Drybench Plasmid.
Coding sequences and reading frames
A CDS, a coding sequence, is the stretch of a gene that is read three bases at a time into a protein, from a start codon to a stop codon.
Triplets and frames
The genetic code is read in non-overlapping triplets from a fixed starting point (Crick et al. 1961), so each strand can be read in three frames and a double-stranded plasmid in six. A CDS is drawn as an arrow in the direction it is read; its length is a multiple of three, stop codon included.
Shifting a frame by one or two bases changes every codon after the shift, which is why an insert placed in a coding sequence must keep the frame to give the intended protein.
From the map to the protein
When the library's part is a CDS with a UniProt entry, the inspector links the protein, so the map and the protein's record stay one step apart. The sequence app translates any part of the plasmid in all six frames.
See it on a real plasmid
Open pBR322: TetR and AmpR read in opposite directions, on opposite strands.
The ribosome reads a coding sequence's codons in frame; the tour shows a human ribosome doing it.
References
- Crick FHC, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature 1961;192:1227-1232. PubMed 13882203
- Sutcliffe JG. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol 1979;43:77-90. PubMed 383387
Statements summarised by the site's builder from the references, for scientific review.