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"+" 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 between 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.
Functionality is shown between brackets, [F] and [P], when the accession number refers to genomic DNA, but not known as being germline or rearranged.

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TRAJ segments are designated by a number according to their localisation from 3' to 5'. Ortholog SEGMENTs in human and mouse have the same numbers.
Invariant TRAV11-TRAJ18 (previously Valpha14-Jalpha281), NK T rearrangements (see Gene table: House mouse (Mus musculus) TRAV).

IMGT gene name IMGT allele name Fct Chromosomal localization R T Pr Positions in the locus IMGT/LIGM-DB reference sequences IMGT/LIGM-DB sequences from the literature
Strain Clone names Accession numbers Positions in the sequence (J-REGION) Secondary accession numbers Strain Clone names Accession numbers Positions in the sequence (J-REGION)
TRAJ1 TRAJ1*01 P (1) 14 (19.7 cM) - - - 83901-85000 (23) B10.D2-H2dm1 (14,18) J1 M64239 [1,18] (18) 84393-84421
TRAJ2 TRAJ2*01 F 14 (19.7 cM) + + 83200-83900 (23) B10.D2-H2dm1 J2 M64239 [1,18] 83418-83483
TRAJ2*02 F 14 (19.7 cM) + + B10.A J-alpha 26 M38103 [2]
TRAJ3 TRAJ3*01 P (2) 14 (19.7 cM) 82401-83200 (23) B10.D2-H2dm1 J3 M64239 [1,18] 82877-82942
TRAJ4 TRAJ4*01 P (16) 14 (19.7 cM) 80601-82400 (23) B10.D2-H2dm1 J4 M64239 [1,18] 81880-81941 129/SvJ AE008686 [19] 449108-449169
AE007512 [19] 1653598-1653659
TRAJ4*02 F 14 (19.7 cM) C57BL/6Jdm1 J4 CT030634 182433-182505 C57BL/6J CT573018 (complement) 133632..133694
TRAJ5 TRAJ5*01 F 14 (19.7 cM) + + 78901-80600 (23) B10.A J6.19 M38105 [2] B10.D2-H2dm1 J5 M64239 [1,18] 79368-79429
TRAJ6 TRAJ6*01 F 14 (19.7 cM) + 77751-78900 (23) B10.D2-H2dm1 J6 M64239 [1,18] 78280-78341
TRAJ7 TRAJ7*01 ORF (3) 14 (19.7 cM) - 75801-77750 (23) B10.D2-H2dm1 J7 M64239 [1,18] 77064-77122
TRAJ8 TRAJ8*01 P (1) 14 (19.7 cM) 75301-75800 (23) B10.D2-H2dm1 M64239 [7] 75508-75543
TRAJ9 TRAJ9*01 F 14 (19.7 cM) + + 73001-76050 (23) BALB/c BDFL II X03761 [3] B10.D2-H2dm1 J8 M64239 [1,18] 74984-75041
TRAJ9*02 (F) 14 (19.7 cM) + + C57BL/Ka X02933 [8] #c
TRAJ10 (21) TRAJ10*01
TRAJ11 TRAJ11*01 F 14 (19.7 cM) - 72351-73000 (23) B10.D2-H2dm1 J9 M64239 [1,18] 72734-72792
TRAJ12 TRAJ12*01 F 14 (19.7 cM) + + 71801-72350 (23) B10.D2-H2dm1 J10 M64239 [1,18] 72149-72207
TRAJ13 TRAJ13*01 F 14 (19.7 cM) + + 70850-71800 (23) B10.D2-H2dm1 J11 M64239 [1,18] 71338-71394
TRAJ14 TRAJ14*01 P (1) 14 (19.7 cM) 70501-70850 (23) B10.D2-H2dm1 M64239 [1,18] 70708-70741
TRAJ15 TRAJ15*01 F 14 (19.7 cM) + + 69201-70500 (23) B10.D2-H2dm1 J12 M64239 [1,18] 70014-70073
TRAJ16 TRAJ16*01 F 14 (19.7 cM) + + 67901-69200 (23) B10.D2-H2dm1 J-alpha 84 X03057 [4] B10.D2-H2dm1 J13 M64239 [1,18] 68729-68789
TRAJ17 TRAJ17*01 F 14 (19.7 cM) + 66501-67900 (23) B10.D2-H2dm1 J14 M64239 [1,18] 67370-67432
TRAJ18 TRAJ18*01 F 14 (19.7 cM) + + 66301-66500 (23) B10.D2-H2dm1 J15 M64239 [1,18] 66372-66437
TRAJ19 TRAJ19*01 ORF (4) 14 (19.7 cM) 65151-66300 (23) B10.D2-H2dm1 M64239 [7] 65983-66043
TRAJ20 TRAJ20*01 P (5) 14 (19.7 cM) 64901-65150 (23) B10.D2-H2dm1 M64239 [7] 65039-65096
TRAJ21 TRAJ21*01 F 14 (19.7 cM) + + 63501-64900 (23) B10.D2-H2dm1 J16 M64239 [1,18] 64387-64443
(F) 14 (19.7 cM) + + C57BL/10 X52448 [9] #c
TRAJ22 TRAJ22*01 F 14 (19.7 cM) + + 61801-63500 (23) B10.D2-H2dm1 J17 M64239 [1,18] 62853-62912
TRAJ23 TRAJ23*01 F 14 (19.7 cM) + + 61501-61800 (23) B10.D2-H2dm1 J18 M64239 [1,18] 61686-61745
TRAJ24 TRAJ24*01 F 14 (19.7 cM) + + 60800-61500 (23) B10.D2-H2dm1 J19 M64239 [1,18] 61244-61305
TRAJ25 TRAJ25*01 ORF (6) 14 (19.7 cM) 60201-60800 (23) B10.D2-H2dm1 M64239 [7] 60421-60477
TRAJ26 TRAJ26*01 F (19) 14 (19.7 cM) + 59001-60200 (23) B10.D2-H2dm1 J20 M64239 [1,18] 60097-60155
TRAJ27 TRAJ27*01 F 14 (19.7 cM) + + 57601-59000 (23) B10.D2-H2dm1 J21 M64239 [1,18] 57913-57971
TRAJ28 TRAJ28*01 F 14 (19.7 cM) + 57001-57600 (23) Std:ddY J1031 X17177 [5] B10.D2-H2dm1 J22 M64239 [1,18] 57270-57334
TRAJ29 TRAJ29*01 ORF (8) 14 (19.7 cM) 56101-57000 (23) B10.D2-H2dm1 M64239 [7] 56554-56613
TRAJ30 TRAJ30*01 F 14 (19.7 cM) + + 54301-56100 (23) B10.D2-H2dm1 J23 M64239 [1,18] 55477-55535
TRAJ31 TRAJ31*01 F 14 (19.7 cM) + + 52001-54300 (23) B10.D2-H2dm1 J24 M64239 [1,18] 53507-53563
TRAJ31*02 (F) 14 (19.7 cM) + + C57BL/6 M16677 [11] (20) #c BALB/c AY639036 [13] (20) #c
TRAJ32 TRAJ32*01 F 14 (19.7 cM) + + 51301-52000 (23) B10.D2-H2dm1 J-alpha TT11 X02858 [4] B10.D2-H2dm1 J25 M64239 [1,18] 51716-51781
TRAJ32*02 (F) 14 (19.7 cM) + + FVB/N BC030392 [12] (20) #c BALB/c AY639038 [13] (20) #c
M31647 [14] (20) #c
X01133 [15] (20) #c
TRAJ33 TRAJ33*01 F 14 (19.7 cM) + + 50501-51300 (23) B10.D2-H2dm1 J26 M64239 [1,18] 50978-51034
TRAJ34 TRAJ34*01 F 14 (19.7 cM) + + 50001-50500 (23) BALB/c J1 X02862 [6] B10.D2-H2dm1 J27 M64239 [1,18] 50319-50376
TRAJ34*02 (F) 14 (19.7 cM) + + B10.S/9R M20875 [10] #c
TRAJ35 TRAJ35*01 F 14 (19.7 cM) + + 48401-50000 (23) B10.D2-H2dm1 J-alpha pHDS58 X03056 [4] B10.D2-H2dm1 J28 M64239 [1,18] 49394-49458
TRAJ35*02 F (15) 14 (19.7 cM) + + BALB/c J2 X02843 [6]
TRAJ36 TRAJ36*01 P (9) 14 (19.7 cM) - - - 47401-48400 (23) B10.D2-H2dm1 J29 M64239 [1,18] 48023-48085
TRAJ37 TRAJ37*01 F 14 (19.7 cM) + + 46701-47400 (23) B10.D2-H2dm1 J30 M64239 [1,18] 47140-47199
TRAJ38 TRAJ38*01 F 14 (19.7 cM) + + 45901-46700 (23) B10.D2-H2dm1 J31 M64239 [1,18] 46196-46257
TRAJ39 TRAJ39*01 F 14 (19.7 cM) + + 44601-45900 (23) B10.D2-H2dm1 J32 M64239 [1,18] 45584-45646
TRAJ40 TRAJ40*01 F 14 (19.7 cM) + + 42501-44600 (23) B10.D2-H2dm1 J-alpha 19 X03058 [4] B10.D2-H2dm1 J33 M64239 [1,18] 43547-43607
TRAJ41 TRAJ41*01 ORF (10) 14 (19.7 cM) 41701-42500 (23) B10.D2-H2dm1 M64239 [7] 41898-41952
TRAJ42 TRAJ42*01 F 14 (19.7 cM) + + 41001-42500 (23) B10.D2-H2dm1 J34 M64239 [1,18] 41400-41463
TRAJ42*02 (F) 14 (19.7 cM) + + C57BL/6 M16675 [11] #c
TRAJ43 TRAJ43*01 F 14 (19.7 cM) + 39901-41000 (23) B10.D2-H2dm1 J35 M64239 [1,18] 40361-40417
TRAJ43*02 (F) 14 (19.7 cM) + + DBA/2 X55823 [9] #c
TRAJ44 TRAJ44*01 ORF (11) 14 (19.7 cM) + + 39001-39900 (23) B10.D2-H2dm1 J36 M64239 [1,18] 39312-39372
TRAJ45 TRAJ45*01 F 14 (19.7 cM) + + 38201-39000 (23) B10.D2-H2dm1 J-alpha 80 X02859 [4] B10.D2-H2dm1 J37 M64239 [1,18] 38450-38512
TRAJ45*02 (F) 14 (19.7 cM) + + M34206 [16] (20) #c M55635 [17] (20) #c
TRAJ46 TRAJ46*01 P (17) 14 (19.7 cM) 37701-38200 (23) B10.D2-H2dm1 J38 M64239 [1,18] 37958-38019
TRAJ47 TRAJ47*01 ORF (12) 14 (19.7 cM) 36501-38000 (23) B10.D2-H2dm1 J39 M64239 [1,18] 37422-37478
TRAJ48 TRAJ48*01 F 14 (19.7 cM) + + 34901-36500 (23) B10.D2-H2dm1 J40 M64239 [1,18] 35436-35496
TRAJ49 TRAJ49*01 F 14 (19.7 cM) + + 34301-34900 (23) B10.D2-H2dm1 J-alpha 65 X03059 [4] B10.D2-H2dm1 J41 M64239 [1,18] 34318-34376
TRAJ50 TRAJ50*01 F 14 (19.7 cM) + + 32601-34300 (23) B10.D2-H2dm1 J42 M64239 [1,18] 33227-33289
TRAJ51 TRAJ51*01 P (1) 14 (19.7 cM) 31501-32600 (23) B10.D2-H2dm1 M64239 [7] 31879-31920
TRAJ52 TRAJ52*01 F 14 (19.7 cM) + + 29701-31500 (23) B10.D2-H2dm1 J44 M64239 [1,18] 30956-31021
TRAJ53 TRAJ53*01 F 14 (19.7 cM) + 28001-29700 (23) B10.D2-H2dm1 J45 M64239 [1,18] 28282-28347
TRAJ54 (22) TRAJ54*01 P (9) 14 (19.7 cM) 27401-28000 (23) B10.D2-H2dm1 J46 M64239 [1,18] 27632-27685
TRAJ55 TRAJ55*01 P (7) 14 (19.7 cM) + 26000-27400 (23) B10.D2-H2dm1 M64239 [7] 27083-27145
TRAJ56 TRAJ56*01 F 14 (19.7 cM) + + 24601-26000 (23) B10.D2-H2dm1 J47 M64239 [1,18] 24907-24969
TRAJ57 TRAJ57*01 F 14 (19.7 cM) + + 23601-24600 (23) B10.D2-H2dm1 J48 M64239 [1,18] 24150-24212
TRAJ58 TRAJ58*01 F 14 (19.7 cM) + + 22401-23600 (23) B10.D2-H2dm1 J49 M64239 [1,18] 22926-22988
TRAJ59 TRAJ59*01 P (13) 14 (19.7 cM) 21701-22400 (23) B10.D2-H2dm1 M64239 [7] 21779-21840
TRAJ60 TRAJ60*01 P (9) 14 (19.7 cM) 21101-21700 (23) B10.D2-H2dm1 M64239 [7] 21579-21632
TRAJ61 TRAJ61*01 P (9) 14 (19.7 cM) - - - 17701-21100 (23) B10.D2-H2dm1 J50 M64239 [1,18] 20652-20723

#c: rearranged cDNA.

IMGT notes:
  1. (1) Pseudogene because germline J-GENE only identified by the presence of the recombination signal upstream of an open reading frame, but without donor splicing site in 5' and without the conserved J-MOTIF Phe (or Trp)-Gly-X-Gly motif.
  2. (2) Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).Non canonical J-NONAMER: GGCTTCTTC instead of GGTTTTTGT.
  3. (3) In coding_start2, the one used by the human TRAJ7 gene, non canonical J-MOTIF: Leu-Gly-X-Gly instead of Phe-Gly-X-Gly. In coding_start1, canonical J-MOTIF: Phe-Gly-X-Gly, but defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).
  4. (4) Non canonical J-HEPTAMER: AAATCTG instead of CACTGTG, and non canonical J-MOTIF: Ser-Gly-X-Glu instead of Phe-Gly-X-Gly.
  5. (5) Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).Non canonical J-HEPTAMER: GCCTGTG instead of CACTGTG, and non canonical J-MOTIF: Val-Glu-X-Val instead of Phe-Gly-X-Gly.
  6. (6) Non canonical J-HEPTAMER: CACTGTA instead of CACTGTG, and non canonical J-MOTIF: Phe-Gly-X-Trp instead of Phe-Gly-X-Gly.
  7. (7) Frameshift in J-REGION.
  8. (8) Non canonical J-NONAMER: GGGGATGAG instead of GGTTTTTGT, and non canonical J-MOTIF: Leu-Gly-X-Glu instead of Phe-Gly-X-Gly.
  9. (9) STOP-CODON in J-REGION.
  10. (10) Non canonical J-NONAMER: GAGGTTGTG instead of GGTTTTTGT, and non canonical J-MOTIF: Leu-Ala-X-Gly instead of Phe-Gly-X-Gly. Defective DONOR-SPLICE (GTN instead of NGT, with splicing occurring before G in both cases).
  11. (11) Non canonical J-MOTIF: Leu-Gly-X-Gly instead of Phe-Gly-X-Gly.
  12. (12) Non canonical J-MOTIF: Cys-Gly-X-Gly instead of Phe-Gly-X-Gly.
  13. (13) Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases). Non canonical J-NONAMER: TTTGGGATT instead of GGTTTTTGT, non canonical J-HEPTAMER: GCCCATC instead of CACTGTG, and non canonical J-MOTIF: Phe-Ala-X-Gly instead of Phe-Gly-X-Gly.
  14. (14) B10.D2-H2dm1 is a congenic strain, B10 is the abbreviated symbol of C57BL/10 and D2 the abbreviated symbol of DBA/2J
  15. (15) INSERTION of one nucleotide G, between positions 6 and 7. This INSERTION may represent a sequencing error. This INSERTION may represent a sequencing error. There is also the possibility that the nucleotide deletion in 5' of the J-REGION, during the V-J rearrangement, deletes the nucleotides up to the extra G included as in the productive cDNA X01134 (N. Bosc and M.-P. Lefranc, 28/01/2002).
  16. (16) Defectuous DONOR-SPLICE '|GT' instead of 'N|GT' due to the deletion of one nucleotide g between positions 50 and 51 in J-REGION. The four amino acids in 3' are in a reading frame different from the one expected ('LCAH' instead of 'AVCP').
  17. (17) Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).
  18. (18) Strain of M64239 is according to [1,18]. The flat file up to March 2000 has no information on the strain. Strain BALB/c was added in EMBL flat file in release 62 (03 March 2000) but without explanation.
  19. (19) The deletion of c26 in the TRAJ26 J-REGION, in M64239 and AE008686, is probably due to a sequencing error. The functionality of TRAJ26 was changed (on 19/01/2007) from pseudogene (due to a frameshift) to functional.
  20. (20) Potentiel allele base on the finding of several sequences in cDNA (IMGT Annotation: Yan Wu, Géraldine Folch, Marie-Paule Lefranc 19/01/2009).
  21. (21) No TRAJ10 has been identified in the mouse[7].
  22. (22) LIGM annotation based on reference [1,18].
  23. (23) These J-GENEs have been identified by Dominique Scaviner (LIGM) based on information provided in reference [7].
IMGT references:
  1. [1] Wilson R.K. et al., Genomics, 13, 1198-1208 (1992). PMID: 1505953
  2. [2] Hue I. et al., J. Immunol., 144, 4410-4419 (1990). PMID: 2160502
  3. [3] Dembic Z. et al., Nature, 320, 232-238 (1986). PMID: 2421164
  4. [4] Winoto A. et al., Nature, 316, 832-836 (1985). PMID: 2993908
  5. [5] Toda M. et al., J. Mol. Biol., 202, 219-231 (1988). PMID: 3172216
  6. [6] Hayday A.C. et al., Nature, 316, 828-832 (1985). PMID: 2993907
  7. [7] Koop B.F. et al., Genomics, 19, 478-493 (1994). PMID: 8188290
  8. [8] Arden B. et al., Nature, 316, 783-787 (1985). PMID: 3839904
  9. [9] Danska J.S. et al., J. Exp. Med., 172, 27-33 (1990). PMID: 1694219
  10. [10] McElligott D.L. et al., J. Immunol., 140, 4123-4131 (1988). PMID: 2453567
  11. [11] Spinella D.G. et al., J. Immunol., 138, 3991-3995 (1987). PMID: 2953795
  12. [12] Strausberg R.L. et al., Proc. Natl. Acad. Sci. U.S.A., 99, 16899-16903 (2002). PMID: 12477932
  13. [13] Hanyecz A. et al., Arthritis Rheum., 48, 2959-2973 (2003). PMID: 14558103
  14. [14] Heuer J. et al., J. Immunol., 146, 775-782 (1991). PMID: 1846162
  15. [15] Chien Y. et al., Nature, 312, 31-35 (1984). PMID: 6548551
  16. [16] Taylor A.H. et al., J. Exp. Med., 172, 1643-1651 (1990). PMID: 1701821
  17. [17] Nakajima P.B. et al., Immunogenetics, 35, 190-198 (1992). PMID: 1371499
  18. [18] Koop, B.F. et al., Genomics, 13, 1209-1230 (1992). PMID: 1505954
  19. [19] Lee I.Y. et al., Unpublished (1998).
Created:
18/09/1998
Last updated:
14/06/2018
Authors:
Joumana Jabado Michaloud and Dominique Scaviner
Editor:
Chantal Ginestoux