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Since DNA is double stranded and each strand is complementary to the other, the codons on each strand will come out to be different after transcription(depending on the reading frame). Does this mean "each strand of DNA" codes for different set of proteins?

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Since DNA is not translated you should think about a different title for your question. –  Chris May 30 at 16:32

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My understanding is that the antisense DNA strand (3'-5') makes the (sense) mRNA hence protein coding DNA strand where as the sense DNA strand (5'-3') is the non-proteins coding DNA strand. Hence the sense DNA produces antisense non-coding RNA, which ultimately acts as a translational regulator (http://en.wikipedia.org/wiki/Antisense_strand). The only reason sense DNA strand is called the the sense strand is because it is complementary to the sense RNA or mRNA.

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There are a few confusions here, I will try to get them resolved without adding more:

First, a gene is always read in the 5' -> 3' direction, no matter on what strand of the double helix is is located. In the traditional way of writing down DNA the forward (or +) strand is written from left to right, the reverse (or -) strand from right to left. So even is you draw a gene map like the one below, the genes which run on the reverse strand.

enter image description here

For the transcription the reverse strand (it doesn't matter if it is the + or - strand) is not important. You can even have different genes on forward and reverse. In many cases the reverse strand doesn't code for any genes though.

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DNA is not always double stranded. Anyway, typically, you have islands of protein-coding genes in both strands in all six frames, i.e. a set of genes in the forward strand, then a set of genes in the reverse strand, then again a set of genes in the forward strand, etc.

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I might be misunderstanding you, but this doesn't sound like an accurate description at all. –  canadianer May 30 at 6:06
    
Care to mention some genome that doesn't conform to the description? –  5heikki May 30 at 6:17
    
I'm saying that protein-coding genes typically occur as islands on both strands. For example, you might have five protein-coding genes in the 5'-3' strand and then downstream ten protein-coding genes in the 3'-5' strand and then downstream twenty protein-coding genes in the 5'-3' strand again, and within these islands, the genes occur typically in all three strand-specific frames. –  5heikki May 30 at 6:55
    
Doesn't only the sense strand have its code forming the protein at the end while the antisense strand serves as a template? –  The Last Word May 30 at 6:56
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The sense strand is the strand that has the same sequence as the transcribed mRNA. Antisense strand is the template. Which strand is sense strand and which strand is antisense strand varies by genomic region. –  5heikki May 30 at 11:44

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