IMGT reference directory in
FASTA format
(IG and TR)
Lefranc, M.-P. and Lefranc, G. The Immunoglobulin FactsBook Academic Press, London, UK (458 pages), (2001)
Lefranc, M.-P. and Lefranc, G. The T cell receptor FactsBook Academic Press, London, UK (398 pages), (2001)
IMGT/V-QUEST reference directory sets
IMGT/GENE-DB reference directory sets
References
Introduction
The IMGT reference directory in FASTA format is constituted by sets of immunoglobulin (IG) or T cell receptor (TR) sequences which are isolated from the IMGT reference sequences.- By definition, the IMGT reference directory sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles.
- In the V-REGION and C-GENE exon sets, IMGT gaps have been introduced according to the IMGT unique numbering [1] [2] [3] [4].
- Gene names with provisional nomenclature (with a letter S) correspond to genes not yet assigned to genomic mapped genes. They correspond to insertion/deletion polymorphism in different strains or to mutated genes. NL: Not Localized.
IMGT/V-QUEST reference directory sets
-
The IMGT/V-QUEST reference directory sets are constituted by sets of sequences which contain the V-REGION,
D-REGION and J-REGION alleles, isolated from the Functional (F), ORF and in-frame pseudogene (P) allele IMGT reference sequences. By definition, these sets contain one sequence for each allele. Allele names of these sequences are shown in red in
Alignments of alleles.
The IMGT/V-QUEST reference directory sets also include orphons. - The human and the mouse IG and TR sets are exhaustive and correspond to the IMGT/GENE-DB content in terms of F+ORF+in-frame P genes and alleles.
- IMGT/V-QUEST reference directory sets comprise IG and TR sets (for one or several species) which are used in IMGT/V-QUEST
for the identification and alignment of the input sequence.
Overview
In the V-REGION sets, IMGT gaps have been introduced according to the IMGT unique numbering [1] [2] [3] [4].
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IMGT/V-QUEST reference directory sets per taxon
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The available IMGT/GENE-DB reference directory sets are the following :
IMGT/GENE-DB reference directory sets
They are divided in:
Note that the IMGT/GENE-DB sets also include the orphons.
IMGT gaps have been introduced according to the
IMGT unique numbering
[1] [2] [3] [4].
IMGT/GENE-DB also provides examples of artificially spliced sequences (for more exhaustive functionalities, please query
IMGT/GENE-DB):
- "L-PART1+L-PART2" (artificially spliced) sets
- "L-PART1+V-EXON" (artificially spliced) sets
- Constant gene artificially spliced exons sets
IG "V-REGION", "D-REGION", "J-REGION", "C-GENE exon" sets
TR "V-REGION", "D-REGION", "J-REGION", "C-GENE exon" sets
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"L-PART1+L-PART2" artificially spliced sets
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"L-PART1+V-EXON" artificially spliced sets
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Constant gene artificially spliced exons sets
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Notes
| (1) | Mouse IG set contains sequences from Mus musculus and Mus spretus. |
| (2) | The IGKV4-52*01 (AJ239198) and the IGKV4-54*01 (AJ231223) V-REGION nucleotide sequences are 100% identical. These two genes differ by one nucleotide in their L-PART2 (at position 12 according to the IMGT numbering). |
| (3) | The IGHV and IGLV genes have a provisional nomenclature which may be updated. The definitive nomenclature will be available once the rat IGH and IGL locus are completely sequenced. |
| (4) | Teleostei IG set contains the sequences from the Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar ), Bastard halibut (Paralichthys olivaceus), Blackfin icefish (Chaenocephalus aceratus), and Channel catfish (Ictalurus punctatus), Charr (Salvelinus alpinus), Chinese perch (Siniperca chuatsi), Common carp (Cyprinus carpio), Emerald rockcod (Trematomus bernachii), European sea bass (Dicentrarchus labrax), Five-ray yellowtail (Seriola quinqueradiata), Goldfish (Carassius auratus), Ladyfish (Elops saurus), Rainbow trout (Oncorhynchus mykiss) , Spotted wolffish (Anarhichas minor), Torafugu (Takifugu rubripes), Turbot (Scophthalmus maximus), Yellowbelly rockcod (Notothenia corriceps), Zebra danio (Danio rerio) IG sets. |
| (5) | Chondrichthyes IG set contains the sequences from Bull shark (Carcharhinus leucas), Sandbar shark (Carcharhinus plumbeus) , Spotted wobbegong shark (Orectolobus maculatus) , Clearnose skate (Raja eglanteria), Horned shark (Heterodontus francisci), Little skate (Raja erinacea), Nurse shark (Ginglyomostoma cirratum), Spotted ratfish (Hydrolagus colliei) |
| (6) | Non-human primates TR set contains Ma's night monkey (Aotus nancymaae) |
| (7) | Note that "F+ORF+all P" sequences are automatically extracted from IMGT/LIGM-DB, except for the BN000872 accession number. |
References:
[1] Lefranc M.-P.
"Unique database numbering system for immunogenetic analysis"
Immunology Today, 18: 509 (1997).
[2] Lefranc M.-P. "The IMGT unique numbering for immunoglobulins, T cell Receptors and Ig-like domains" The immunologist, 7,132-136 (1999).
[3] Lefranc M.-P. et al. "IMGT unique numbering for immunoglobulin and Tcell receptor variable domains and Ig superfamily V-like domains" Dev. Comp. Immunol., 27, 55-77 (2003).
[4] Lefranc M.-P. et al.
"IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains"
Dev. Comp. Immunol., 2005, 29, 185-203
PMID: 15572068
Last updated: Thursday, 29-Jul-2010 18:51:38 CEST
Authors: Véronique Giudicelli (veronique.giudicelli@igh.cnrs.fr) and Marie-Paule Lefranc (marie-paule.lefranc@igh.cnrs.fr)
IMGT/V-QUEST Documentation
IMGT/V-QUEST Search page
Contact: Marie-Paule Lefranc
Software material and data coming from IMGT server may be used for academic research only,
provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics
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(founder and director: Marie-Paule Lefranc, Montpellier, France)."
References to cite:
Lefranc, M.-P. et al.,
Nucleic Acids Research, 27, 209-212 (1999)
Cover of NAR;
Ruiz, M. et al.,
Nucleic Acids Research, 28, 219-221 (2000);
Lefranc, M.-P.,
Nucleic Acids Research, 29, 207-209 (2001);
Lefranc, M.-P.,
Nucleic Acids Res., 31, 307-310 (2003);
Lefranc, M.-P. et al.,
In Silico Biol., 5, 0006 (2004) [Epub],
5, 45-60 (2005);
Lefranc, M.-P. et al.,
Nucleic Acids Res., 33, D593-D597 (2005)
Full text;
Lefranc, M.-P. et al.,
Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838
Full text.
For any other use please contact Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr.
IMGT founder and director: Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr
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Veronique.Giudicelli@igh.cnrs.fr
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