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LOCALIZATION

The 'LOCALIZATION' axiom is one of the seven axioms of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope [1-3].

The 'LOCALIZATION' axiom postulates that molecules, cells, organs, organisms or populations and their processes and relations have to be localized in time or space. At the molecular level in the field of immunogenetics, the concepts of localization allow to characterize the localization of IG and TR genes. The 'LOCALIZATION' axiom has generated concepts of localization, for example:

The 'Locus' concept includes for a standardized description:

Gene order is the relative position (order) of a gene, in a locus from the 5' end of a locus to its 3' end. The number '0' indicates that the relative position is unknown.

The Gene order concept provides a localization of the genes at fixed intervals, used for graphs and tables of IMGT® tools, when the query or analysis results do not require the real genomic coordinates positions.

The Gene order concept allows the display of inserted genes of copy number variations (CNV).

'Gene order' tables are available in 'Locus description'

All known genes in a locus are listed in Gene order. Non-IG and non-TR genes of interest may be included in the list and assigned a gene order when their position is useful for relative gene mapping.

References:
[1] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999). PMID: 10745995, LIGM:221 pdf
[2] Giudicelli, V. and Lefranc, M.-P. "Le paradigme IMGT-ONTOLOGY" In: Biologie Systémique Standards et modèles (Roux M. Ed.), Collection Ecrin, Omniscience, Presses Universitaires de France, Paris, 2007, Chapitre 6, pp143-164. ISBN: 978-2-916097-12-1
[3] Duroux, P. et al., "IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm", Biochimie, 90, 570-583 (2008). Epub 2007 Sep11. PMID: 17949886