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Position

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[1].

Gene positions

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:

For example:

where amino acids are shown by capital letters (one-letter code), and nucleotides are shown by small letters.

Mutation positions

Mutation positions are described in Tables of alleles (IMGT Repertoire).

Reference:
[1] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999). PMID: 10745995 LIGM:221 pdf
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