IMGT reference directory in
FASTA format
(IG and TR)
Citing IMGT reference directory:
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)
IntroductionLefranc, 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/V-QUEST reference directory sets per IMGT Group
- IMGT/V-QUEST reference directory sets per taxon
- IMGT/V-QUEST reference directory sets for several taxons
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 from IMGT/GENE-DB.- 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 reference sequence and gene orientation:
An IMGT reference sequence for a given IG or TR gene in the IMGT reference directory in FASTA format (IMGT/GENE-DB, IMGT/V-QUEST) is provided in the 5' > 3' DNA strand orientation corresponding to the 'sense', 'plus' or 'coding strand' of that gene (DNA strand orientation).
The orientation (direct or opposite) of an IG or TR gene in a given IMGT locus is given in Locus Gene order (Genomic orientation)
IMGT Repertoire (IG and TR) > 1. Locus and genes > 3. Locus descriptions > Locus gene order
IMGT/V-QUEST reference directory sets release 202330-1 (24 July 2023)
-
The IMGT/V-QUEST reference directory sets are constituted by sets of sequences in FASTA format 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. - 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 Download
IMGT/V-QUEST reference directory sets per IMGT Group
In the V-REGION sets, IMGT gaps have been introduced according to the IMGT unique numbering [1] [2] [3] [4].IMGT/V-QUEST reference directory sets per taxon
| F+ORF+in-frame P | |||
| IMGT Groups | IG | TR | |
| MAMMALIA EUTHERIA (placentals) | Homo sapiens (human) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
| Mus musculus, Mus spretus (mouse) (1) |
IGHV,
IGHD,
IGHJ IGKV (2), IGKJ IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Aotus nancymaae (Ma's night monkey) |
TRAV ,
TRAJ TRBV , TRBJ TRGV , TRGJ TRDV , TRDJ |
||
| Bos taurus (bovine) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Camelus dromedarius (Arabian camel) |
IGKV, IGKJ |
TRBV,
TRBD,
TRBJ TRDV TRGV, TRGJ |
|
| Canis lupus familiaris (dog) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ, |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Capra hircus (goat) |
IGKV,
IGKJ IGLV, IGLJ |
||
| Equus caballus (horse) |
IGKV,
IGKJ IGHV, IGHD, IGHJ |
||
| Felis catus (Domestic cat) |
IGKV, IGKJ, IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Gorilla gorilla gorilla (lowland gorilla) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ |
TRGV,
TRGJ |
|
| Heterocephalus glaber (Naked mole-rat) |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
||
| Lemur catta (Ring-tailed lemur) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ |
||
| Macaca fascicularis (crab-eating macaque) |
IGHV, IGHD, IGHJ | TRBV, TRBD, TRBJ | |
| Macaca mulatta (Rhesus monkey) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Mustela putorius furo (ferret) |
TRBV, TRBD, TRBJ | ||
| Oryctolagus cuniculus (rabbit) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRAV,
TRAJ TRBV, TRBD, TRBJ TRDV, TRDD, TRDJ TRGV, TRGJ |
|
| Ovis aries (sheep) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRAV,
TRAJ, TRBV, TRBD, TRBJ, TRDV, TRDD, TRDJ |
|
| Pongo abelii (Sumatran orangutan) |
IGKV,
IGKJ |
||
| Rattus norvegicus (Norway rat) (3) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
||
| Sus scrofa (pig) |
IGHV,
IGHD,
IGHJ IGKV, IGKJ IGLV, IGLJ |
TRBV,
TRBD,
TRBJ |
|
| Tursiops truncatus (bottlenose dolphin) |
TRAV,
TRAJ TRDV, TRDD, TRDJ TRGV, TRGJ |
||
| Vicugna pacos (alpaca) |
IGHV, IGHD, IGHJ | ||
| MAMMALIA PROTHERIA (monotremes) | Ornithorhynchus anatinus (platypus) |
IGHV, IGHD, IGHJ | |
| AVES (birds) | Gallus gallus (chicken) |
IGHV,
IGHD,
IGHJ IGLV, IGLJ |
|
| TELEOSTEI (4) | Danio rerio (zebrafish) |
IGHV,
IGHD,
IGHJ IGIV, IGIJ |
TRAV
TRAJ TRDV, TRDD, TRDJ |
| Gadus morhua (Atlantic cod) |
IGHV | ||
| Ictalurus punctatus (Channel catfish) |
IGHV | ||
| Oncorhynchus mykiss (Rainbow trout) |
IGHV, IGHD, IGHJ, | TRBV, TRBD, TRBJ | |
| Salmo salar (Atlantic salmon) |
IGHV , IGHD , IGHJ | ||
| CHONDRICHTHYES (5) | |||
IMGT/V-QUEST reference directory sets for several taxons
Teleostei: IGHV , IGIVThe Teleostei IGHV and IGIV sets contain pooled sequences from several species (detailed in the table below).These sets are not included in IMGT/HighV-QUEST. The Teleostei pooled IGHD and IGHJ sets are not currently available.
|
Chondrichthyes: IGHV , IGHD , IGHJThe Chondrichthyes IGHV , IGHD and IGHJ sets contain pooled sequences from several species sets(detailed in the table below). These sets are not included in IMGT/HighV-QUEST.
|
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| (1) | Mouse IG set contains sequences from Mus musculus plus 9 from Mus spretus (IGKV: Musspr_IGKV10-94*01, Musspr_IGKV10-96*01; IGLV: Musspr_IGLV2*01, Musspr_IGLV3*01, Musspr_IGLV4*01, Musspr_IGLV4*02, Musspr_IGLV8*01; IGLJ Musspr_IGLJ4*01, Musspr_IGLJ5*01,). |
| (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 are available as separate sets for 5 species as shown in the table per taxon and as pooled with sequences of other species (in the set 'Teleostei' for several taxons). |
| (5) | Chondrichthyes are currently only available as pooled sequences of several species (in the set 'Chondrichthyes' for several taxons). |
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
"L-PART1+L-PART2" artificially spliced sets
|
|
"L-PART1+V-EXON" artificially spliced sets
|
|
Constant gene artificially spliced exons sets
|
|
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
Created: 09/04/1998
Last updated: 22/09/23
Last updated: 22/09/23
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