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) TRBJ 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 (*)
TRBJ1-1 TRBJ1-1*01 F 6B1 (20.5 cM)
RTPr
++
 JT1 B10.A (2) X01018 [5] MAP 73-120 * J1S1 BALB/c AE000665 [2,8,9] 153956-154003 *
C57BL/6J IMGT000132 [3,4] 655043-655118
Jbeta1.1 SJL/J U77843 [1] 664-711 *
TRBJ1-1 TRBJ1-1*02 (F) 6B1 (20.5 cM)
RTPr
++
 Jbeta1 BALB/cxC56BL/6(F1) M11456 [7] #c 371-417 *
TRBJ1-2 TRBJ1-2*01 F 6B1 (20.5 cM)
RTPr
++
 JT2 B10.A X01018 [5] MAP 209-256 * J1S2 BALB/c AE000665 [2,8,9] 154093-154140 *
C57BL/6J IMGT000132 [3,4] 655180-655255
Jbeta1.2 SJL/J U77843 [1] 800-847 *
TRBJ1-3 TRBJ1-3*01 F 6B1 (20.5 cM)
RTPr
++
 JT3 B10.A X01018 [5] MAP 549-598 * J1S3 BALB/c AE000665 [2,8,9] 154415-154464 *
C57BL/6J IMGT000132 [3,4] 655502-655579
Jbeta1.3 SJL/J U77843 [1] 1122-1171 *
TRBJ1-4 TRBJ1-4*01 F 6B1 (20.5 cM) JT4 B10.A X01018 [5] 1036-1086 *
TRBJ1-4 TRBJ1-4*02 F 6B1 (20.5 cM)
RTPr
++
 J1S4 BALB/c AE000665 [2,8,9] MAP 154903-154953 * C57BL/6J IMGT000132 [3,4] 655990-656068
Jbeta1.4 SJL/J U77843 [1] 1609-1659 *
TRBJ1-5 TRBJ1-5*01 F (3) 6B1 (20.5 cM)
RTPr
++
 J1S5 BALB/c AE000665 [2,8,9] MAP (3) 155176-155225 * C57BL/6J IMGT000132 [3,4] 656263-656340
TRBJ1-5 TRBJ1-5*02 F (3) 6B1 (20.5 cM) JT5 B10.A X01018 [5] (3) 1309-1357 *
TRBJ1-5 TRBJ1-5*03 F 6B1 (20.5 cM) Jbeta1.5 SJL/J U77843 [1] 1882-1931 *
TRBJ1-6 TRBJ1-6*01 ORF (4) 6B1 (20.5 cM)
RTPr
++
 JT6 B10.A X01018 [5] MAP 1778-1830 * J1S6 BALB/c AE000665 [2,8,9] 155646-155698 *
C57BL/6J IMGT000132 [3,4] 656733-656813
Jbeta1.6 SJL/J U77843 [1] 2351-2403 *
TRBJ1-7 TRBJ1-7*01 ORF (5) 6B1 (20.5 cM) JT7 B10.A X01018 [5] MAP 1867-1912 * J1S7 BALB/c AE000665 [2,8,9] 155734-155779 *
C57BL/6J IMGT000132 [3,4] 656822-656894
TRBJ2-1 TRBJ2-1*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.1 B10.A K02802 [6] MAP 405-454 * J2S1 BALB/c AE000665 [2,8,9] 162836-162885 *
Jbeta2-1 BALB/c X00934 [12] 762-811 *
C57BL/6J IMGT000132 [3,4] 663933-664010
TRBJ2-2 TRBJ2-2*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.2 B10.A K02802 [6] MAP 608-658 * J2S2 BALB/c AE000665 [2,8,9] 163039-163089 *
C57BL/6J IMGT000132 [3,4] 664136-664214
TRBJ2-3 TRBJ2-3*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.3 B10.A K02802 [6] MAP 874-922 * J2S3 BALB/c AE000665 [2,8,9] 163305-163353 *
C57BL/6J IMGT000132 [3,4] 664402-664478
TRBJ2-4 TRBJ2-4*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.4 B10.A K02802 [6] MAP 1013-1061 * J2S4 BALB/c AE000665 [2,8,9] 163444-163492 *
C57BL/6J IMGT000132 [3,4] 664541-664617
TRBJ2-5 TRBJ2-5*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.5 B10.A K02802 [6] MAP 1104-1152 * J2S5 BALB/c AE000665 [2,8,9] 163535-163583 *
C57BL/6J IMGT000132 [3,4] 664632-664708
TRBJ2-6 TRBJ2-6*01 P (1) 6B1 (20.5 cM) Jbeta2.psi B10.A K02802 [6] MAP 1248-1295 * J2S6 BALB/c AE000665 [2,8,9] 163680-163727 *
C57BL/6J IMGT000132 [3,4] 664777-664852
TRBJ2-7 TRBJ2-7*01 F 6B1 (20.5 cM)
RTPr
++
 Jbeta2.7 B10.A K02802 [6] MAP 1460-1506 * J2S6 BALB/c AE000665 [2,8,9] 163892-163938 *
C57BL/6J IMGT000132 [3,4] 664989-665063
TRBJ2-7 TRBJ2-7*02 (F) 6B1 (20.5 cM)
RTPr
++
 C57BL/6 M16122 [10,11] #c 573-618 *
IMGT notes: ↑
  1. pseudogene because no sequence consensus
  2. B10.A is a congenic strain, B10 is the abbreviated symbol of C57BL/10 and A the abbreviated symbol of A/J.
  3. Nucleotide G, at position 10 of TRBJ5 in AE000665, is deleted in X01018. This DELETION leads to a frameshift. However it is not excluded that V-D-J rearrangements allow to reestablish the normal ORF. In those cases, the STOP-CODON needs to be eliminated by the rearrangements. For these reasons the TRBJ1-5*02 is considered as functional.
  4. Non canonical J-REGION: Phe-Ala-X-Gly instead of Phe-Gly-X-Gly.
  5. Non canonical J-REGION: His-Gly-X-Gly instead of Phe-Gly-X-Gly. Non canonical DONOR-SPLICE: ATA instead of NGT.
IMGT references: ↑
  1. Bahk Y.Y. et al., Association between susceptibility to Theiler's virus-induced demyelination and T-cell receptor Jbeta1-Cbeta1 polymorphism rather than Vbeta deletion, J. Virol, vol. 71, no. 5, 1997, pp. 4181-4185. PUBMED: 9094705
  2. Chen F. et al., Differential transcriptional regulation of individual TCR V beta segments before gene rearrangement, J. Immunol, vol. 166, no. 3, 2001, pp. 1771-1780. PUBMED: 11160223
  3. Church,D.M. et al., Lineage-specific biology revealed by a finished genome assembly of the mouse, PLoS Biol (2009), PUBMED: 19468303
  4. Church,D.M. et al., Modernizing reference genome assemblies, PLoS Biol, vol. 9, no. 7, 2011, PUBMED: 21750661
  5. Gascoigne N.R. et al., Genomic organization and sequence of T-cell receptor beta-chain constant- and joining-region genes, Nature, vol. 310, no. 5976, 1984, pp. 387-391. DOI: 10.1038/310387a0
  6. Malissen M. et al., Mouse T cell antigen receptor: structure and organization of constant and joining gene segments encoding the beta polypeptide, Cell, vol. 37, no. 3, 1984, pp. 1101-1110. DOI: 10.1016/0092-8674(84)90444-6
  7. Morinaga T. et al., Isolation of cDNA clones encoding a T-cell receptor beta-chain from a beef insulin-specific hybridoma, Proc. Natl. Acad. Sci. U.S.A, vol. 82, no. 23, 1985, pp. 8163-8167. PUBMED: 3906657
  8. Rowen L. et al., Comparison of the human and mouse T cell receptor beta and trypsinogen loci, Unpublished.
  9. Rowen L. et al., Sequence of the mouse T cell receptor locus, Unpublished.
  10. Sherman D.H, Unpublished.
  11. Sherman D.H. et al., Molecular analysis of antigen recognition by insulin-specific T-cell hybridomas from B6 wild-type and bm12 mutant mice, Mol. Cell. Biol, vol. 7, no. 5, 1987, pp. 1865-1872. PUBMED: 2439899
  12. Siu G. et al., The structure, rearrangement and expression of D beta gene segments of the murine T-cell antigen receptor, Nature, vol. 311, no. 5984, 1984, pp. 344-350. DOI: 10.1038/311344a0