IMGT Repertoire (IG and TR)
Gene table: house mouse (Mus musculus) TRDV
- 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.
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. AE008686 (461875 bp) contains TRDV1 to TRDV5.
The 10 TRAV/DV genes which belong to 7 TRAV subgroups are reported in the TRAV Mouse (Mus musculus) Gene table.
| IMGT subgroup | 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 | Secondary accession numbers | Strain | Clone names | Accession numbers | Positions in the sequence | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV1 | TRDV1 | TRDV1*01 | F | 14 (19.7 cM) | + | + | 112447-113058 | (6) | 129/SvJ | VDelta 2 | MAP | M94080 | [5] | 129/Sv/J | TRDV1 | MAP | AC005938 | [7] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| AE007512 | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV1*02 | F | 14 (19.7 cM) | 1463645-1464289 | (8) | C57BL/6J | IMGT000082 | [8] | MAP | 1463645-1464289 | (8) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV2 | TRDV2-1 | TRDV2-1*01 | F | 14 (19.7 cM) | 169281-169868 | (6) | 129/SvJ | TRDV2-1 | MAP | AC003993 | [7] | AC005835 | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| AE007512 | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV2-1*02 | F | 14 (19.7 cM) | 1528106-1528732 | C57BL/6J | (8) | IMGT000082 | [8] | MAP | 1528106-1528732 | (8) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV2-2 | TRDV2-2*01 | F | 14 (19.7 cM) | + | + | 180112-180712 | (6) | 129/SvJ | TRDV2-2 | MAP | AC003993 | [7] | AC005835 | [7] | C57BL/6J | IMGT000082 | [8] | MAP | 1543026-1543674 | (8) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
| AE007512 | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV2-2*02 | [F] | 14 (19.7 cM) | B10.A | (1) | VDelta 4.2 | U28810 | [6] | ° | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV3 | TRDV3 | TRDV3*01 | P | (5) | 14 (19.7 cM) | + | + | 226595-226894 | (7) | 129/SvJ | TRDV3P | MAP | AC005835 | [7] | AE007512 | [7] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV3*02 | P | (10) | 14 (19.7 cM) | 1582992-1583286 | C57BL/6J | (9) | IMGT000082 | [8] | MAP | 1582992-1583286 | (9) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV4 | TRDV4 | TRDV4*01 | F | 14 (19.7 cM) | + | + | 314801-315312 | (6) | 129/SvJ | TRDV4 | MAP | AC003057 | [7] | AE007512 | [7] | C57BL/6J | IMGT000082 | [8] | MAP | 1657037-1657587 | (8) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV5 | TRDV5 | (4) | TRDV5*01 | F | 14 (19.7 cM) | BALB/c | VDelta 5 | MAP | M23382 | [2] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV5*02 | F | 14 (19.7 cM) | + | + | + | B10.D2-H2dm1 | (2) | VDelta 7.3 | MAP | M23095 | [3] | B10.D2-H2dm1 | VDelta 7.3 | MAP | M23098 | [3] | (3) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| C57BL/6J | IMGT000082 | [8] | MAP | complement(1730656,1731234) | (8) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV5*03 | F | 14 (19.7 cM) | + | + | + | 381551-382090 | (6) | B10.D2-H2dm1 | TRDV5 | MAP | M64239 | [4] | AE007512 | [7] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| TRDV5*04 | (F) | 14 (19.7 cM) | + | + | BALB/c x 129 (F1) | VDelta 5 | MAP | M37281 | [1] | #c | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
#c: rearranged cDNA.
°: DNA genomic sequence, but not known as being germline or rearranged.
MAP: Mapped reference sequences.
- (1) B10.A is a congenic strain, B10 is the abbreviated symbol of C57BL/10 and A the abbreviated symbol of A/J.
- (2) B10.D2-H2dm1 is a congenic strain (see MGD for Strain Nomenclature Guidelines), B10 is the abbreviated symbol of C57BL/10 and D2 the abbreviated symbol of DBA/2J.
- (3) V-GENE is partial (no L-PART1, no L-PART2), and V-REGION is partial: AA 1 to 71 are missing (no FR1-IMGT, no CDR1-IMGT, no FR2-IMGT, no CDR2-IMGT and partial FR3-IMGT).
- (4) The TRDV5 gene is localized in 3' from the TRDC gene and is in an inverted orientation of transcription.
- (5) Frameshifts in V-REGION.
- (6) Limits from INIT-CODON (ATG) to the last nucleotide of V-REGION in the AE008586 accession number.
- (7) For the pseudogene TRDV3 which has no L-PART1, limits are from the first nucleotide to the last nucleotide of V-EXON.
- (8) Position of V-GENE-UNIT
- (9) Position of V-REGION
- (10) frameshifts in V-REGION: several insertions and deletions, no L-PART1
- [1] Elliott J.F. et al., Nature, 331, 627-631 (1988). PMID:2963227
- [2] Iwashima M. et al., Proc. Natl. Acad. Sci. USA., 85, 8161-8165 (1988). PMID:3263646
- [3] Korman A.J. et al., Proc. Natl. Acad. Sci. USA., 86, 267-271 (1989). PMID:2789518
- [4] Koop B.F. et al., Genomics, 13, 1209-1230 (1992). PMID:1505954
- [5] Seto D. et al., Genomics, 20, 258-266 (1994). PMID:8020973
- [6] Balboni I. et al., Unpublished (1996).
- [7] Lee I.Y. et al., Unpublished (1998).
- [8] Deanna C. et al, PLoS Biol., (9)7 (2011). PMID:21750661
- Created:
- 15/02/2000
- Last updated:
- 22/09/2023
- Authors:
- Nathalie Bosc and Guilhem Zeitoun
