It's my first time here and I really thank you all for the usefull content you submit. I read a couple of questions about forward and reverse convention and it really came as a grate relief to see that I wasn't the only person who was wondering about such a basic but sometimes confusing thing.
I'm investigating a gene which is in the reverse strand so, according to the discussions I've read, the forward strand given by the databases is the remplate or antisense strand. Am I right?
Then, the poly(A) signal that usually is 5'-AAUAAA-3' in mRNA appears as its complementary sequence in the forward strand: 5'-TTTATT-3'
forward strand/template strand (antisense): 5'-TTTATT-3'
reverse strand/coding strand (sense): 3'-AAATAA-5'
What happens is that there are a 5'-TTTATT-3' and a 5'-AAATAA-3' sequences in the 3'UTR of this gene and I wasn't sure about which one could be the putative poly(A) signal.
Do you know if there is a program to predict the presence of regulatory sequences such as promoters, splicing sites, polyadenilation sites, etc. ?
Thank you very much in advanced!
I cite Bio_X2Y's answer, which was very helpful:
DNA is double-stranded. By convention, for a reference chromosome, one whole strand is designated the "forward strand" and the other the "reverse strand". This designation is arbitrary. Sometimes the terms "plus strand" and "minus strand" are used instead.
*Visually (I'm not talking about the transcription machinery yet), you would typically read the sequence of a strand in the 5-3 direction. For the forward strand, this means reading left-to-right, and for the reverse strand it means right-to-left.
*A gene can live on a DNA strand in one of two orientations. The gene is said to have a coding strand (also known as its sense strand), and a template strand (also known as its antisense strand). For 50% of genes, its coding strand will correspond to the chromosome's forward strand, and for the other 50% it will correspond to the reverse strand.
The cDNA (and protein) sequence of a gene corresponds to the DNA sequence as read (again, visually) from the gene's coding strand. So the cDNA sequence always corresponds to the 5-3 coding sequence of a gene.
Now, the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand (e.g. left-to-right for a forward strand gene). It reads the bases from the template strand (so it is reading in the 3-5 direction from the point-of-view of the template strand), and builds the cDNA as it goes. This means that the cDNA matches the coding sequence of the gene, not the template sequence. (This diagram from Wikipedia illustrates).
Annotations such as Ensembl and UCSC are concerned with the coding sequences of genes, so when they say a gene is on the forward strand, it means the gene's coding sequence is on the forward strand. To follow through again, that means that during transcription of this forward-strand gene, the gene's template sequence is read from the reverse strand, producing a cDNA that matches the sequence on the forward strand.