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I am wondering whether majority of transcripts are transcribed from the 5'->3' strand? Because I encounter a lot of expressions like "anti-sense transcripts". Could anybody help clarify this? Thanks.

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Could you elaborate on your question? Anti-sense transcripts are also transcribed in the 5'->3' direction. What type of data are you looking at? –  GWW Apr 25 '12 at 4:28
    
Thanks, GWW. Maybe I was wrong, i thought the "anti-sense strand" as the 3'->5' strand. So you mean, for example, the DNA is "AAAAATTTTT", some transcript could be "AATTT" and some could be "TTTAA"? Could you please further clarify it? –  Cai Shaojiang Apr 25 '12 at 5:07
    
do you have questions after reading en.wikipedia.org/wiki/Sense_%28molecular_biology%29 ? –  Michael Kuhn Apr 25 '12 at 7:11
    
Thanks, @biocs. Clearer now. –  Cai Shaojiang Apr 25 '12 at 11:49

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up vote 9 down vote accepted

From my understanding sense and anti sense is contextual. If you are looking at a gene from 5'->3'(which is convention) that strand is the sense strand and the complement to the gene is the anti sense strand.

However further along the DNA there could be a gene on the 'original' anti sense strand, if you are discussing this new gene, there is a new context and it is now on the sense strand (oriented 5'->3'), and it's complement on the anti sense strand.

I hope that's clear.

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Thanks, @Ben. I found this on Wiki: "The only real biological information that is important for labeling strands is the location of the 5' phosphate group and the 3' hydroxyl group because these ends determine the direction of transcription and translation." May I have this conclusion: the cell is going to read the DNAs ONLY from 5' end to 3' end, regardless whether it is reading the 5'->3' strand or 3'->5' strand? And whichever strand is used as a template to produce the transcript, it is called "antisense" strand? Moreover, when aligning, result "+" means aligned to sense strand? –  Cai Shaojiang Apr 25 '12 at 12:13
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You are indeed correct, as the antisense strand is used as the template to make the mRNA translation of the DNA sense strand. –  Ben Apr 25 '12 at 14:21

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