Hi
I apologise for the really basic question. I've probably said this a million times now but I'm returning to this field after a long time and I keep confusing myself by mis-remembering or half-remembering things from the past and it's not helping me. It would be easier coming to the field from fresh i think. Anyhow...
As i remember it, sequence databases always store the forward strand of a DNA chromsome in the 5' to 3' direction.
A gene is read in the 3' to 5' direction and so its complementary strand in the 5' to 3' direction is the same as the mRNA transcript. So i thought if a gene was on the reverse strand of a DNA molecule then the forward strand in the 5' to 3' direction gives the sequence on the corresponding mRNA (ignoring introns for simplicity).
However I'm just looking at a gene now in ensembl and this gene is described as being on the forward strand. If you look at the forward strand it contains the exact same sequence as the gene's mRNA. So to me then, if the mRNA runs on the forward strand in the 5' to 3' direction the actual gene is on the reverse strand is it not?
Is this a convention issue that I have mis-remembered? Is a gene classed as being on the forward strand if its mRNA sequence is 'on' the forward strand.
thanks for your help
Also trying to get this straight in my head. @Bio_X2Y:
you mention
Not trying to be obtuse here, but doesn't the RNAP make RNA which would be complementary to the template which is identical to (except U's instead of T's) the coding strand?
Wouldn't the cDNA then, which is complementary to the mRNA (and coding sequence), be identical to the template?
I thought that was exactly what i said in my question? I quote: Is a gene classed as being on the forward strand if its mRNA sequence is 'on' the forward strand.
I've just always called the coding strand the mRNA sequence. Like you say the template strand, which to me is the actual gene, is on the reverse strand. I should have been clearer wih my wording
forgot to say thank-you!
Fair enough, I guess the answer is "yes" then :) I partially used the answer to clarify things in my own head too. I can understand why you consider the template strand to be "actual" gene, but I would always have conceptualised it as the other way around (feels easier to me anyway). Things must get interesting in your view when you consider anti-sense transcription :)
Great answer, thanks for putting the time into crafting a detailed explanation!
@Bio_X2Y : Your first mention that the designation of forward and reverse strands is arbitrary. Are you sure about this ? I imagined that the forward strand was the one with the 5' end closest to centromere, no ?
@tony, I think you're correct - I ended up posting a follow up question here: Conventions For Designating Forward And Reverse Strands
Also trying to get this straight in my head. @Bio_X2Y:
you mention "the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand ... and builds the cDNA as it goes."
Not trying to be obtuse here, but doesn't the RNAP make RNA which would be complementary to the template which is identical to (except U's instead of T's) the coding strand?
"This means that the cDNA matches the coding sequence of the gene, not the template sequence."
Wouldn't the cDNA, which is complementary to the mRNA (and coding sequence), be identical to the template?
Maybe I am misunderstanding the answer...
Quote: "the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand ... and builds the cDNA as it goes." Not trying to be obtuse here, but doesn't the RNAP make RNA which would be complementary to the template? Quote: "This means that the cDNA matches the coding sequence of the gene, not the template sequence." I would have thought that the cDNA, which is complementary to the mRNA (and coding sequence), is identical to the template, and not the coding sequence. Am I thinking about this wrong?
Would you please elaborate where these numbers are coming from? And why exactly 50-50%? Thanks!
that statement is not correct, it is not exactly 50% - what it is trying to get at is that there is no preference for one strand vs another.
Amazing explanation! Probably the most concise answer to differentiate between forward/reverse (+/-), coding/template, sense/anti-sense strand conventions.