Question

mRNA transcript sequence analysis

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5.8 years ago

alexille5640 ▴ 10

By convention, i understand that when a mRNA sequence is obtained, it is automatically formatted as cDNA for computational analysis. (the U nucleotide is automatically formatted as T)

I am having trouble finding publications which illustrate mRNA sequence analysis in text or in figures showing convention in practice - showing an mRNA sequence illustrated in cDNA format or simply in AGTC versus AGUC format.

MAIN POINT: I have transcriptome data, and I'm outlining some SNPs within a single transcript. By convention, this transcript should be presented as cDNA. I would like to see some publications who have done this or something similar, literally writing out their mRNA sequence using DNA nucleotides. Anyone know any such articles so I can see it within a publication?

I have only been able to find one article so far which illustrates this: https://www.sciencedirect.com/science/article/pii/S0888754313000682

mRNA cDNA • 1.4k views

ADD COMMENT • link updated 5.8 years ago by h.mon 35k • written 5.8 years ago by alexille5640 ▴ 10

score 2 · Accepted Answer · 2018-07-17

Short answer: if you do you intend to highlight genomic SNPs obtained from RNAseq data, use ATCG. If you are intend to highlight mRNA editing, use AUCG.

By convention, i understand that when a mRNA sequence is obtained, it is automatically formatted as cDNA for computational analysis. (the U nucleotide is automatically formatted as T)

This is true, but also false. cDNA can have more than one meaning, depending on context. And your use of "obtained" doesn't make clear as to what do you mean, if sequencing RNA, or about the representation of transcripts on a in silico context.

Why is this false?

In molecular biology, complementary DNA is a DNA molecule synthesized by reverse transcriptase from messenger RNA (or other single stranded RNA). For the molecular biology cDNA, it is not a convention to use T instead of U, because the cDNA molecule is indeed DNA. And as what we call RNAseq is in fact cDNAseq, when using ATCG we are representing the actual bases being sequenced.

Why is this true?

In bioinformatics, cDNA is a representation of the mRNA using DNA bases rather than RNA bases, and in this case you are indeed right, this is just a convention.