Configuration
The 'configuration' concept defines the status of the V, D and J genes before or after DNA rearrangements, respectively. The two main instances of that concept are:
- germline which defines DNA with unjoined IG and TR V-GENE, D-GENE and/or J-GENE or corresponding sequence in cDNA, and
- rearranged which defines DNA with joined IG and TR V-GENE, D-GENE and/or J-GENE or corresponding sequence in cDNA.
The 'configuration' concept is particularly important because it is unique, in the animal and plant genomes, to the vertebrate IG and TR genes.
The 'configuration' concept is part of the 'IDENTIFICATION' concept of the IMGT-ONTOLOGY [1].
Note that the C-GENEs do not rearrange directly and therefore their configuration is undefined.
IMGT note:
- 1. In the absence of a germline sequence, a "consensus sequence" may be used sometimes in the literature. In IMGT/LIGM-DB, such a consensus sequence is assigned with the "unknown configuration" in the keywords and with a "consensus sequence" note in the qualifiers.
Reference:
[1] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999)
PMID: 10745995, LIGM:221
