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Functionality

The definition of functionality is based on the sequence analysis [1].

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

For IG and TR "Germline" entities and for "C-GENE"

A germline entity (V-GENE, D-GENE or J-GENE) or a C-GENE can be functional, ORF or pseudogene.

FUNCTIONAL
A germline entity (V-GENE, D-GENE or J-GENE) or a C-GENE is functional if the coding region has an open reading frame without stop codon, and if there is no described defect in the splicing sites, recombination signals and/or regulatory elements.
ORF (Open Reading Frame)
A germline entity (V-GENE, D-GENE or J-GENE) or a C-GENE is qualified as ORF (Open Reading Frame) if the coding region has an open reading frame, but:
  • alterations have been described in the splicing sites, recombination signals and/or regulatory elements.
  • and/or changes of conserved amino acids have been suggested by the authors to lead to uncorrect folding.
  • and/or the entity is an orphon.
PSEUDOGENE
A germline entity (V-GENE, D-GENE or J-GENE) or a C-GENE is qualified as pseudogene if the coding region has stop codon(s) and/or frameshift mutation(s).
In particular, a V-GENE is considered as pseudogene if these defects occur in the L-PART1 and/or V-EXON, or if there is a mutation in the L-PART1 INIT-CODON atg.
A J-GENE is considered as pseudogene if it has been identified by the presence of a recombination signal upstream of an open reading frame, but it has no donor splicing site in 5' or the donor splice is not in the expected sf1 or if no J-MOTIF is identified.

Functionality in IMGT annotation rules

For IG and TR "Rearranged" entities

PRODUCTIVE
A rearranged IG or TR (genomic or cDNA) entity is productive if the coding region has an open reading frame, with no stop codon and no defect described in the initiation codon, splicing sites and/or regulatory elements, and an in-frame JUNCTION.
UNPRODUCTIVE
An unproductive rearranged IG or TR (genomic or cDNA) entity is characterized by an out-of-frame JUNCTION and/or the presence of stop codon(s) and/or frameshift mutation(s), and/or a defect described in the splicing sites and/or the regulatory element(s), and/or unusual features (TRANSLOCATED, GENE FUSION...) and/or changes of conserved amino acids demonstrated as leading to uncorrect folding.

For germline V and J genes and alleles with a STOP-CODON region end

The IMGT functionality of germline V and J genes and alleles which have as unique defect an in-frame STOP-CODON at their region end (3' last codon for V-REGION, 5' first codon for J-REGION based on IMGT [3]) is functional.
Indeed, this STOP-CODON may very frequently disappear during V-(D)-J rearrangements owing to the mechanisms of junctional and/or N-diversity. The resulting rearranged sequences are classically either productive or unproductive.

For partial sequences

Functionality is assigned taking into account, whenever possible, the data from other sequences of the same gene.
A partial sequence with an open reading frame will be considered as ORF, and not functional, except if clearly mentioned by the authors.

For genes other than IG or TR

For genes other than IG or TR, the functionality instances are the same as 'For IG and TR "Germline" entities and for "C-GENE"', that is FUNCTIONAL, ORF and PSEUDOGENE.

Reference to cite for Functionality:
Lefranc, M.-P. "IMGT Locus on Focus: A new section of Experimental and Clinical Immunogenetics", Exp. Clin. Immunogenet., 15, 1-7 (1998).
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
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