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Coordinates of CDS sequence

Hi all,

I can't seem to get my head around the Genbank CDS coordinate numbers (see here: https://www.ncbi.nlm.nih.gov/nuccore/NC_000022.11?report=genbank&from=44881162&to=45010005&strand=true)

If I have a list of a CDS sequence here:

CDS sequence from a gene

And the gene itself (both introns and exons) starts at place 0, would the coordinate of the first CDS be:

0+457 = 457

Or would this relate to the beginning of the first exon, which would start at place 100:

100+457 = 557

In image format:

enter image description here Apologies if this is a stupid question!

cds genbank fasta
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updated by Mensur Dlakic Mensur Dlakic • written by hemr3 • hemr3

Which specific gene are you referring to? There may be a 5'-UTR there.

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written by GenoMax GenoMax

Hi! This is the CDS without any UTR in them (I believe), but I'm referring to PHF21B.

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written by hemr3 • hemr3

1 answer

Counting starts from 1, not from 0. All the counts are from the very first nucleotide in that particular record, which is to say that they have the same frame of reference. That would be your option #1.

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written by Mensur Dlakic Mensur Dlakic

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