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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.

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

See also:

• IMGT-ONTOLOGY
• IDENTIFICATION
• Sterile transcript ("germline transcript")

Created: 22/05/2001
Last updated: Monday, 11-Jan-2010 17:25:32 CET
Authors: Véronique Giudicelli and Marie-Paule Lefranc
Editors: Manuel Ruiz and Chantal Ginestoux
Contact: Marie-Paule Lefranc

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For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

     

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