Citing IMGT dynamic tools: Sanou G., Zeitoun G. et al. IMGT® at scale: FAIR, Dynamic and Automated Tools for Immune Locus Analysis, Nucleic Acids Research. 2025;,gkaf1024. doi: 10.1093/nar/gkaf1024 (Free Article) PMID: 41091930.
Program version: v. 

Add information about removed genes/alleles.
May 15th, 2025.

Add the possibility to obtain a gene table per strain (for mouse now and for other species later) and allotypes/isotypes for human.
September 25th, 2024.

Bibliographical references in alphabetic order, small design changes and addition of "NL" for non-localized gene.
June 14th, 2024.

Addition of 'Score for IMGT allele confirmation' as well as NCBI TPA accession numbers.
September 20th, 2023.

Implementation of the dynamic gene table.

Gene table legend:

"+" or "-" indicates if the gene sequences have been found (+) or not been found (-) rearranged (R), transcribed (T) and/or translated into protein (Pr). Arbitrarily that information is shown on the first line of each gene, when the data have been confirmed by several studies.

Functionality is shown in parentheses, (F) and (P), when the accession number refers to rearranged genomic DNA or cDNA and the corresponding germline gene has not yet been isolated.

IMGT allele confirmation: A scoring system is employed to indicate the number of IMGT/LIGM-DB reference sequences and other sequences from the literature in which an IG or TR gene allele has been identified and annotated.

Removed genes/alleles
If a gene/allele existence or name has to be changed, the old name or gene/allele would be deleted and its name won't be reused. They are kept in the gene table for historical reasons.
A single star ()
indicates that an IG or TR gene allele is annotated in the reference sequence only.
Two stars ()
indicate that an IG or TR gene allele is annotated in its reference sequence and in one sequence from the literature.
Three stars ()
indicate that an IG or TR gene allele is annotated in its reference sequence and in at least two sequences from the literature.
In the Excel file, the stars are represented by the plus symbol (+).

Click on:
  • IMGT gene name to get the corresponding IMGT/GENE-DB entry (link).
  • IMGT allele name to see the corresponding Alignments of alleles (link).
  • Accession number to get the corresponding IMGT/LIGM-DB entry (link).
  • MAP: mapped sequences. Click to access GENE-DB «LOCALIZATION IN GENOME ASSEMBLIES» (link).
  • [number] to access the corresponding IMGT reference (popover).
  • (number) to see the corresponding IMGT note (popover).
Options:
  • You can show/hide columns (), download data () or put the table in fullscreen () using buttons.
See also (IMGT Scientific chart):
Select a species and a IMGT group to get the gene table:
Only IMGT available species/group are shown in the drop-down list.
The gene table can take several seconds to appear, please be patient.
Gene table of house mouse (Mus musculus) TRDJ IMGT group:
IMGT gene nameIMGT allele nameScore for
IMGT allele
confirmation		FctChromosomosal
localization		R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)		Secondary
accession
numbers		Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
TRDJ1 TRDJ1*01 F 14C2 (19.7 cM)
RTPr
+++
 Jdelta1 BALB/c (2) AF019412 [15] MAP 31627-31705 AE008686 [13] 129/SvJ AE007512 [13] 1567342-1567420
C57BL/6J IMGT000082 [7,8] 1705143-1705223
TRDJ2 TRDJ2*01 F 14C2 (19.7 cM)
RTPr
+++
 Jdelta2 BALB/c X64903 [6] MAP 10-97 AE008686 [13] 129/SvJ AE007512 [13] 1574171-1574258
B10.D2-H2dm1 (3) M64239 [1-5,9-12,14,16,19-22] 2454-2540
C57BL/6J IMGT000082 [7,8] 1718783-1718872
TRDJ2 TRDJ2*02 F (1) 14C2 (19.7 cM) Jdelta2 Std:ddY X17179 [18] 728-813
IMGT notes: ↑
  1. Nucleotide T, at position 24 (according to the IMGT allele mutation numbering) of TRDJ2 in X64903, is deleted in X17179. This DELETION leads to a frameshift downstream of codon 8. However it is not excluded that V-D-J rearrangements allow to reestablish the normal ORF. For these reasons the TRDJ2*02 is considered as functional.
  2. It is not excluded that the source of the sequence is from B10.D2-H.2dm1 instead of BALB/c, as the cosmid clone is coming from the Kai Wang's library [4].
  3. B10.D2-H2dm1 is a congenic strain, B10 is the abbreviated symbol of C57BL/10 and D2 the abbreviated symbol of DBA/2J.
IMGT references: ↑
  1. Arden B. et al., Diversity and structure of genes of the alpha family of mouse T-cell antigen receptor, Nature, vol. 316, no. 6031, 1985, pp. 783-787. DOI: 10.1038/316783a0
  2. Baer R. et al., Organization of the T-cell receptor alpha-chain gene and rearrangement in human T-cell leukaemias, Mol. Biol. Med, vol. 3, no. 3, 1986, pp. 265-277. PUBMED: 3016457
  3. Becker D.M. et al., Variability and repertoire size of T-cell receptor V alpha gene segments, Nature, vol. 317, no. 6036, 1985, pp. 430-434. DOI: 10.1038/317430a0
  4. Chien Y.-H. et al., A third type of murine T-cell receptor gene, Nature, vol. 312, no. 5989, 1984, pp. 31-35. DOI: 10.1038/312031a0
  5. Chien Y.H. et al., A new T-cell receptor gene located within the alpha locus and expressed early in T-cell differentiation, Nature, vol. 327, no. 6124, 1987, pp. 677-682. DOI: 10.1038/327677a0
  6. Chien Y.H. et al., T-cell receptor delta gene rearrangements in early thymocytes, Nature, vol. 330, 1987, pp. 24-31.
  7. Church,D.M. et al., Lineage-specific biology revealed by a finished genome assembly of the mouse, PLoS Biol (2009), PUBMED: 19468303
  8. Church,D.M. et al., Modernizing reference genome assemblies, PLoS Biol, vol. 9, no. 7, 2011, PUBMED: 21750661
  9. Dembic Z. et al., Transfer of specificity by murine alpha and beta T-cell receptor genes, Nature, vol. 320, no. 6059, 1986, pp. 232-238. DOI: 10.1038/320232a0
  10. Hayday A.C. et al., Unusual organization and diversity of T-cell receptor alpha-chain genes, Nature, vol. 316, no. 6031, 1985, pp. 828-832. DOI: 10.1038/316828a0
  11. Hochgeschwender U. et al., Dominance of one T-cell receptor in the H-2Kb/TNP response, Nature, vol. 326, no. 6110, 1987, pp. 307-309. DOI: 10.1038/326307a0
  12. Iwashima M. et al., Variable region (V delta) gene segment most frequently utilized in adult thymocytes is 3' of the constant (C delta) region, Proc. Natl. Acad. Sci. U.S.A, vol. 85, no. 21, 1988, pp. 8161-8165. PUBMED: 3263646
  13. Lee I.Y. et al., Large-scale Sequence Analysis of the Mouse T-cell Receptor Alpha/Delta Locus, Unpublished.
  14. Patten P. et al., Structure, expression and divergence of T-cell receptor beta-chain variable regions, Nature, vol. 312, no. 5989, 1984, pp. 40-46. DOI: 10.1038/312040a0
  15. Rowen L. et al., The mouse T cell receptor delta locus: partial sequence, Unpublished.
  16. Saito H. et al., A third rearranged and expressed gene in a clone of cytotoxic T lymphocytes, Nature, vol. 312, no. 5989, 1984, pp. 36-40. DOI: 10.1038/312036a0
  17. Takeshita S. et al., Excision products of the T cell receptor gene support a progressive rearrangement model of the alpha/delta locus, EMBO J, vol. 8, no. 11, 1989, pp. 3261-3270. PUBMED: 2583098
  18. Toda M. et al., Structure of extrachromosomal circular DNAs excised from T-cell antigen receptor alpha and delta-chain loci, J. Mol. Biol, vol. 202, no. 2, 1988, pp. 219-231. DOI: 10.1016/0022-2836(88)90453-6
  19. Wilson R.K. et al., Nucleotide sequence analysis of 95 kb near the 3' end of the murine T-cell receptor alpha/delta chain locus: strategy and methodology, Genomics, vol. 13, no. 4, 1992, pp. 1198-1208. DOI: 10.1016/0888-7543(92)90038-T
  20. Winoto A. and Baltimore D, Alpha beta lineage-specific expression of the alpha T cell receptor gene by nearby silencers, Cell, vol. 59, no. 4, 1989, pp. 649-655. DOI: 10.1016/0092-8674(89)90010-X
  21. Winoto A. and Baltimore D, A novel, inducible and T cell-specific enhancer located at the 3' end of the T cell receptor alpha locus, EMBO J, vol. 8, no. 3, 1989, pp. 729-733. PUBMED: 2524381
  22. Winoto A. et al., Predominant use of a V alpha gene segment in mouse T-cell receptors for cytochrome c, Nature, vol. 324, no. 6098, 1986, pp. 679-682. DOI: 10.1038/324679a0