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Allele

An allele is a polymorphic variant of a gene.

The 'allele' concept is part of the 'CLASSIFICATION' concept of IMGT-ONTOLOGY[8]

Alleles are defined (i) for the sequence polymorphisms described at the nucleotide level, and (ii) for the Restriction Fragment Length Polymorphisms (RFLP) detected by Southern hybridization.

IMGT sequence polymorphisms

How are alleles determined?

Alleles displayed in the Alignments of alleles represent "potential" alleles. They are based on nucleotide differences in the core region of the genomic germline V, D and J genes (V-REGION, D-REGION, J-REGION) and of the C genes (C-REGION).

For each potential allele, one sequence (accession number in red) is selected as "reference sequence" (based on one or, whenever possible, several of the following criteria: germline sequence, first sequence published, longest sequence, mapped sequence).

Alignments of alleles allow to know how many times the alleles have been sequenced. Alleles which have been sequenced once may represent either rare alleles or sequencing errors. When a sequencing error is strongly suspected, the nucleotide and amino acid differences are shown in italics and in black and/or a note is added.

When the allele has been confirmed by several groups (identical sequence found by more than one investigator, evidence they are not PCR errors), by genetic studies (segregated in family studies) or by expression studies (both alleles expressed in antibodies in one person), a plus + is added in the column "confirmed by genetics and/or data" in Table of alleles).

Requirements for the assignment of new alleles

Requirements for the assignment of new alleles for variable (V), diversity (D) and joining (J) genes of immunoglobulin (IG) and T cell receptor (TR) genes are the following:

  1. sequences of new alleles should be from genomic DNA and from V, D and J genes in germline configuration.
  2. sequences of new alleles should include the complete gene unit, that is:
  3. sequences should be submitted to GenBank, EMBL-Bank or DDBJ.

Be aware that:

Therefore authors who would like to keep the anteriority of new alleles, should contact the IMGT nomenclature committee with the submitted sequences and accession numbers.

IMGT RFLP polymorphisms

IMGT RFLP polymorphisms are described in the section "Probes and RFLP" of the IMGT Repertoire.

References:
[1] Lefranc, M.-P. et al., Nucleic Acids Res., 26, 297-303 (1998) PMID: 9399859, LIGM:195.
[2] Pallarès, N. et al., Exp. Clin. Immunogenet., 15, 8-18 (1998) PMID: 9619396, LIGM:200 pdf
[3] Barbié, V. and Lefranc, M.-P., Exp. Clin. Immunogenet., 15, 171-183 (1998) PMID: 9813414, LIGM:207 pdf
[4] Martinez, C. and Lefranc, M.-P., Exp. Clin. Immunogenet., 15, 184-193 (1998) PMID: 9813415, LIGM:208 pdf
[5] Pallarès, N. et al., Exp. Clin. Immunogenet., 16, 36-60 (1999) PMID: 10087405, LIGM:210 pdf
[6] Ruiz, M. et al., Exp. Clin. Immunogenet., 16, 173-184 (1999) PMID: 10394055, LIGM:211 pdf
[7] Lefranc, M.-P., The Immunologist, 7, 132-136 (1999) LIGM:217.
[8] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995, LIGM:221 pdf
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