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.
Gene table of Atlantic salmon (Salmo salar) IGHJ IMGT group:
IMGT gene nameIMGT allele nameScore for
IMGT allele
confirmation		FctChromosomosal
localization		R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)		Secondary
accession
numbers		Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
IGHJ1 IGHJ1*01 F ssa06 GU129139 [2] 792258-792347 g6.3 Y12391 [1] 6887-6975
IGHJ1D IGHJ1D*01 F ssa03 GU129140 [2] 967580-967669 g5.1 Y12392 [1] 993-1081
IGHJ1T1D IGHJ1T1D*01 P (1) ssa03 GU129140 [2] 349757-349847
IGHJ1T2 IGHJ1T2*01 F ssa06 GU129139 [2] 333944-334029
IGHJ1T2D IGHJ1T2D*01 F ssa03 GU129140 [2] 529484-529570
IGHJ1T3 IGHJ1T3*01 F ssa06 GU129139 [2] 405311-405397
IGHJ1T4 IGHJ1T4*01 F ssa06 GU129139 [2] complement(660491-660576)
IGHJ1T5 IGHJ1T5*01 P (2) ssa06 GU129139 [2] 710952-711005 *
IGHJ2 IGHJ2*01 ORF (3) ssa06 GU129139 [2] 792428-792516 g6.3 Y12391 [1] F (5) 7056-7144
IGHJ2D IGHJ2D*01 F ssa03 GU129140 [2] 967750-967838 g5.1 Y12392 [1] 1162-1250
IGHJ2T2 IGHJ2T2*01 F ssa06 GU129139 [2] 334420-334511
IGHJ2T2D IGHJ2T2D*01 F ssa03 GU129140 [2] 529974-530064
IGHJ2T3 IGHJ2T3*01 F ssa06 GU129139 [2] 405843-405934
IGHJ2T4 IGHJ2T4*01 F ssa06 GU129139 [2] complement(660009-660099)
IGHJ2T5 IGHJ2T5*01 F ssa06 GU129139 [2] 711321-711412
IGHJ3 IGHJ3*01 F ssa06
RTPr
++
 GU129139 [2] 792632-792721 g6.3 Y12391 [1] 7261-7349
IGHJ3D IGHJ3D*01 F ssa03
RTPr
++
 GU129140 [2] 967954-968043 g5.1 Y12392 [1] 1364-1453
IGHJ4 IGHJ4*01 F ssa06 GU129139 [2] 792993-793082 g6.3 Y12391 [1] 7622-7710
IGHJ4D IGHJ4D*01 F ssa03 GU129140 [2] 968315-968404 g5.1 Y12392 [1] 1725-1814
IGHJ5 IGHJ5*01 F ssa06 GU129139 [2] 793378-793469
IGHJ5 IGHJ5*02 ORF (4) ssa06 g6.3 Y12391 [1] (6) 8006-8096
IGHJ5D IGHJ5D*01 F ssa03 GU129140 [2] 968703-968794
IGHJ5D IGHJ5D*02 ORF (4) ssa03 g5.1 Y12392 [1] (6) 2113-2203
IMGT notes: ↑
  1. No J-TRP: STOP-CODON instead of TRP
  2. No V-NONAMER
  3. Noncanonical J-NONAMER: tgattttat instead of ggtttttgt
  4. Noncanonical J-HEPTAMER: cacagct instead of cactgtg, howewer rearrangement is not excluded (see publication)
  5. Functionality different from the reference sequence: functional
  6. Sequence not in locus reference sequences (GU129139 and GU129140)
IMGT references: ↑
  1. Hordvik I et al., Structure and organization of the immunoglobulin M heavy chain genes in Atlantic salmon, Salmo salar, Mol. Immunol, vol. 34, no. 8-9, 1997, pp. 631-639.
  2. Yasuike M. et al., Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar, BMC Genomics, vol. 11, 2010, pp. 486-486. DOI: 10.1186/1471-2164-11-486