NAR Molecular Biology Database Collection entry number 503

http://imgt.cines.fr/cgi-bin/GENElect.jv

Giudicelli, V., Lefranc, M.-P.

Université Montpellier II, CNRS, Montpellier, FRANCE

Contact lefranc@ligm.igh.cnrs.fr

IMGT/GENE-DB is the IMGT comprehensive genome database for immunoglobulins (IG) and T cell receptors (TR) genes from human and mouse, and, in developement, from other vertebrates. IMGT/GENE-DB is part of IMGT, the international ImMunoGeneTics information system® (1,2), the high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrate species. IMGT/GENE-DB annotated data are extracted from IMGT Repertoire, the global ImMunoGeneTics Web Resource, and from the IMGT/LIGM-DB database. All the human IMGT gene names (3,4) were approved by the Human Genome Organization (HUGO) Nomenclature Committee (HGNC) in 1999 (5), and entered in the Genome DataBase GDB (Canada) and in LocusLink at NCBI (USA). IMGT/GENE-DB allows a search of IG and TR gene entries by locus, group, subgroup, based on the CLASSIFICATION concept of IMGT-ONTOLOGY (6). A short cut allows to search genes by a selection on gene name (according to the IMGT nomenclature) or on clone name(s) (data from the "Reference sequences" and "Sequences from the literature" columns in IMGT Repertoire>Germline genes tables). IMGT/GENE-DB entries provide, for each gene, the chromosomal localization, the gene name and definition, the number of alleles, links to IMGT Repertoire and to external sequence (EMBL, GenBank, DDBJ) and genome (e.g., GDB, LocusLink, OMIM) databases. IMGT/GENE-DB provides for each allele, the functionality, the clone names, the IMGT/LIGM-DB reference sequence accession numbers (with link to the flat file), and the "IMGT/GENE-DB reference sequences in FASTA format" (nucleotide and amino acid sequences of the coding regions extracted from the IMGT/LIGM-DB reference sequence), with gaps according to the IMGT unique numbering (7) (based on the IMGT Scientific chart rules and on the NUMEROTATION concept of IMGT-ONTOLOGY). IMGT/GENE-DB was implemented by Véronique Giudicelli, and has been available on the Web since February 2003.

In July 2003, IMGT/GENE-DB contained 1,375 genes and 2,201 alleles (673 IG and TR genes and 1,024 alleles from Homo sapiens, and 702 IG and TR genes and 1,177 alleles from Mus musculus, Mus cookii, Mus pahari, Mus spretus, Mus saxicola, Mus minutoides).

IMGT is funded by the European Union's 5th PCRDT programme QLG2-2000-01287, the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.

1. Lefranc, M.-P., IMGT, the international ImMunoGeneTics database®, Nucleic Acids Res., 2003, 31, 307-310, PMID:12520009
2. Lefranc M.-P. IMGT, the international ImMunoGeneTics database®: a high-quality information system for comparative immunogenetics and immunology. Dev. Comp. Immunol., 2002, 26, 697-705, PMID:12206833
3. Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, Harcourt, 458 pages, 2001, ISBN:012441351X
4. Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, Harcourt, 398 pages, 2001, ISBN:0124413528
5. Wain, H.M., Bruford E.A., Lovering R.C., Lush M.J., Wright M.W. and Povey S., Guidelines for human gene nomenclature, Genomics, 2002, 79, 464-470, PMID:11944974.
6. Giudicelli, V. and Lefranc, M.-P. Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID: 10745995
7. Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc, G. "IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains", Dev. Comp. Immunol., 2003, 27, 55-77, PMID:12477501

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