What Does Cds And Exon Mean In A Gtf File?

Question

[dfernan]

Hi,

I have a hg19 GTF file that I ordered according to chromosome start and end positions, and group by gene_id.

Here is an example of a few lines of the file:

lines 45-47

chr1  refGene transcript  367659  368597  . + . gene_id "OR4F29"; transcript_id "NM_001005221"; gene_name "OR4F29";
chr1  refGene exon  367659  368597  . + . gene_id "OR4F29"; transcript_id "NM_001005221"; exon_number "1"; exon_id "NM_001005221.1"; gene_name "OR4F29";
chr1  refGene CDS 367659  368594  . + 0 gene_id "OR4F29"; transcript_id "NM_001005221"; exon_number "1"; exon_id "NM_001005221.1"; gene_name "OR4F29";

lines 143-146

chr1  refGene transcript  861121  879961  . + . gene_id "SAMD11"; transcript_id "NM_152486"; gene_name "SAMD11";
chr1  refGene exon  861121  861180  . + . gene_id "SAMD11"; transcript_id "NM_152486"; exon_number "1"; exon_id "NM_152486.1"; gene_name "SAMD11";
chr1  refGene exon  861302  861393  . + . gene_id "SAMD11"; transcript_id "NM_152486"; exon_number "2"; exon_id "NM_152486.2"; gene_name "SAMD11";
chr1  refGene CDS 861322  861393  . + 0 gene_id "SAMD11"; transcript_id "NM_152486"; exon_number "2"; exon_id "NM_152486.2"; gene_name "SAMD11";

I was wondering what the CDS means. I mean the transcript is one isoform of the gene, the exon are the exon positions of the given isoforms, but what'd the CDS mean?

Sorry about such basic Q but I got confused.

Answer 1

[Istvan Albert]

Don't feel bad this is not a basic question at all. The terminology is not nearly as obvious as it should be moreover the exact definitions may carry many subtle details. It is the so called Sequence Ontology that specifies the meaning of each term:

CDS: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon."

http://www.sequenceontology.org/browser/current_cvs/term/SO:0000316

Exon: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing."

http://www.sequenceontology.org/browser/current_cvs/term/SO:0000147

[Istvan Albert]

Ironically I have come to believe that this definition is incorrect. The CDS should not actually include the stop codon and most annotations that label a feature as CDS do not include the stop codon. Which IMHO is the correct behavior the stop codon is not actually translated into an amino acid so it is not actually coding.

Answer 2

[Sangwoo Kim]

IMHO, exon contains both of UTR and CDS. So the CDS is the sequence that actually makes proteins. In you example of SAMD11, the region upstream of 861322 is thought to be 5' UTR which is transcribed to mRNA but does not build a protein.

[epigene]

This clarify things better. 5' UTR, CDS and 3'UTR make up exons.

Answer 3

[fo3c]

CoDing Sequence