IMGT Repertoire (IG and TR)


Assignment of rearranged cDNAs and gDNAs to germline genes: Mouse (Mus musculus) TRAJ

In this table are listed representative rearranged complementary DNAs (cDNAs) and genomic DNAs (gDNAs).

Rearranged cDNAs (#c) and gDNAs (#g) TRAJ sequences have been assigned to IMGT TRAJ genes and alleles as described in Germline gene tables, Alignments of alleles and Tables of alleles.
Assignments were performed using IMGT/V-QUEST.

Click here for Assignement of rearranged cDNAs and gDNAs to germline genes: Mouse (Mus musculus TRAV).

For Mouse (Mus musculus) TRAJ1, TRAJ3, TRAJ8, TRAJ14, TRA19, TRA20, TRA25, TRA26, TRA29, TRA36, TRAJ41, TRAJ46, TRAJ47, TRAJ51, TRAJ54, TRAJ55, TRAJ59 and TRAJ60, no rearanged cDNA was found, in agreement with their functionality (P or ORF) and/or the defect in their sequence.
No TRAJ10 has been identified in the mouse.

TRAJ
gene name		 Reference sequences Rearranged cDNAs and gDNAs CDR lengths JUNCTION (1)
Allele name Strain (5) Accession numbers Clone name Strain Accession numbers
TRAJ1 TRAJ1*01 B10.D2-H2dm1 M64239
TRAJ2 TRAJ2*01 B10.D2-H2dm1 M64239[1] TA26 C57B1/Ka X02930 (2) -
TRAJ2*02 B10.A M38103 J6.19 B10.A M38102 [43]#g [5.4.10] +
TRAJ3 TRAJ3*01 B10.D2-H2dm1 M64239 [1]
TRAJ4 TRAJ4*01 B10.D2-H2dm1 M64239 [1] HL228 M61133 [46]#c [6.6.13] +
M14T-1 BALB/c M33587 [42]p5'#c [x.4.13] +
7/6AH1 BALB/c M34216 [41]p5'#c [x.4.12] +
D10 AKR U83242 [102]p5'#c [6.6.10] +
TRAJ5 TRAJ5*01 B10.A M38105 A26 BALB/c M22660 [26]#c [8.6.13] +
M14T-1 BALB/c M33589 [42]p5'#c [x.6.x] -
TRAJ6 TRAJ6*01 B10.D2-H2dm1 M64239 [1] Hb(46-76)/I-Ek B10.BR U46581 [56]#c [5.6.11] +
C9 C57BL/6 X56717 [47]#c [6.4.13] +
SJL-HE-1.1 SJL/J X57397 [50]#c [6.6.8] +
M14T-6 BALB/c M33590 [42]p5'#c [x.6.12] +
M14T-7 BALB/c M33591 [42]p5'#c [x.6.12] +
TRAJ7 TRAJ7*01 B10.D2-H2dm1 M64239 [1] B2-13 C57BL/6 X56716 [47]p5'#c [x.4.12] +
TRAJ8 TRAJ8*01 B10.D2-H2dm1 M64239 [7]
TRAJ9 TRAJ9*01 BALB/c X03761 5B6 SJL U07658 [66]#c [6.6.11] +
SPL1.1 SJL U07654 [66]#c [6.6.13] +
TRAJ9*02 C57BL/Ka X02933 TA72 C57BL/ka X02933 [6.6.11] +
TRAJ10 (6)
TRAJ11 TRAJ11*01 B10.D2-H2dm1 M64239 [1] CD3+,4+,5+,8- BALB/c X67127 [63]#c [5.4.12] +
TRAJ12 TRAJ12*01 B10.D2-H2dm1 M64239 [1] 5/10-20D C57BL/10 X05733 [12]#c [6.5.11] +
Q1.1B6 SJL AF037038 [94]#c [6.5.10] +
8/10-2 C57BL/10 X05732 [12]#c [6.4.12] +
TRAJ13 TRAJ13*01 B10.D2-H2dm1 M64239 [1] BB1.D5 C57BL/10 M16676 [13]#c [8.6.10] +
PL214.12 B10.PL M21863 [25]#c [6.6.11] +
TA39 C57BL/Ka X02929 [2]#c [6.6.9] +
PL23.1 B10.PL M21857 [25]#c [6.6.11] +
PL51.4.1 B10.PL M21858 [25]#c [6.6.11] +
PL83.12 B10.PL M21859 [25]#c [6.6.11] +
PL127.6 B10.PL M21860 [25]#c [6.6.11] +
PL172.10 B10.PL M21861 [25]#c [6.6.11] +
PL183.2 B10.PL M21862 [25]#c [6.6.11] +
PL23.1 SJL/J M35486 [6.6.11] +
    M35487 [34]#c [6.6.11] +
    M35488 [34]#c [6.6.11] +
    M35489 [34]#c [6.6.11] +
    M35490 [34]#c [6.6.11] +
    M35491 [34]#c [6.6.11] +
TRAJ14 TRAJ14*01 B10.D2-H2dm1 M64239 [1]
TRAJ15 TRAJ15*01 B10.D2-H2dm1 M64239 [1] 4000 SJL U07659 [66]#c [5.4.11] +
F5 C57BL/6 X14387 [33]#c [6.6.12] +
N30.7 C57BL/6 U95921 [81]#c [6.6.12] +
TRAJ16 TRAJ16*01 B10.D2-H2dm1 X03057 2H10 B10.A M73262 [48]#c [5.4.12] +
B10 B10.A X03860 [6]#c [5.4.12] +
CF.6 B10.A X03858[6]#c [5.4.11] +
4.C3 B10.A X03861[6]#c [5.4.12] +
pXTL63 C57BL/10 D16596 [64]p5'#c [x.x.14] +
TA84 C57BL/Ka X02926 [2]#c [6.5.13] +
RF33.21.22 C57BL/6 L34678 [79]#c [6.6.12] +
TRAJ17 TRAJ17*01 B10.D2-H2dm1 M64239 [1] pXTL66 C57BL/10 D16599 [64]p5'#c [x.4.11] +
TRAJ18 TRAJ18*01 B10.D2-H2dm1 M64239 [1] 1B8 BALB/c M98568 [58]#c [6.4.x] -
2-3-B9 BALB/cJ U05047 [85]#c [6.4.13] +
S518-5a BALB/c U21415 [75]p5'#c [5.4.13] +
FN1-18 C57BL/6 M13376 [9]p5'#c [5.4.11] +
TRAJ19 TRAJ19*01 B10.D2-H2dm1 M64239 [7]
TRAJ20 TRAJ20*01 B10.D2-H2dm1 M64239 [7]
TRAJ21 TRAJ21*01 B10.D2-H2dm1 M64239 [1] 50,01 C57BL/10 X52448 [45]#c [6.6.12] +
C11.A2 B10.A x AKR M26423 [35]p5'#c [6.5.10] +
TRAJ21*02 C57BL/10 X52448
TRAJ22 TRAJ22*01 B10.D2-H2dm1 M64239 [1] N2-36 B10.BR M73761 [54]p5'#c [6.6.12] +
3D1 BALB/c U05048[85]#c [7.4.12] +
TRAJ23 TRAJ23*01 B10.D2-H2dm1 M64239[1] C9 C57BL/6 X05734 [12]#c [6.4.12] +
TRAJ24 TRAJ24*01 B10.D2-H2dm1 M64239 [1] BL4L-30 C57BL/6 D12897 [62]p5'#c [x.4.12] +
TRAJ25 TRAJ25*01 B10.D2-H2dm1 M64239 [7]
TRAJ26 TRAJ26*01 B10.D2-H2dm1 M64239 [1]
TRAJ27 TRAJ27*01 B10.D2-H2dm1 M64239 [1] MT1-6 BALB/c M34202 [41]p5'#c [6.6.13] +
TA61 C57BL/Ka X02936 [2](4)#c [x.6.11] +
TRAJ28 TRAJ28*01 Std:ddY X17177 pXTL64 B10 D16597
TRAJ29 TRAJ29*01 B10.D2-H2dm1 M64239 [7]
TRAJ30 TRAJ30*01 B10.D2-H2dm1 M64239 [1] MA25 C3H AJ311366 [30]#c [6.6.11] +
7H5 BALB/c M98566 [58]p5'#c [x.6.12] +
HD8 BALB/c L16803 [68]p5'#c [x.5.10] +
1B8 BALB/c M98567 [58]p5'#c [x.6.11] +
1C6 BALB/c M98569 [58]p5'#c [6.6.x] -
L-9.10 SWR x NZB (F1) U07878 [67]#c [6.6.10] +
TRAJ31 TRAJ31*01 B10.D2-H2dm1 M64239 [1] TA39 C57BL/Ka X02969 [3]#c [6.6.9] +
HD3 BALB/c L16801 [68](3)p5'#c [x.6.10] +
  BALB/c M29272 [37]#c [6.6.10] +
BW51H7 AKR X16935 [40]#c [6.6.10] +
TRAJ32 TRAJ32*01 B10.D2-H2dm1 X02858 5/10-20K C57BL/10 X05012 [12]#c [6.6.15] +
BN4-3 C57BL/6 x CBA (F1) AF296661 [104]#c [7.4.15] +
TRAJ33 TRAJ33*01 B10.D2-H2dm1 M64239 [1] MT113 Std:ddY X05492
TRAJ34 TRAJ34*01 B10.D2-H2dm1 M64239 [1] BALB/c X02862
TRAJ34*02 B10.S/9R M20875 5C.C7 B10.A X03859[6]#c [5.4.12] +
B5-46 C57BL/6 X56707 [47]#c [6.4.12] +
C9 C57BL/6 X56712 [47]#c [6.4.12] +
C7 C57BL/6 D45221 [73]p5'#c [6.4.12] +
C7 C57BL/6 D45225 [73]p5'#c [6.4.12] +
6.9R.D6 B10.S/9R M20875 [21]p5'#c [5.4.11] +
A2-21 B10.BR M73765 [54]p5'#c [x.6.12] +
TRAJ35 TRAJ35*01 B10.D2-H2dm1 X03056
TRAJ35*02 BALB/c X02843 pHDS58 BALB.B E01014 [7]#c [6.4.10] +
LD3 BALB/c M34196 [41]#c [6.6.12] +
TRAJ36 TRAJ36*01 B10.D2-H2dm1 M64239 [1]
TRAJ37 TRAJ37*01 B10.D2-H2dm1 M64239 [1] SJL AF012190
TRAJ38 TRAJ38*01 B10.D2-H2dm1 M64239 [1] X03668
TRAJ39 TRAJ39*01 B10.D2-H2dm1 M64239 [1] SB1-180 BALB/c U21451 [74]#c [7.6.13] +
F3-26 C57BL/6 X04330 [4]#c [6.6.10] +
42H11 C57BL/6 M16118[14]#c [7.4.13] +
TRAJ40 TRAJ40*01 B10.D2-H2dm1 X03058 H-2I-A NOD U80816 [89]#c [6.6.10] +
MR1.3 C57BL/6 x DBA/2 (F1) AF126456 [100]#c [5.6.10] +
pXTL72 C57BL/10 D16605 [64]p5'#c [x.x.10] +
TRAJ41 TRAJ41*01 B10.D2-H2dm1 M64239 [7]
TRAJ42 TRAJ42*01 B10.D2-H2dm1 M64239 [1] pXTL68 C57BL/10 D16601 [64]p5'#c [x.x.11] +
TRAJ42*02 C57BL/6 M16675 DA.33.C2 C57BL/6 M16675 [13]#c [6.6.14] +
4C1 BALB/c M98574 [58]p5'#c [6.6.13] +
TRAJ43 TRAJ43*01 B10.D2-H2dm1 M64239 [1] N2-7 B10.BR M73762 [54]p5'#c [x.6.11] +
TRAJ43*02 DBA/2 X55823 8,2 X55823 [44]p5'#c [6.6.11] +
TRAJ44 TRAJ44*01 B10.D2-H2dm1 M64239 [1]
TRAJ45 TRAJ45*01 B10.D2-H2dm1 X02859 TA80 C57BL/Ka X02939 [2]p5'#c [6.6.x] -
P14A.1 B10.BR X06773 [11]#c [5.6.x] -
TRAJ46 TRAJ46*01 B10.D2-H2dm1 M64239 [1]
TRAJ47 TRAJ47*01 B10.D2-H2dm1 M64239 [1]
TRAJ48 TRAJ48*01 B10.D2-H2dm1 M64239 [1] MDA BALB/c X02967 [3]#c [6.6.10] +
TA31 C57BL/Ka X02928 [2]#c [6.5.x] -
NA5 BALB/c M27352 [10]#c [6.5.12] +
bm4T17.2 C57BL/6 M87852 [52]#c [6.4.11] +
  BALB/c M34194 [41]#c [6.4.11] +
L-9.2 SWR x NZB (F1) U07879 [67]#c [5.4.10] +
P14A-2 B10.BR X06771 [11]#c [6.6.10] +
1C6 BALB/c M98570[58]p5'#c [x.4.13] +
5.6.18 C57BL/6 M16119[14]#c [7.4.12] +
TRAJ49 TRAJ49*01 B10.D2-H2dm1 X03059 BN1-5 C57BL/6 x CBA (F1) AF296659 [104]#c [6.6.10] +
L-3A SWR x NZB (F1) U07877 [67]#c [6.6.x]
TA65 C57BL/Ka X02932 [2]#c [6.6.12] +
E1 BALB/c X63928 [3]#c [6.5.11] +
P71 BALB/c X02970 [3]#c [7.6.10] +
C57BL/6 AF034161 [92]p5'#c [x.x.15] +
TRAJ50 TRAJ50*01 B10.D2-H2dm1 M64239 [1] 9C217 BALB/c U88296[93]#c [6.6.11] +
TRAJ51 TRAJ51*01 B10.D2-H2dm1 M64239 [7]
TRAJ52 TRAJ52*01 B10.D2-H2dm1 M64239 [1] C5 C57BL/6 X63927 [3]#c [6.5.13] +
2E.5 SJL U07655 [66]#c [6.6.12] +
P1F12C4 BALB/c M34210 [41]#c [7.6.14] +
TRAJ53 TRAJ53*01 B10.D2-H2dm1 M64239 [1] S630-62a1 BALB/c U21448 [74]p5'#c [8.6.14] +
TRAJ54 (7) TRAJ54*01 B10.D2-H2dm1 M64239 [1]
TRAJ55 TRAJ55*01 B10.D2-H2dm1 M64239 [7]
TRAJ56 TRAJ56*01 B10.D2-H2dm1 M64239 [1] S322-507a BALB/c U21406 [75]#c [7.6.12] +
1E10 BALB/c M34214 [41]p5'#c [x.4.12] +
TRAJ57 TRAJ57*01 B10.D2-H2dm1 M64239 [1] Hb(64-76)/I-Ek CE/J U46580 [56]#c [6.6.13] +
TA27 C57BL/Ka X02935 [2]#c [7.4.15] +
TRAJ58 TRAJ58*01 B10.D2-H2dm1 M64239 [1] NA3(V2B4) BALB/c nu/nu M27351 [10]#c [5.4.12] +
TA1 C57BL/Ka X02934 [2]#c [7.4.12] +
TRAJ59 TRAJ59*01 B10.D2-H2dm1 M64239 [7]
TRAJ60 TRAJ60*01 B10.D2-H2dm1 M64239 [7]
TRAJ61 TRAJ61*01 B10.D2-H2dm1 M64239 [1] MT114 Std:ddY X17181

#c : rearranged cDNA
#g : rearranged genomic DNA

IMGT notes:
  1. (1) + indicates in-frame JUNCTION, - indicates out-of-frame JUNCTION, n.d. indicates not defined JUNCTION (for example for partial sequences), a blank indicates that the information is not relevant (germline gene).
  2. (2) Rearranged to TRAJ2*01 with a gene containing a long deletion of 126 bp which may be due to cloning artefact. (deletion of 127 bp and insertion of 1nt (a), assignment to TRAV9D-3 was made by alignment with X05732)
  3. (3) Mutations in FR2-IMGT (g140>t, c141>a, G47>V; a142>g, K48>E; g145>a, G49>S according to the IMGT numbering) are probably sequencing or typing errors.
  4. (4) Pseudogene because a DELETION of 3 nucleotides (a279-g281>del(3nt)#) leading to a frameshift in FR3-IMGT.
  5. (5) M37286 has a deletion of 134 nucleotides compared to the IMGT reference sequence TRAV15-2/DV6-2 (M37287). It is not known if these differences result from a cloning artefact and/or typing or sequencing error.
  6. (6) No TRAJ10 has been identified in the mouse [7].
  7. (7) LIGM annotation based on reference [1].
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Created:
17/11/2006
Last updated:
22/09/2023
Authors:
Yan Wu and Marie-Paule Lefranc