The coding region of a gene, also known as the coding sequence or CDS (from coding DNA sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein. The region is bounded nearer the 5' end by a start codon and nearer the 3' end with a stop codon. The coding region in mRNA is bounded by the five prime untranslated region (5'-UTR) and the three prime untranslated region (3'-UTR), which are also parts of the exons. The CDS is that portion of an mRNA transcript that is translated by a ribosome.
Difference with cDNA
A cDNA sequence is derived from the transcript by reverse transcription, but in this case it also contains the 5' and 3' UTRs, which are not part of the CDS (they are transcribed, but not translated). Due to this, a CDS will -almost- always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG). These stop codons are called the stop signal.
Coding sequence annotation
While identification of open reading frames within a DNA sequence is straightforward, identifying coding sequences is not, because the cell translates only a subset of all open reading frames to proteins. Currently CDS prediction uses sampling and sequencing of mRNA from cells, although there is still the problem of determining which parts of a given mRNA are actually translated to protein. CDS prediction is a subset of gene prediction, the latter also including prediction of DNA sequences that code not only for protein but also for other functional elements such as RNA genes and regulatory sequences.
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