IMGT®, the international ImMunoGeneTics information system®

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Functionality

The definition of functionality is based on the sequence analysis (IMGT Scientific chart) [1].

The 'functionality' concept is part of the 'IDENTIFICATION' axiom of IMGT-ONTOLOGY [2] [3] [4]

As examples, for the IG and TR genes, the instances functional (for germline V-GENE, D-GENE, J-GENE, and for C-GENE) and productive (for rearranged V-J and V-D-J genomic or cDNA entities) mean that the coding regions have an open reading frame without stop codon, and that there is no described defect in the splicing sites, and/or recombination signals, and/or regulatory elements. According to the gravity of the identified defects and to the gene configuration, the functionality can be defined as ORF or pseudogene (for germline V-GENE, D-GENE or J-GENE, and for C-GENE) and unproductive (for rearranged V-J and V-D-J genomic or cDNA entities).

For genes other than IG and TR, the functionality instances are the same as "For Germline IG and TR entities and for C-GENE".

Functionality can be queried from the "Taxonomy,..." module in IMGT/LIGM-DB.

Functionality is shown between:

References:
[1] Lefranc, M.-P. IMGT Locus on Focus : a new section of Experimental and Clinical Immunogenetics. Exp. Clin. Immunogenet., 15, 1-7 (1998) PMID: 9619395, LIGM: 199 pdf
[2] Giudicelli, V. and Lefranc, M.-P. Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995, LIGM: 221 pdf
[3] Giudicelli, V. and Lefranc, M.-P., IMGT-ONTOLOGY 2012. Front Genet. 3:79 (2012). doi: 10.3389/fgene.2012.00079. Epub 2012 May 23 Online access PMID:22654892, LIGM: 401
[4] Lefranc M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. Feb 05;5:22 (2014). doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447, LIGM: 429