The 'position' concept corresponds to the classification of terms and rules which are necessary to position a component of the IG or TR sequences, genes, locus or proteins in a system of coordinates.
The 'position' concept is part of the 'LOCALIZATION' axiom of IMGT-ONTOLOGY.
Gene positions may be given on a chromosome, in a locus, in a clone or on a sequence. The human IG and TR gene positions are given in 'Gene positions' (IMGT Repertoire).
Nucleotide, codon, amino acid positions
The rules to position a nucleotide or a codon in a nucleotide sequence, an amino acid in a protein sequence, in a Collier de Perles or a 3D structure are described in the Numbering section of IMGT Scientific chart. They are based on the IMGT unique numbering for V-REGION, the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN and the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN.
Nucleotide positions are frequently deduced from the amino acid position in the IMGT unique numbering:
- multiply amino acid position number by 3, minus 2 for first nucleotide in codon
- multiply amino acid position number by 3, minus 1 for second nucleotide in codon
- multiply amino acid position number by 3, for third nucleotide in codon
- C at position 23 is encoded by codon tgt (t67, g68, t69)
- W at position 41 is encoded by codon tgg (t121, g122, g123)
where amino acids are shown by capital letters (one-letter code), and nucleotides are shown by small letters.
Mutation positions are described in Tables of alleles (IMGT Repertoire).