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. 

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.

In the realm of 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.
Gene table of Naked mole-rat (Heterocephalus glaber) TRDV IMGT group:
IMGT sub­groupIMGT gene nameIMGT allele nameFctScore for
IMGT allele
confirmation
Chromosomosal
localization
R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
IsolateClone namesAccession
numbers
Positions
in the sequence
(L-V-GENE-UNIT)
or V-REGION (*)
Secondary
accession
numbers
IsolateClone namesAccession
numbers
Positions
in the sequence
(L-V-GENE-UNIT)
or V-REGION (*)
TRDV1TRDV1-1 TRDV1-1*01 (1) 2 BK064754 [1] MAP 290429-291023 IMGT000071 452888-453482
TRDV1TRDV1-2 TRDV1-2*01 ORF (2) 2 BK064754 [1] MAP 392404-392979 IMGT000071 576850-577425
TRDV1TRDV1-3 TRDV1-3*01 (3) 2 IMGT000071 663653-664206
TRDV1TRDV1-4 TRDV1-4*01 F 2 BK064754 [1] MAP 483686-484239 IMGT000071 676189-676742
TRDV1TRDV1-5 TRDV1-5*01 F 2 BK064754 [1] MAP 526104-526715 IMGT000071 720393-721004
TRDV1TRDV1-6 TRDV1-6*01 F 2 BK064754 [1] MAP 602105-602705 IMGT000071 796437-797037
TRDV2TRDV2 TRDV2*01 (4) 2 IMGT000071 1592159-1592673
TRDV2TRDV2 TRDV2*02 (4) 2 BK064754 [1] MAP 1208644-1209158
TRDV3TRDV3 TRDV3*01 ORF (5) 2 BK064754 [1] MAP complement(1274577-1275213) IMGT000071 complement(1668387-1669023)
TRDV4TRDV4 TRDV4*01 (6) 2 BK064754 [1] MAP 1182872-1183398 IMGT000071 1566383-1566909
TRDV5TRDV5 TRDV5*01 F 2 BK064754 [1] MAP 1130743-1131313 IMGT000071 1514437-1515007
TRDVATRDVA TRDVA*01 (7) 2 BK064754 [1] MAP 464544-465165 IMGT000071 648895-649516
TRDVBTRDVB TRDVB*01 (8) 2 BK064754 [1] MAP 782301-782895 IMGT000071 1009775-1010369
TRDVCTRDVC TRDVC*01 (9) 2 IMGT000071 1023313-1023897

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

IMGT notes:
  1. STOP-CODON in L-PART1, frameshift in L-PART1, several STOP-CODON in V-REGION
  2. noncanonical ACCEPTOR-SPLICE: ntgnn instead of nagnn, noncanonical V-NONAMER: acaggggcc instead of acaaaaacc
  3. frameshift in L-PART1, frameshifts in V-REGION: several insertions and deletions
  4. no INIT-CODON: Leu instead of Met, no DONOR-SPLICE, frameshift in V-REGION: several insertions and deletions
  5. no 1st-CYS: Tyr instead of Cys
  6. STOP-CODON in L-PART1, STOP-CODON in V-REGION: position 38, frameshift in V-REGION: deletion of 1 nt in FR3-IMGT
  7. STOP-CODON in V-REGION: position 16, frameshifts in V-REGION: several insertions and deletions
  8. no INIT-CODON: Leu instead of Met, STOP-CODON in V-REGION: position 8
  9. no INIT-CODON: Leu instead of Met, frameshift in V-REGION: deletion of 1 nt and deletion of 1 nt in FR2-IMGT
IMGT references:
  1. 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