nucleus, the sequence is an exon. That's an interesting nomenclature problem, and very relevant for my work (I often target splice-blocking Morpholinos).

Here's another - what do you do if there are alternative start codons in different exons? I suppose we just arbitrarily number the exon bearing the most 5' start site as exon 1. Two start codons in adjacent exons with a 5'-UTR intron upstream becomes even more interesting (yikes).

There is no subject so simple that it cannot be obfuscated with nomenclature.

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I am asking the question because I was reading an article when they show a map as: exon1-ATG-exon2...

so not sure what they mean

when we say exon we mean that the atg position should be at the beginning of exon 1? or the exon 1 can be upstream of the ATG?

thanks[/quote]

If you’re talking about codifying sequences, yes, the start of the protein (ATG) should be at the beginning of the exon 1.
[/quote]

Hmmm. But there are cases of introns in the 5'-UTR, so what do you call the exon upstream of the UTR intron? Exon zero? If it comes out of the nucleus, the sequence is an exon. That's an interesting nomenclature problem, and very relevant for my work (I often target splice-blocking Morpholinos).

Here's another - what do you do if there are alternative start codons in different exons? I suppose we just arbitrarily number the exon bearing the most 5' start site as exon 1. Two start codons in adjacent exons with a 5'-UTR intron upstream becomes even more interesting (yikes).

There is no subject so simple that it cannot be obfuscated with nomenclature.
[/quote]

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the atg of my gene ( the one am studying ) is in exon 2.

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ok so what we call exon it's not from ATG but include 5'UTR

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Here's how PPAR Gamma was broken down in my former research.

Exons 1-6 were in each of the splice variants - Exon 1 started with 8 nucleotides, then the ATG

The 5'UTR exons were called A1, A2, B, C, and D (I think due to when they were found), some of these exons had their own ATGs, so in some cases slightly different protein isoforms are created.

So, I think exon 1 usually 'starts' with ATG, or near the main ATG. I guess it depends on how it splices, if there are multiple splice variants, I think, people usually name them to try and sort out the splice variants - rather than keeping to a universal nomenclature rule.

You can check out the sequences at http://e-lab-book.com/?p=140
???

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