IMGT Repertoire (IG and TR)

Gene table: house mouse (Mus musculus) TRAJ

Here you are: IMGT Web resources > IMGT Repertoire (IG and TR) > 1. Locus and genes

• Fct: FUNCTIONALITY
  • F: Functional
  • P: Pseudogene
  • ORF: Open Reading Frame
• R: Rearranged
• T: Transcribed
• Pr: Translated into protein

"+" 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.

Click on:

• IMGT gene name to get the corresponding IMGT/GENE-DB entry,
• IMGT allele name to see the corresponding Alignments of alleles,
• accession number to get the corresponding IMGT/LIGM-DB entry.

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 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 Phe (or Trp)-Gly-X-Gly motif.
2. (2) Non canonical J-NONAMER: GGCTTCTTC instead of GGTTTTTGT. Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).
3. (3) In coding_start2, the one used by the human TRAJ7 gene, non canonical J-REGION: Leu-Gly-X-Gly instead of Phe-Gly-X-Gly. In coding_start1, canonical J-REGION: 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-REGION: Ser-Gly-X-Glu instead of Phe-Gly-X-Gly.
5. (5) Non canonical J-HEPTAMER: CCTGTG instead of CACTGTG, and non canonical J-REGION: Val-Glu-X-Val instead of Phe-Gly-X-Gly. Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).
6. (6) Non canonical J-HEPTAMER: CACTGTA instead of CACTGTG, and non canonical J-REGION: 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-REGION: 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-REGION: 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-REGION: Leu-Gly-X-Gly instead of Phe-Gly-X-Gly.
12. (12) Non canonical J-REGION: Cys-Gly-X-Gly instead of Phe-Gly-X-Gly.
13. (13) Non canonical J-NONAMER: TTTGGGATT instead of GGTTTTTGT, non canonical J-HEPTAMER: GCCCATC instead of CACTGTG, and non canonical J-REGION: Phe-Ala-X-Gly instead of Phe-Gly-X-Gly. Defective DONOR-SPLICE (NNGT instead of NGT, with splicing occurring before G in both cases).
14. (14) B10.D2-H2^dm1 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) Defective DONOR-SPLICE (GTN instead of NGT, with splicing occurring before G in both cases).
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

See also (IMGT Scientific chart):

• IMGT reference sequences
• IMGT/LIGM-DB standardized labels
• IMGT gene name nomenclature for IG and TR of human and other vertebrates
• IMGT allele nomenclature for sequence polymorphisms
• IMGT annotation rules

Created: 18/09/1998
Last updated: 21/12/2012
Authors: Dominique Scaviner
Editor: Chantal Ginestoux

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