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In the transcription process, RNA is produced from the template strand of DNA (that is 3'-5') so the RNA molecule produced has the direction 5'-3'.
When working with genes in bioinformatics, there are many genes that we indicate with a (-) sign meaning they are from the reverse (coding strand).
I am really confused here. If RNA is only transcribed from the template strand, shouldn't all genes have the same direction?
I'd appreciate your input a lot!
There is a difference between the forward / reverse (also top / bottom) strand of DNA, and the template / coding strand during transcription. The designation of forward / reverse is rather arbitrary, one of the strands has to be forward (left (5') to right (3')), the other reverse, but it makes no practical difference which goes into which direction. DNA is double stranded and both strands go from 5' -> 3' in opposite directions. The template and coding strand during transcription are a specific feature of transcribed DNA sequences, and typically relate to features of the 5' -> 3' sequence of the DNA, such as promoters and coding sequences.
For example this short double stranded DNA sequence:
5' ATTTACGTATGTACAT 3'
3' TAAATGCATACATGTA 5'
There is an ATG start codon in 5' -> 3' direction on the bottom strand, and this could serve as the start codon of a coding strand after RNA transcription of a protein coding sequence. In this case, the template strand would be the top strand, the bottom strand is the coding strand. Transcription would happen on the top strand from right to left, so in reverse (-).
