Could you give more detail on what you mean by "run either way?" For instance, in my example above, why does C>G nucleotide change match for both the gDNA and cDNA position? Whereas in another example, say CEP290:c.74 C>T and chr12:g.88535011G>A, the cDNA location has a C>T change yet the gDNA location has a G>A change.
Is it possible for a single DNA nucleotide to match its cDNA complement, and not invert?
This is likely a simple biology question but I am having trouble understanding. I am reading about a single nucleotide mutation, with the mutation in the cDNA described as: RDH12:c.505C>G.
However, the gDNA change is similarly described as chr14:g.68193754C>G.
I checked the reference sequence, and at this position the reference nucleotide is indeed C.
How is it possible for the cDNA at that position to also have C? Shouldn't it be the reverse complement?
1 answer
Well, for example: CEP290:c.74 C>T and chr12:g.88535011G>A both describe the same nucleotide change, but why does the g.DNA show G>A and the c.DNA C>T? Yet with RDH12:c.505C>G and chr14:g.68193754C>G, but show the same C>G change. Thanks in advance for your patience in explaining this; just trying to learn.
Ok, sure. It's my understanding that the cDNA is the reverse complement of the gDNA since we don't know which rung it is being formed from and as such can go in either direction. So in that case at a particular gDNA position, the cDNA should either match the gDNA nucleotide (A-A, T-T, C-C, G-G), or be the inverse (A-T, T-A, G-C, C-G). But where I am confused is that when describing a mutation for a particular gDNA position, the cDNA always seems to follow some kind of standard - always matches, or always the reverse - and I can't figure out what guide is being used to set that. Is there some kind of a separate reference that is used when describing cDNA positions that facilities this? Again, I apologize if my understanding is basic and thank you in advance for helping me to understand this
Well, the gDNA location describes the specific position aligned to a reference genome. the cDNA location describes the position from the beginning of the coding region for the gene. So one SNP position can be described by either of these two coordinate systems. Is that correct?
If so, I am still confused as to the relationship between gDNA and cDNA nucleotides at the same position, as mentioned above
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