canonical sequence


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canonical sequence

[kə′nän·ə·kəl ′sē·kwəns]
(cell and molecular biology)
An archetypical nucleotide or amino acid sequence to which all variants are compared.
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If the genome has been fragmented and expanded based on recombination events in an analogous manner to plant organellar genomes, this may be a way of protecting against damage by having "extra" genetic material that can be modified by oxidative damage and/or recombination and subsequently edited back to the canonical sequence. There seems to be limits to the ability of the editing machinery to make a canonical transcript evidenced by the large number of synonymous substitutions primarily at the third codon position.
The canonical sequence of separating points (a, b, c, d) of a is defined as follows:
The resulting gene sequence is different slightly from the canonical sequence of the reference genome without modification in the amino acid sequence of the protein.
As an example, in the transcript variant X1 (XM_005252446) of the Human IL2RA the canonical 3'ss TTCCAG immediately upstream of exon 4 is silenced and the fourth exon (216 nt; 72 aa) of the canonical sequence (NM_000417) is lacking in this variant.
Results for each peptide are expressed as percent cleavage by furin compared with the canonical sequence.