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) TRGJ IMGT group:
IMGT 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
(J-GENE-UNIT)
or J-REGION (*)
Secondary
accession
numbers
IsolateClone namesAccession
numbers
Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
TRGJ1-1 TRGJ1-1*01 ORF (1) 1 BK064756 [1] MAP 49361-49449 BK064755 [1] 49358-49446
MEF-2018 IMGT000072 49230-49318
TRGJ1-2 TRGJ1-2*01 F 1 BK064756 [1] MAP 53686-53763 BK064755 [1] 53685-53762
MEF-2018 IMGT000072 53579-53656
TRGJ2-1 TRGJ2-1*01 (2) 1 BK064756 [1] MAP 161675-161760 BK064755 [1] 171188-171273
MEF-2018 IMGT000072 161219-161304
TRGJ3-1 TRGJ3-1*01 ORF (3) 1 BK064756 [1] MAP 226420-226510 BK064755 [1] 235988-236078
MEF-2018 IMGT000072 227592-227682
TRGJ3-2 TRGJ3-2*01 (4) 1 BK064756 [1] MAP 227147-227236 MEF-2018 IMGT000072 228319-228408
TRGJ3-2 TRGJ3-2*02 (4) 1 BK064755 [1] MAP 236714-236803
TRGJ3-3 TRGJ3-3*01 ORF (5) 1 BK064756 [1] MAP 231261-231339 BK064755 [1] 240829-240907
MEF-2018 IMGT000072 232432-232510
TRGJ4-1 TRGJ4-1*01 ORF (6) 1 BK064756 [1] MAP 259434-259520 BK064755 [1] 268988-269074
MEF-2018 IMGT000072 260588-260674
TRGJ4-1 TRGJ4-1*02 ORF (6) 1 NMR 29 IMGT000083 327044-327130
TRGJ4-2 TRGJ4-2*01 ORF (7) 1 BK064756 [1] MAP 261775-261852 BK064755 [1] 271332-271409
MEF-2018 IMGT000072 263816-263893
TRGJ5-1 TRGJ5-1*01 (2) 1 BK064756 [1] MAP 306171-306255 BK064755 [1] 313375-313459
MEF-2018 IMGT000072 310280-310364
TRGJ5-2 TRGJ5-2*01 (2) 1 BK064756 [1] MAP 306899-306990 BK064755 [1] 314102-314193
MEF-2018 IMGT000072 311007-311098
TRGJ5-3 TRGJ5-3*01 F 1 BK064756 [1] MAP 310426-310503 BK064755 [1] ORF (8) 317629-317706
MEF-2018 IMGT000072 ORF (8) 314520-314597 (9)
NMR 29 IMGT000083 377675-377752

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

IMGT notes:
  1. noncanonical J-HEPTAMER: cattatg instead of cactgtg
  2. frameshift in J-REGION: deletion of 1 nt
  3. noncanonical J-NONAMER: gagatttat instead of gatttttgt, noncanonical J-HEPTAMER: gactatg instead of cactgtg, noncanonical J-MOTIF: FAXG instead of FGXG
  4. STOP-CODON in J-REGION
  5. noncanonical J-MOTIF: FSXG instead of FGXG
  6. noncanonical J-NONAMER: agactttaa instead of agtttttga, noncanonical J-HEPTAMER: gacaatg instead of cactgtg, no J-PHE: Ser instead of Phe
  7. noncanonical J-NONAMER: gttttttta instead of gatttttgt, noncanonical J-MOTIF: FSXG instead of FGXG
  8. noncanonical J-HEPTAMER: cgttgtg instead of cactgtg
  9. The litterature sequence has a canonical J-HEPTAMER: cattgtg -> therefore, the functionality of the litterature sequence is functional (F).
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