Is it possible for a single DNA nucleotide to match its cDNA complement, and not invert?

Question

[adam]

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?

[Ram]

Please do not delete posts that have received feedback. In your case, your question seems to have been answered. If the answer resolved your question, you should mark it as accepted. If an answer was not really helpful or did not work, provide detailed feedback so others to analyze that answer deeper.

Answer 1

[swbarnes2]

No. The genome always runs one way, the transcripts can run either way.

[adam]

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.

[swbarnes2]

Do you understand that transcripts can run in either direction compared to how the genome runs?

[adam]

Yes I do. But I don't understand how at the same position there can be a single nucleotide discrepancy between the cDNA and gDNA change when they are both describing the same mutation.

[swbarnes2]

Why do you think they have different numerical coordinates?

[adam]

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.

[swbarnes2]

I'm trying to explain it to you. Don't just tell me the coordinates, tell me why the same SNP has two different coordinates.

[adam]

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

[swbarnes2]

Convention sets the forward direction of genomic DNA. It's fixed. But again, why do you think the same SNP has two different coordinates?

[adam]

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

[swbarnes2]

Okay, so you accept that there are two valid coordinate systems for measuring the position. You really can't imagine why some transcripts would have a coordinate system in the same direction as the genome, and others would have the opposite?

[adam]

That is the root of my confusion! Specifically when you say that some transcripts are in the same direction and others run opposite - what determines the direction of a particular transcript?

[swbarnes2]

Nothing "determines" the direction. Some transcripts are forward, some are reverse. You just have to look up the transcript to know how it runs with respect to the conventional forward of the genome, or not.

[adam]

Apologies if my question is too elementary to warrant a complete response but I am still genuinely trying to learn the answer. Is it possible to send a reading link that might bridge my gap in understanding?