Citing IMGT databases: Manso T. et al. IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res. 2022 Jan 7;50(D1):D1262-D1272. doi: 10.1093/nar/gkab1136 PMID: 34875068 Free PMC article.
Program version: v. 

Add the possibility to obtain a gene table per strain (for mouse now and for other species later) and allotypes/isotypes for human.
September 25th, 2024.

Bibliographical references in alphabetic order, small design changes and addition of "NL" for non-localized gene.
June 14th, 2024.

Addition of 'Score for IMGT allele confirmation' as well as NCBI TPA accession numbers.
September 20th, 2023.

Implementation of the dynamic gene table.

Gene table legend:

"+" 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 in 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.

IMGT allele confirmation: a scoring system is employed to signify the frequency of occurrences of a specific allele within sequence data. A single star () indicates that no instances of the allele have been identified in the literature. Two stars () indicate the discovery of one literature sequence containing the allele. If more than one literature sequence is found to contain the allele, it is designated with three stars (). In the Excel file, the stars are represented by the plus symbol (+).

Click on:
  • IMGT gene name to get the corresponding IMGT/GENE-DB entry (link).
  • IMGT allele name to see the corresponding Alignments of alleles (link).
  • Accession number to get the corresponding IMGT/LIGM-DB entry (link).
  • MAP: mapped sequences. Click to access GENE-DB «LOCALIZATION IN GENOME ASSEMBLIES» (link).
  • [number] to access the corresponding IMGT reference (popover).
  • (number) to see the corresponding IMGT note (popover).
Options:
  • You can show/hide columns (), download data () or put the table in fullscreen () using buttons.
See also (IMGT Scientific chart):
Select a species and a IMGT group to get the gene table:
Only IMGT available species/group are shown in the drop-down list.
The gene table can take several seconds to appear, please be patient.

Due to the poor quality of the assembly Btau3.1 only clearly identified genes are annotated. Moreover some duplications such as TRDV1-4 in Btau3.1_ChrUn.139 and TRDV1-8 in Btau3.1_ChrUn.41 may result from assembly errors.

This article was also used for annotation:
Takeuchi N, Ishiguro N, Shinagawa M. Molecular cloning and sequence analysis of bovine T-cell receptor gamma and delta chain genes. Immunogenetics. 1992;35(2):89-96. PMID: 1346526.

Gene table of bovine (Bos taurus) TRDV IMGT group:
IMGT sub­groupIMGT gene nameIMGT allele nameScore for
IMGT allele
confirmation		FctChromosomosal
localization		R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
Clone namesBreedAccession
numbers		Positions
in the sequence
(L-V-GENE-UNIT)
or V-REGION (*)		Secondary
accession
numbers		Clone namesBreedAccession
numbers		Positions
in the sequence
(L-V-GENE-UNIT)
or V-REGION (*)
TRDV1TRDV1-1 TRDV1-1*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 336584-337189 TRDV1S8*01 Hereford Btau3.1_Chr10.28 [1] (11) complement(245668-246273)
TRDV1TRDV1-1 TRDV1-1*02 F 10 TRDV1S30*01 Hereford Btau3.1_ChrUn.129 [1] (11,12) 300288-300894
TRDV1TRDV1-2 TRDV1-2*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 381222-381830 TRDV1S7-1*01 Hereford Btau3.1_Chr10.28 [1] (11) complement(198246-198854)
TRDV1S7-2*01 Hereford Btau3.1_ChrUn.5529 [1] (11) complement(9562-10170)
TRDV1TRDV1-3 TRDV1-3*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 422753-423347 TRDV1S6-1*01 Hereford Btau3.1_Chr10.28 [1] (11) 132846-133440
TRDV1S6-2*01 Hereford Btau3.1_ChrUn.857 [1] (11) 50213-50807
TRDV1TRDV1-4 TRDV1-4*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 466128-466732 TRDV1S18-1*01 Hereford Btau3.1_ChrUn.139 [1] (11) 16460-17064
TRDV1TRDV1-5 TRDV1-5*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 647182-647779 TRDV1S20*01 Hereford Btau3.1_ChrUn.139 [1] (11) 314906-315504
TRDV1TRDV1-6 TRDV1-6*01 P (1) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 669770-670375 Hereford Btau3.1_ChrUn.139 [1] (11) 341005-341610
TRDV1TRDV1-7 TRDV1-7*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 685347-685955 TRDV1S21-1*01 Hereford Btau3.1_ChrUn.139 [1] (11) 356577-357185
TRDV1S21-2*01 Hereford Btau3.1_ChrUn.4913 [1] (11) complement(10636-11244)
TRDV1TRDV1-8 TRDV1-8*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 724738-725238 TRDV1S13-1*01 Hereford Btau3.1_ChrUn.41 [1] (11) 282485-282985
TRDV1TRDV1-8 TRDV1-8*02 F 10 TRDV1S3*01 Hereford Btau3.1_Chr10.28 [1] (11,12) 84670-85170
TRDV1TRDV1-9 TRDV1-9*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 737253-737855 TRDV1S17*01 Hereford Btau3.1_ChrUn.41 [1] (11) 642343-642945
TRDV1TRDV1-10 TRDV1-10*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 756768-757370 TRDV1S15-2*01 Hereford Btau3.1_ChrUn.41 [1] (11) 661894-662496
TRDV1TRDV1-10D TRDV1-10D*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2866264-2866866) TRDV1S15-1*01 Hereford Btau3.1_ChrUn.41 [1] (11) 313360-313962
TRDV1TRDV1-11 TRDV1-11*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 1817505-1818107 TRDV1S19*01 Hereford Btau3.1_ChrUn.139 [1] (11) 303549-304151
TRDV1TRDV1-11 TRDV1-11*02 F 10
RTPr
++
 TRDV1S32*01 Hereford Btau3.1_ChrUn.129 [1] (11,12) 414487-415095
TRDV1TRDV1-12 TRDV1-12*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 1857773-1858273 TRDV1S39*01 Hereford Btau3.1_ChrUn.298 [1] (11) 263421-263921
TRDV1TRDV1-13 TRDV1-13*01 F (2) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 1886230-1886824
TRDV1TRDV1-13 TRDV1-13*02 F (2) 10
RTPr
++
 TRDV1S44*01 Hereford Btau3.1_ChrUn.1227 [1] (11,12) complement(79886-80480)
TRDV1TRDV1-14 TRDV1-14*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 1902814-1903424 TRDV1S43*01 Hereford Btau3.1_ChrUn.1227 [1] (11) complement(62953-63563)
TRDV1TRDV1-15 TRDV1-15*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 1926154-1926760
TRDV1TRDV1-15 TRDV1-15*02 F 10 TRDV1S42*01 Hereford Btau3.1_ChrUn.1227 [1] (11,12) complement(39656-40263)
TRDV1TRDV1-15 TRDV1-15*03 F 10 TRDV1S48*01 Hereford Btau3.1_ChrUn.2188 [1] (11,12) 33687-34294
TRDV1TRDV1-16 TRDV1-16*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 2172532-2173139 TRDV1S35*01 Hereford Btau3.1_ChrUn.158 [1] (11) complement(237072-237679)
TRDV1TRDV1-17 TRDV1-17*01 ORF (3) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 2199793-2200408 TRDV1S25-2*01 Hereford Btau3.1_ChrUn.129 [1] (11) 390952-391567
TRDV1S25-1*01 Hereford Btau3.1_ChrUn.221 [1] (11) complement(174821-175436)
TRDV1TRDV1-17 TRDV1-17*02 ORF (4) 10
RTPr
++
 TRDV1S34*01 Hereford Btau3.1_ChrUn.158 [1] (11,12) complement(209501-210077)
TRDV1TRDV1-18 TRDV1-18*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 2231429-2232025 TRDV1S33*01 Hereford Btau3.1_ChrUn.158 [1] (11) complement(178884-179480)
TRDV1TRDV1-19 TRDV1-19*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 2251584-2252184
TRDV1TRDV1-20 TRDV1-20*01 P (5) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 2280113->2280262 * Hereford Btau3.1_ChrUn.158 [1] (11) complement(<155920-156069) *
TRDV1TRDV1-21 TRDV1-21*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2325118-2325689)
TRDV1TRDV1-22 TRDV1-22*01 ORF (6) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2348378-2348976)
TRDV1TRDV1-23 TRDV1-23*01 P (7) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2376289-2376889)
TRDV1TRDV1-24 TRDV1-24*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2394644-2395246) TRDV1S14*01 Hereford Btau3.1_ChrUn.41 [1] (11) 294987-295589
TRDV1TRDV1-25 TRDV1-25*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2407292-2407792) TRDV1S12*01 Hereford Btau3.1_ChrUn.41 [1] (11) 272858-273358
TRDV1TRDV1-26 TRDV1-26*01 P (8) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2425319-2425892) Hereford Btau3.1_ChrUn.41 [1] (11) 254764-255330
TRDV1TRDV1-27 TRDV1-27*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2429767-2430405) TRDV1S11*01 Hereford Btau3.1_ChrUn.41 [1] (11) 250250-250888
TRDV1TRDV1-27 TRDV1-27*02 F 10 TRDV1S52-1*01 Hereford Btau3.1_ChrUn.3620 [1] (11,12) 538-1168 TRDV1S52-2*01 Hereford Btau3.1_ChrUn.3793 [1] (11) 3915-4545
TRDV1TRDV1-28 TRDV1-28*01 P (9) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2447224-2447837) TRDV1S9*01 Hereford Btau3.1_ChrUn.41 [1] (11) complement(161485-162099)
TRDV1TRDV1-29 TRDV1-29*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2473337-2473933) TRDV1S10*01 Hereford Btau3.1_ChrUn.41 [1] (11) complement(188072-188668)
TRDV1TRDV1-29 TRDV1-29*02 F 10 TRDV1S46*01 Hereford Btau3.1_ChrUn.1758 [1] (11,12) complement(57989-58581)
TRDV1TRDV1-29 TRDV1-29*03 F 10 TRDV1S23*01 Hereford Btau3.1_ChrUn.221 [1] (11,12) complement(6038-6638)
TRDV1TRDV1-30 TRDV1-30*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2497562-2498155) TRDV1S24*01 Hereford Btau3.1_ChrUn.221 [1] (11) complement(30244-30837)
TRDV1TRDV1-31 TRDV1-31*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2659878-2660487) TRDV1S26*01 Hereford Btau3.1_ChrUn.221 [1] (11) complement(220716-221325)
TRDV1TRDV1-32 TRDV1-32*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2679937-2680544) TRDV1S27-1*01 Hereford Btau3.1_ChrUn.221 [1] (11) complement(240695-241302)
TRDV1S27-2*01 Hereford Btau3.1_ChrUn.2578 [1] (11) complement(31652-32259)
TRDV1TRDV1-33 TRDV1-33*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(2703621-2704226) TRDV1S51-2*01 Hereford Btau3.1_ChrUn.2982 [1] (11) 15173-15778
TRDV1S51-1*01 Hereford Btau3.1_ChrUn.3458 [1] (11) complement(16933-17538)
TRDV1TRDV1-33 TRDV1-33*02 F 10 TRDV1S50*01 Hereford Btau3.1_ChrUn.10149 [1] (11,12) complement(1804-2409)
TRDV1TRDV1-33 TRDV1-33*03 F 10 TRDV1S28*01 Hereford Btau3.1_ChrUn.221 [1] (11,12) complement(264398-265003)
TRDV1TRDV1-33 TRDV1-33*04 F 10 TRDV1S36*01 Hereford Btau3.1_ChrUn.298 [1] (11,12) 28570-29175
TRDV1TRDV1-33 TRDV1-33*05 F 10
RTPr
++
 TRDV1S16*01 Hereford Btau3.1_ChrUn.41 [1] (11,12) 480039-480644
TRDV1TRDV1S1 NL TRDV1S1*01 F 10 Hereford Btau3.1_Chr10.28 [1] (11,12) complement(20340-20949)
TRDV1TRDV1S2 NL TRDV1S2*01 ORF (4) 10 TRDV1S2-1*01 Hereford Btau3.1_Chr10.28 [1] (11,12) 58187-58762 TRDV1S2-2*01 Hereford Btau3.1_ChrUn.4123 [1] (11) 14961-15536
TRDV1TRDV1S4 NL TRDV1S4*01 F 10 TRDV1S4-1*01 Hereford Btau3.1_Chr10.28 [1] (11,12) 97187-97789 TRDV1S4-2*01 Hereford Btau3.1_ChrUn.857 [1] (11) 4172-4774
TRDV1S4-3*01 Hereford Btau3.1_ChrUn.3566 [1] (11) 19054-19657
TRDV1TRDV1S5 NL TRDV1S5*01 F 10 TRDV1S5-1*01 Hereford Btau3.1_Chr10.28 [1] (11,12) 115470-116065 TRDV1S5-2*01 Hereford Btau3.1_ChrUn.857 [1] (11) 28383-28978
TRDV1TRDV1S22 NL TRDV1S22*01 ORF (4) 10 Hereford Btau3.1_ChrUn.139 [1] (11,12) 373301-373876
TRDV1TRDV1S29 NL TRDV1S29*01 F 10 Hereford Btau3.1_ChrUn.129 [1] (11,12) 5640-6247
TRDV1TRDV1S29 NL TRDV1S29*02 F 10 TRDV1S41*01 Hereford Btau3.1_ChrUn.857 [1] (11,12) 74024-74631
TRDV1TRDV1S31 NL TRDV1S31*01 F 10 Hereford Btau3.1_ChrUn.129 [1] (11,12) 331405-332015
TRDV1TRDV1S37 NL TRDV1S37*01 F 10 Hereford Btau3.1_ChrUn.298 [1] (11,12) 206764-207364
TRDV1TRDV1S38 NL TRDV1S38*01 F 10
RTPr
++
 Hereford Btau3.1_ChrUn.298 [1] (11,12) 223460-224056
TRDV1TRDV1S40 NL TRDV1S40*01 F 10 Hereford Btau3.1_ChrUn.857 [1] (11,12) 19494-20094
TRDV1TRDV1S45 NL TRDV1S45*01 F 10 Hereford Btau3.1_ChrUn.1758 [1] (11,12) complement(21904-22497)
TRDV1TRDV1S47 NL TRDV1S47*01 F 10 TRDV1S47-1*01 Hereford Btau3.1_ChrUn.2188 [1] (11,12) 10476-11070 TRDV1S47-2*01 Hereford Btau3.1_ChrUn.3970 [1] (11) 9390-9984
TRDV1TRDV1S49 NL TRDV1S49*01 F 10 Hereford Btau3.1_ChrUn.3566 [1] (11,12) 5067-5567
TRDV1TRDV1S53 NL TRDV1S53*01 (F) 10
RTPr
++
 EF175171 [5] (12) #c <1-224 *
TRDV1TRDV1S54 NL TRDV1S54*01 (F) 10
RTPr
++
 EF175172 [5] (12) #c 61-339 *
TRDV1TRDV1S56 NL TRDV1S56*01 (F) 10
RTPr
++
 D16113 [2] (12) #c 61-348 *
TRDV2TRDV2 TRDV2*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 3105697-3106225 Hereford Btau3.1_ChrUn.158 [1] (11) complement(22632-23160)
TRDV3TRDV3 TRDV3*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP complement(3236267-3236888) TRDV4*01 Hereford Btau3.1_Chr10.30 [1] (11) 396663-397284
TRDV4TRDV4 TRDV4*01 ORF (10) 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 3078995-3079535 Hereford Btau3.1_ChrUn.158 [1] (11) complement(49100-49640)
TRDV5TRDV5-1 TRDV5-1*01 F 10
RTPr
++
 CM008177.2 Hereford BK064707✤ [3,4] MAP 3000922-3001486
TRDV5TRDV5-1 TRDV5-1*02 F 10 TRDV3S2*01 Hereford Btau3.1_ChrUn.1002 [1] (11,12) 77577-78141
TRDV5TRDV5-1 TRDV5-1*03 F 10 TRDV3S1*01 Hereford Btau3.1_ChrUn.7503 [1] (11,12) complement(3103-3667)
TRDV5TRDV5-2 TRDV5-2*01 F 10 CM008177.2 Hereford BK064707✤ [3,4] MAP 3035223-3035778

✤ : NCBI accession number that correspond to a previously internal IMGT accession number. See the correspondence table.

IMGT notes: ↑
  1. STOP-CODON in V-REGION: position 92
  2. STOP-CODON at position 108 (last 3' codon of germline CDR3-IMGT) may disappear during rearrangements
  3. insertions and deletions in V-REGION: 11 AA are added and 9 AA are missing
  4. deletions in V-REGION: 9 AA are missing
  5. deletions in V-REGION: AA 56 to 108 are missing
  6. deletions in V-REGION: 4 AA are missing
  7. frameshift in L-PART1
  8. frameshift in V-REGION: deletion of 2 nt in FR2-IMGT
  9. no INIT-CODON: Ile instead of Met
  10. noncanonical V-NONAMER: tcaaatctc instead of acaaaaacc
  11. The localization of the sequences in the Btau3.1 project is indicated in the accession number after the underscore
  12. Sequence not in locus reference sequence (assembly ARS-UCD1.2)
IMGT references: ↑
  1. Herzig C.T. et al., Annotation and classification of the bovine T cell receptor delta genes, BMC Genomics, vol. 11, 2010, pp. 100-100. DOI: 10.1186/1471-2164-11-100
  2. Ishiguro N. et al., Molecular structure of bovine T cell receptor gamma and delta chains predominantly expressed on peripheral blood lymphocytes, Unpublished.
  3. Manso,T. et al., IMGT(R) databases, related tools and web resources through three main axes of research and development, Nucleic Acids Res, vol. 50, no. D1, 2022, pp. D1262-D1272. PUBMED: 34875068
  4. Pegorier P et al., IMGT((R)) Biocuration and Comparative Analysis of Bos taurus and Ovis aries TRA/TRD Loci, Genes (Basel), vol. 12, no. 1, 2020, pp. E30-. PUBMED: 33379283
  5. Van Rhijn I. et al., Highly diverse TCR delta chain repertoire in bovine tissues due to the use of up to four D segments per delta chain, Mol. Immunol, vol. 44, no. 12, 2007, pp. 3155-3161. DOI: 10.1016/j.molimm.2007.02.003