IMGT®, the international ImMunoGeneTics information system®

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:

• parentheses, (F) and (P), when the accession number refers to rearranged genomic DNA or cDNA and the corresponding germline gene has not yet been isolated.
• brackets, [F] and [P], when the accession number refers to genomic DNA, but not known as being germline or rearranged.