Protein coding sequences

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Protein coding sequences are DNA sequences that are transcribed into mRNA and in which the corresponding mRNA molecules are translated into a polypeptide chain. Every three nucleotides, termed a codon, in a protein coding sequence encodes 1 amino acid in the polypeptide chain. In some cases, different chassis may either map a given codon to a different sequence or may use different codons more or less frequently. Therefore some protein coding sequences may be optimized for use in a particular chassis.

In the Registry, protein coding sequences begin with a start codon (usually ATG) and end with a stop codon (usually with a double stop codon TAA TAA). Protein coding sequences are often abbreviated with the acronym CDS.

Although protein coding sequences are often considered to be basic parts, in fact proteins coding sequences can themselves be composed of one or more regions, called protein domains. Thus, a protein coding sequence could either be entered as a basic part or as a composite part of two or more protein domains.

  1. The N-terminal domain of a protein coding sequence is special in a number of ways. First, it always contains a start codon, spaced at an appropriate distance from a ribosomal binding site. Second, many coding regions have special features at the N terminus, such as protein export tags and lipoprotein cleavage and attachment tags. These occur at the beginning of a coding region, and therefore are termed Head domains.
  2. A protein domain is a sequence of amino acids which fold relatively independently and which are evolutionarily shuffled as a unit among different protein coding regions. The DNA sequence of such domains must maintain in-frame translation, and thus is a multiple of three bases. Since these protein domains are within a protein coding sequence, they are called Internal domains. Certain Internal domains have particular functions in protein cleavage or splicing and are termed Special Internal domains.
  3. Similarly, the C-terminal domain of a protein is special, containing at least a stop codon. Other special features, such as degradation tags, are also required to be at the extreme C-terminus. Again, these domains cannot function when internal to a coding region, and are termed Tail domains.

For more details on protein domains including how to assemble protein domains into protein coding sequences, please see Protein domains.

Protein coding sequences should be as follows


Design: Are you interested in designing a new protein coding sequence? Here are some guidelines to help you design new protein coding sequences.
Help: A glossary, FAQ, and further reading on translational units, protein coding sequences and protein domains.

Commonly used protein coding sequences

Reporters: Reporters are proteins that can be used to measure gene expression or other intracellular event. Reporters generally produce a measurable signal such as fluorescence, color, or luminescence.
Transcriptional regulators: Proteins involved in activation or repression of transcription are listed here.
Selection markers: Proteins involved in conferring a selective advantage or disadvantage to cells including antibiotic resistance markers. These protein coding sequences are useful for selecting cells with a particular trait, such as containing a plasmid.


Biosynthesis: Enzymes involved in the production or degradation of chemicals and metabolites are listed here.
DNA modification: Enzymes used during DNA cleavage, excision, integration, ligation, chromatin remodeling and replication.
Proteases: Proteases cleave or degrade other proteins. Some proteases can even cleave themselves.
Post-translational modification enzymes: Some enzymes post-translationally modify other proteins by, for example, adding or removing a phophate or methyl group.

Other protein coding sequences

Membrane proteins: Surface display peptides, transporters, channels, and pumps are listed here.
Receptors and ligands: Receptors and ligands not associated with the cell membrane.
Lysis proteins: Proteins involved in killing cells through disruption of the membrane.