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It's not clear from the question but for example:

AAAAAAA

TTTTTTT

The top strand would create a different protein than the bottom, and with the huge amount of nucleotide in a gene, I think it's very unlikely that the same region on both gene could create proteins that are similar to each other, even though they're alleles of the same gene. This would also affect codominance/incomplete dominance, since I'm assuming that only one of the strand would create a functional protein.

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  • $\begingroup$ Welcome to SE-Biology. However I'm not clear what you are asking. The use of 'can' in your question suggests that you think that this happens, in which case your assumption is wrong. The actual question suggests that you are asking a hypothetical question (in which case you should change 'can' to 'could'). However as you go on to say that in this hypothetical case you assume only one strand would create a functional protein, this seems less of a question and more thinking aloud. Please clarify. $\endgroup$ – David Oct 20 '16 at 12:31
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    $\begingroup$ Is this a duplicate of this? $\endgroup$ – user137 Oct 20 '16 at 13:42
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You are confusing the the forward and reverse strands of DNA as two alleles. They are not. Remember you have a double stranded DNA from each parent. Each of those two pieces of double stranded DNA represent alleles for a given locus.

For the example you gave, you can have different genes that overlap the same region of DNA. One is on one strand and a different gene is on the other. The DNA is read 5' to 3' so we think of one strand as forward and one strand as reverse.

See embedded pic for examples from this publication about different kinds of overlap and whether they are conserved across species.

enter image description here

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  • $\begingroup$ But the poster is asking about proteins, and not all those genes pictured are protein coding. $\endgroup$ – swbarnes2 Oct 20 '16 at 17:08
  • $\begingroup$ The figure shows both protein coding and non-protein coding. I addressed the misunderstanding of alleles, which seemed to be the reason for the confusion on how two "alleles" could produce a protein what was supposed to be very similar. This stemmed from a misunderstanding of coding/template strands for a given allele vs. two separate alleles. At least that was my interpretation. $\endgroup$ – akaDrHouse Oct 20 '16 at 17:55
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I think it's very unlikely that the same region on both gene could create proteins that are similar to each other, even though they're alleles of the same gene

I think your reasoning is faulty here. It's not that the two alleles are in the same chromosome and each in one strand. Each allele is in a different chromosome (one from each parent).

Overlapping or nested genes are a different topic altogether.

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  • $\begingroup$ So brown eye allele is at the 5' end of the maternal DNA, which means the paternal's green eye allele is at the other 5' end, so that they're at opposite ends? $\endgroup$ – L to the V Oct 20 '16 at 21:55
  • $\begingroup$ I made a diagram since perhaps it's the easiest way: s21.postimg.org/kap5b2gsn/Untitled.png $\endgroup$ – M.G. Oct 21 '16 at 8:18
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In general, protein-coding genes don't overlap, so the problem you've identified doesn't come up.

And no, complementary strands are not different alleles. If that were so, bacteria and gametes would have two alleles of every gene, because they each contain one double stranded copy of the genome.

You have two copies of each double-stranded chromosome, that is why you have two alleles for each gene.

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Usually not the whole gene overlaps, and it's not usually in-frame, this makes it a lot easier.

You also have some flexibility because of the redundant codons (20 AA for 64 codons), so you can more or less change every 3rd base to fit the "other" gene.

"Similar" could mean anything, possibly referring to two proteins that are not even 20% identical. At 20% identity you can still be sure that that enzyme is of the same class, catalyzing the same reaction. It might accept different substrates, but it could also still accept the same substrates.

Together, this means that on the non-coding strand of every gene you can put a gene coding for a protein that's more or less doing the same thing.

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