IMGT Repertoire (IG and TR)
Gene table: house mouse (Mus musculus) TRAV
Citing this page:
Bosc, N. and Lefranc, M.-P., Dev. Comp. Immunol., 27, 465-497 (2003)
PMID: 12697305
UPDATE: 30/04/2003
- 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.
In this table, are reported the 10 TRAV/DV genes identified so far:
- Eight TRAV/DV genes (TRAV4-4/DV10, TRAV6-7/DV9, TRAV13-4/DV7, TRAV14D-3/DV8, TRAV15D-1/DV6D-1, TRAV15-1/DV6-1, TRAV16D/DV11 and TRAV21/DV12) which have been found rearranged to TRAJ genes and to (D)J-GENEs of the TRD locus.
- TRAV15-2/DV6-2 and TRAV15D-2/DV6D-2, which are assigned to the TRAV15 subgroup on the basis of sequence alignment, although they have not yet been found rearranged to TRAJ genes.
This does not exclude that other TRAV genes may be found rearranged to TRDD-TRDJ.
Clones used for the complete sequencing of the TRA/TRD locus (see IMGT/GeneView and Accession numbers of the Reference sequences) were later used to construct four contigs: AE008683 to AE008686.
- AE008683 (404892 bp) contains TRAV1 to TRAV7D-3.
- AE008684 (400099 bp) contains TRAV6D-4 to TRAV7-3.
- AE008685 (400099 bp) contains TRAV6-4 to TRAV12-4.
- AE008686 (461875 bp) contains TRAV13-5 to TRAV23.
The original contigs (AE008683, AE008684, AE008685 and AE008686) have been merged in EMBL into one sequence of 1666365 bp (AE007512). The four contigs has become secondary accession number of AE007512 which is annotated.
In the TRA locus of Mus musculus C57BL/6J, there is an insertion of 300 kb between TRAV15D-3 and TRAV7-2, that corresponds to a triplication of part of the TRAV genes. The triplicated genes are indicated with the letter N in their name. They comprise 34 TRAV genes (of which 27 are functional and 7 are pseudogene).
The "invariant" TR alpha chain of the murine NK1.1+ (NKR-P1C, CD161) T cells which recognize CD1d results from the TRAV11-TRAJ18 (previously Valpha14-Jalpha281) rearrangement (it remains to be demonstrated if both the TRAV11 and TRAV11D genes, which have a 100 % identical V-REGION, are involved). CD161 is expressed by ~ 1 % of mouse T cells and a large fraction of these CD161+ T cells are invariant NK T cells [Exley, M.A. et al., Current Protocols in Immunology, Wiley, J. and Sons, New York, 14, 14.11.1-14.11.13 (2002)].
Click here for the Correspondence between nomenclatures.
#c: rearranged cDNA
#g: rearranged genomic DNA.
MAP: mapped sequences.
IMGT notes:
- (1) B10.A is a congenic strain (see MGD for Strain Nomenclature Guidelines), B10 is the abbreviated symbol of C57BL/10.
- (2) In frame STOP-CODON at codon 6 in FR1-IMGT (positions 16-18 in IMGT unique numbering), INSERTION of 1 nucleotide c in FR1-IMGT (between positions 54 and 55), DELETION of 2 nucleotides in FR3-IMGT (positions 221-222).
- (3) In frame STOP-CODON at codon 83 in FR3-IMGT (positions 247-249 in IMGT unique numbering).
- (4) INSERTION of 12 nucleotides CCCAGCTGGAGG in FR3-IMGT (between positions 293 and 294 in IMGT unique numbering). This INSERTION is a duplication of positions 280-293 (Bosc, N., IMGT comment, 01/02/2001) and may represent a sequencing error.
- (5) INIT-CODON not conserved in L-PART1: ATC instead of ATG.
- (6) In frame STOP-CODONs at codon 58 in CDR2-IMGT (positions 172-174 in IMGT unique numbering), at codons 99 and 104 in FR3-IMGT (positions 295-297 and 310-312), the 2nd-CYS is not conserved.
- (7) No L-PART1, in frame STOP-CODON at codon 5 in FR1-IMGT (positions 13-15 in IMGT unique numbering) and DELETION of 1 nucleotide in FR1-IMGT (position 42), DELETION of 6 nucleotides in frame (positions 229-234) and of 16 nucleotides in FR3-IMGT (position 262-277), STOP-CODON at codon 99 in FR3-IMGT (positions 295-297).
- (8) V-REGION is partial: AA 1 to 22 are missing (partial FR1-IMGT).
- (9) V-REGION is partial: AA 1 is missing (partial FR1-IMGT).
- (10) In frame STOP-CODONs at codon 58 in CDR2-IMGT (positions 172-174 in IMGT unique numbering) and at codon 99 in FR3-IMGT (positions 295-297).
- (11) No L-PART1, in frame STOP-CODON at codon 5 in FR1-IMGT (positions 13-15 in IMGT unique numbering) and DELETION of 1 nucleotide in FR1-IMGT (position 42) , DELETION of 6 nucleotides in frame (positions 229-234) and of 4 nucleotides in FR3-IMGT (positions 281-284), STOP-CODON at codon 99 in FR3-IMGT (positions 295-297).
- (12) Sterile transcript
- (13) V-REGION is partial: AA 1 to 15 are missing (partial FR1-IMGT).
- (14) V-GENE is partial: partial V-SPACER and no V-NONAMER.
- (15) V-REGION is partial: AA 1 to 10 are missing (partial FR1-IMGT).
- (16) V-REGION is partial: AA 1 to 25 are missing (partial FR1-IMGT).
- (17) V-REGION is partial: AA 1 to 8 are missing (partial FR1-IMGT).
- (18) V-REGION is partial: AA 1 to 9 are missing (partial FR1-IMGT).
- (19) DELETION of 1 nucleotide in CDR2-IMGT (position 83 in IMGT unique numbering).
- (20) V-REGION is partial: AA 1 to 11 are missing (partial FR1-IMGT).
- (21) V-REGION is partial: AA 1 to 69 are missing (no FR1-IMGT, no CDR1-IMGT, no FR2-IMGT, no CDR2-IMGT, partial FR3-IMGT).
- (22) V-REGION is partial: AA 1 to 19 are missing (partial FR1-IMGT).
- (23) V-REGION is partial: AA 1 to 44 are missing (no FR1-IMGT, no CDR1-IMGT, partial FR2-IMGT).
- (24) V-REGION is partial: AA 1 to 51 are missing (no FR1-IMGT, no CDR1-IMGT and partial FR2-IMGT).
- (25) No L-PART1, limits are from the first nucleotide to the last nucleotide of V-EXON.
- (26) No L-PART1 and frameshifts in V-REGION..
- (27) Although the V-HEPTAMER is unusual (CACAGTA instead of CACAGTG), the gene has been found rearranged and is therefore functional.
- (28) V-REGION is partial: AA 1 to 56 are missing (no FR1-IMGT, no CDR1-IMGT, no FR2-IMGT and partial CDR2-IMGT).
- (29) DELETION of 1 nucleotide in FR3-IMGT (position 299 in IMGT unique numbering). V-REGION is partial: AA 1 to 43 are missing (no FR1-IMGT, no CDR1-IMGT and partial FR2-IMGT).
- (30) V-REGION is partial: AA 1 to 38 are missing (no FR1-IMGT, no CDR1-IMGT and no FR2-IMGT).
- (31) V-REGION is partial: AA 1 and 2 are missing (partial FR1-IMGT).
- (32) Although the V-HEPTAMER is unusual (CACACTG instead of CACAGTG), the gene has been found rearranged and is therefore functional.
- (33) INSERTION of 1 nucleotide leads to a frameshift in L-PART1.
- (34) Although the V-HEPTAMER is unusual (CACCATG instead of CACAGTG), the gene has been found rearranged and is therefore functional.
- (35) V-REGION is partial: AA 1 and 2, 106 and 107 are missing (partial FR1-IMGT and partial CDR3-IMGT). It is not known if this sequence is an allele of TRAV11 or of TRAV11D (see note (49)).
- (36) V-REGION is partial: AA 1 to 42 are missing (no FR1-IMGT, no CDR1-IMGT and partial FR3-IMGT), DELETION of 3 nucleotides in frame in FR3-IMGT (positions 279-281 in IMGT unique numbering, S93 is encoded by TCG instead of TCA) .
- (37) ORF because unusual V-HEPTAMER sequence: CACAGCG instead of CACAGTG.
- (38) No L-PART1, V-REGION is partial: AA 1 to 3 are missing (partial FR1-IMGT), in frame STOP-CODONs at codon 40 in FR2-IMGT (positions 118-120 in IMGT unique numbering) and at codon 91 in FR3-IMGT (positions 271-273), DELETION of 9 nucleotides in FR3-IMGT (positions 296-304) leading to a frameshift.
- (39) V-REGION is partial: AA 1 to 4 are missing (partial FR1-IMGT), in frame STOP-CODON at codon 40 (positions 118-120 in IMGT unique numbering) and DELETION of 1 nucleotide in FR2-IMGT (position 149).
- (40) V-REGION is partial: AA 1 to 17 are missing (partial FR1-IMGT).
- (41) ORF because unusual V-HEPTAMER sequence: GAGGGTG instead of CACAGTG.
- (42) ORF because no CONSERVED-TRP
- (43) V-REGION is partial: AA 1 to 27 are missing (no FR1-IMGT and partial CDR1-IMGT).
- (44) Although the V-HEPTAMER is unusual (CACGGTA instead of CACAGTG), the gene has been found rearranged and therefore is functional.
- (45) In frame STOP-CODON at codon 2 in FR1-IMGT (positions 4-6 in IMGT unique numbering), DELETION of 11 nucleotides in FR3-IMGT (positions 262-272) , STOP-CODON at codon 104 in FR3-IMGT (positions 310-312).
- (46) Several STOP-CODON in V-REGION, frameshift in V-REGION: deletion of 1 nt in FR1-IMGT
- (47) Sequence submitted to EMBL by IMGT curators (Bosc, N., 21/04/2001).
- (48) For the TRAV11 subgroup, sequences of the TRAV11D gene cannot be differentiated from those of the TRAV11 gene, when these sequences are not mapped. These unmapped sequences are therefore described as "TRAV11 alleles" and compared to the allele *01 of TRAV11 (AC005240). However it is not excluded that some of these "alleles" belong exclusively to the TRAV11D gene.
- (49) ORF because the 1st-CYS is not conserved, V-REGION is partial: AA 1 is missing (partial FR1-IMGT).
- (50) U04312 and AC005402 have the same V-REGION but L-PART1 and L-PART2 are different.
- (51) DELETION of 12 nucleotides in CDR1-IMGT (positions 85-96 in IMGT unique numbering), in frame STOP-CODON at codon 43 in FR2-IMGT (positions 127-129) and INSERTION of 6 nucleotides in CDR2-IMGT (between positions 169/170).
- (52) INIT-CODON not conserved in L-PART1: AAG instead of ATG, DELETION of 12 nucleotides in CDR1-IMGT (positions 85-96 in IMGT unique numbering), in frame STOP-CODON at codon 43 in FR2-IMGT (positions 127-129) and INSERTION of 6 nucleotides in CDR2-IMGT (between positions 169/170), no CONSERVED-TRP.
- (53) DELETION 1 nucleotide in FR1-IMGT (position 32 in IMGT unique numbering), no CONSERVED-TRP, and V-REGION is partial: AA 43 to 90 are missing (partial FR2-IMGT, no CDR2-IMGT and partial FR3-IMGT).
- (54) INSERTION of 13 nucleotides in FR3-IMGT (between positions 281/282 in IMGT unique numbering).
- (55) V-GENE is partial (no L-PART1, no L-PART2), and V-REGION is partial: AA 1 is absent (FR1-IMGT is partial).
- (56) It is not known if this sequence is an allele of TRAV11 or of TRAV11D (see note (49)).
- (57) In frame STOP-CODON at codon 25 in FR1-IMGT (positions 73-75 in IMGT unique numbering). It is not known if this sequence is an allele of TRAV11 or of TRAV11D (see note (49)).
- (58) X53732 differs by one undefined nucleotide at codon 7 (position 20 in IMGT unique numbering).
- (59) Potentiel allele base on the finding of several sequences in cDNA (IMGT Annotation: Yan Wu, Géraldine Folch, Marie-Paule Lefranc 19/01/2009).
- (60) 10 AA missing in CDR2-IMGT and FR3-IMGT.
- (61) Frameshift in V-REGION, Some amino acids are deleted in FR1-IMGT and FR3-IMGT.
- (62) Frameshift in FR3-IMGT.
- (63) STOP-CODON in frame at codon 25 in FR1-IMGT.
- (64) Frameshift in V-REGION.
- (65) No L-PART1, in frame STOP-CODON in V-REGION.
- (66) Limits from INIT-CODON (ATG) to the last nucleotide of V-REGION in the following Accession numbers: AE008683, AE008684, AE008685 and AE008686.
- (67) The V-REGION of allele TRAV14-3*01 is 100% identical to the V-REGION of allele TRAV14D-3/DV8*08.
- (68) The V-REGION of allele TRAV14D-3/DV8*01 is 100% identical to the V-REGION of allele TRAV14N-3*01.
- (69) The V-REGION of allele TRAV15D-2/DV6D-2*03 is 100% identical to the V-REGION of allele TRAV15N-2*01.
- (70) The V-REGION of allele TRAV16*01 is 100% identical to the V-REGION of allele TRAV16D/DV11*02.
- (71) Frameshift in V-REGION: deletion of 1nt in FR1-IMGT
- (72) Following a question from M. Le Moine, the assignment of L77149 and L77150 [61] was revised. L77149 has been assigned to TRAV14-1*01 (instead of TRAV14D-1*01) and L77150 has been assigned to TRAV14D-1*01 (instead of TRAV14-1*01) (J Jabado-Michaloud and M-P. Lefranc, 12/05/2021).
- (73) Position of L-V-GENE-UNIT
- (74) Position of V-REGION
- (75) frameshifts in V-REGION: several insertions and deletions
- (76) STOP-CODON in V-REGION: position 83
- (77) noncanonical V-HEPTAMER: caccatg instead of cacagtg
- (78) STOP-CODON in V-REGION: position 58, frameshift in L-PART1: insertion of 1 nt causing defectuous DONOR-SPLICE
- (79) noncanonical V-NONAMER: acactgacc instead of acaaaaact
- (80) several STOP-CODON in V-REGION, no 2nd-CYS: STOP-CODON instead of Cys, no L-PART1
- (81) no L-PART2, truncated pseudogene, frameshifts in V-REGION: several insertions and deletions
- (82) frameshift in V-REGION: deletion of 30 nt in CDR2-IMGT
- (83) frameshift in V-REGION: deletion of 1 nt in FR1-IMGT, truncated pseudogene, no V-RS
- (84) STOP-CODON in V-REGION: position 25
- (85) STOP-CODON in V-REGION: position 58
- (86) several STOP-CODON in V-REGION, no CONSERVED-TRP: STOP-CODON instead of Trp, no L-PART1
- (87) frameshift in V-REGION: insertion of 2 nt in FR1-IMGT
- (88) no INIT-CODON: Val instead of Met, frameshifts in V-REGION: several insertions and deletions, truncated pseudogene, no V-RS
- (89) STOP-CODON in V-REGION: position 40, no INIT-CODON: Thr instead of Met, frameshift in L-PART1: insertion of 1 nt causing defectuous DONOR-SPLICE, no L-PART2
- (90) noncanonical V-NONAMER:cccaaaccc instead of acacaaacc
- (91) noncanonical V-NONAMER: caaaatctg instead of acacaaacc
- (92) several STOP-CODON in V-REGION, frameshifts in V-REGION: several insertions and deletions
- (93) frameshift in V-REGION: insertion of 13 nt in FR3-IMGT
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More information:
See also (IMGT Scientific chart):
- Created:
- 28/03/2001
- Last updated:
- 22/09/2023
- Authors:
- Joumana Jabado-Michaloud, Nathalie Bosc, Guilhem Zeitoun and Géraldine Folch
