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.

Haplotypes have been described in Mattila, P.S et al., Eur. J. Immunol., 25, 2578-2582 (1995).

Gene table of human (Homo sapiens) 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 namesAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)		Secondary
accession
numbers		Clone namesAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
IGHJ1 IGHJ1*01 F 14q32.33
RTPr
++
 J1 J00256 [3,16,19] MAP (5) 686-774 BK063799✤ [12] 1014349-1014438
BK063800✤ [12] 1024441-1024530
BK063801✤ [12] 970118-970207
BK063802✤ [12] 957835-957924
BK068298✤ [12] 1046697-1046786
BK068299✤ [12] 1028222-1028311
JADDFX010000192 [21] complement(86370-86459)
X86355 [13] (6) 247-336
X86356 [13] (6) 247-336
X86357 [13] (6) 247-336
X86358 [13] (6) 247-336
X86359 [13] (6) 247-336
X97051 [1,6,13,18-20] 87524-87613
IGHJ1P IGHJ1P*01 P (1) 14q32.33 J1P J00256 [3,16,19] (5) 467-557
IGHJ1P IGHJ1P*02 P (1) 14q32.33 X97051 [1,6,13,18-20] MAP 87306-87396 CM000676.2 BK063799✤ [12] 1014131-1014221
BK063800✤ [12] 1024223-1024313
BK063801✤ [12] 969900-969990
BK063802✤ [12] 957617-957707
BK068298✤ [12] 1046479-1046569
BK068299✤ [12] 1028004-1028094
IMGT000112 [5] 1074761-1074851
JADDFX010000192 [21] complement(86587-86677)
X86355 [13] 30-120
X86356 [13] 30-120
X86357 [13] 30-120
X86358 [13] 30-120
X86359 [13] 30-120
IGHJ2 IGHJ2*01 F 14q32.33
RTPr
++
 J2 J00256 [3,16,19] MAP (5) 893-984 BK063799✤ [12] 1014556-1014646
BK063800✤ [12] 1024648-1024738
BK063801✤ [12] 970325-970415
BK063802✤ [12] 958042-958132
BK068298✤ [12] 1046904-1046994
BK068299✤ [12] 1028429-1028519
JADDFX010000192 [21] complement(86162-86252)
X86355 [13] (6) 454-544
X86356 [13] (6) 454-544
X86357 [13] (6) 454-544
X86358 [13] (6) 454-544
X86359 [13] (6) 454-544
X97051 [1,6,13,18-20] 87731-87821
IGHJ2P IGHJ2P*01 P (1) 14q32.33
RTPr
++
 J2P J00256 [3,16,19] (5) 1284-1380
IGHJ2P IGHJ2P*02 P (1) 14q32.33 CM000676.2 BK063799✤ [12] MAP 1014955-1015054 BK063800✤ [12] 1025047-1025146
BK063801✤ [12] 970724-970823
BK063802✤ [12] 958441-958540
BK068298✤ [12] 1047303-1047402
BK068299✤ [12] 1028828-1028927
JADDFX010000192 [21] complement(85754-85853)
X86355 [13] 853-952
IGHJ3 IGHJ3*01 F 14q32.33
RTPr
++
 J3 J00256 [3,16,19] (5) 1498-1586 M25625 [17] 31-119
IGHJ3 IGHJ3*02 F 14q32.33
RTPr
++
 J3 X86355 [13] MAP (6) 1068-1156 BK063799✤ [12] 1015170-1015258
BK063800✤ [12] 1025262-1025350
BK063801✤ [12] 970939-971027
BK063802✤ [12] 958656-958744
BK068298✤ [12] 1047518-1047606
BK068299✤ [12] 1029043-1029131
JADDFX010000192 [21] complement(85550-85638)
J3 X86356 [13] (6) 1068-1156
J3 X86357 [13] (6) 1068-1156
J3 X86358 [13] (6) 1068-1156
J3 X86359 [13] (6) 1068-1156
X97051 [1,6,13,18-20] 88345-88433
IGHJ3P IGHJ3P*01 P (2) 14q32.33
RTPr
++
 J3P J00256 [3,16,19] (5) 2709-2797 M25625 [17] 1241-1329
IGHJ3P IGHJ3P*02 P (2) 14q32.33
RTPr
+
 J3P X86355 [13] MAP (6) 2239-2326 BK063799✤ [12] 1016342-1016429
BK063800✤ [12] 1026434-1026521
BK063801✤ [12] 972111-972198
BK063802✤ [12] 959828-959915
BK068298✤ [12] 1048690-1048777
BK068299✤ [12] 1030215-1030302
IMGT000199 [10,11] ° 675266-675353
IMGT000207 775393-775480
IMGT000208 [4,7,9] ° 304731-304818
JADDFX010000192 [21] complement(84379-84466)
J3P X86356 [13] (6) 2239-2326
J3P X86357 [13] (6) 2239-2326
J3P X86358 [13] (6) 2239-2326
J3P X86359 [13] (6) 2239-2326
X97051 [1,6,13,18-20] (6) 89517-89604
IGHJ3P IGHJ3P*03 P (3) 14q32.33
RTPr
+
 IMGT000158 [7-9] 882331-882418
IGHJ4 IGHJ4*01 F 14q32.33
RTPr
++
 J4 J00256 [3,16,19] (5) 1873-1959
IGHJ4 IGHJ4*02 F 14q32.33
RTPr
++
 J4 X86355 [13] MAP (6) 1441-1527 BK063799✤ [12] 1015544-1015630
BK063800✤ [12] 1025636-1025722
BK063801✤ [12] 971313-971399
BK063802✤ [12] 959030-959116
BK068298✤ [12] 1047892-1047978
BK068299✤ [12] 1029417-1029503
IMGT000207 774595-774681
IMGT000208 [4,7,9] ° 303933-304019
JADDFX010000192 [21] complement(85178-85264)
J4 X86356 [13] (6) 1441-1527
J4 X86357 [13] (6) 1441-1527
J4 X86358 [13] (6) 1441-1527
J4 X86359 [13] (6) 1441-1527
X97051 [1,6,13,18-20] 88719-88805
IGHJ4 IGHJ4*03 F 14q32.33
RTPr
++
 J4 M25625 [17] (7) 407-493
IGHJ5 IGHJ5*01 F 14q32.33
RTPr
++
 J5 J00256 [3,16,19] (5) 2317-2404 M25625 [17] 855-942
IGHJ5 IGHJ5*02 F 14q32.33
RTPr
++
 J5 X86355 [13] MAP (6) 1840-1928 BK063799✤ [12] 1015942-1016031
BK063800✤ [12] 1026035-1026123
BK063801✤ [12] 971712-971800
BK063802✤ [12] 959429-959517
BK068298✤ [12] 1048291-1048379
BK068299✤ [12] 1029815-1029904
IMGT000208 [4,7,9] ° 304332-304420
JADDFX010000192 [21] complement(84777-84865)
J5 X86356 [13] (6) 1840-1928
J5 X86357 [13] (6) 1840-1928
J5 X86358 [13] (6) 1840-1928
J5 X86359 [13] (6) 1840-1928
X97051 [1,6,13,18-20] 89118-89206
IGHJ5 IGHJ5*03 P (4) 14q32.33
RTPr
++
 IMGT000158 [7-9] 881967-882017 *
IGHJ5 IGHJ5*04 F 14q32.33 IMGT000207 MAP 774993-775082
IGHJ6 IGHJ6*01 F 14q32.33
RTPr
++
 J6 J00256 [3,16,19] (5) 2909-3009
IGHJ6 IGHJ6*02 F 14q32.33
RTPr
++
 M25625 [17] MAP (7) 1442-1542 BK063800✤ [12] 1026639-1026739
BK063801✤ [12] 972316-972416
BK068298✤ [12] 1048895-1048995
BK068299✤ [12] 1030420-1030520
IMGT000199 [10,11] ° 675471-675571
IMGT000207 775598-775698
M63031 [14] 20-120
J6 X86355 [13] (8) 2444->2543
J6 X86357 [13] (8) 2482->2543 *
J6 X86358 [13] (8) 2482->2543 *
X97051 [1,6,13,18-20] 89722-89822
IGHJ6 IGHJ6*03 F 14q32.33
RTPr
++
 M63030 [14] MAP (9) 20-120 CM000676.2 BK063799✤ [12] 1016547-1016647
BK063802✤ [12] 960033-960133
IMGT000208 [4,7,9] ° 304936-305036
JADDFX010000192 [21] complement(84161-84261)
J6 X86356 [13] (10) 2444->2543
J6 X86359 [13] (10) 2482->2543 *
IGHJ6 IGHJ6*04 F 14q32.33
RTPr
++
 AJ879487 [15] 1-101
IGHJ6 IGHJ6*05 F 14q32.33
RTPr
++
 IMGT000158 [7-9] 882535-882635

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

IMGT notes: ↑
  1. no DONOR-SPLICE
  2. J-psi-3
  3. frameshift in J-REGION
  4. no J-RS
  5. Sequenced in haplotype a.
  6. Sequenced in haplotypes b1, b1c, b2, b3 and c, respectively.
  7. Sequenced in haplotype d.
  8. Sequenced in haplotypes b1, b2 and b3, respectively.
  9. Has a complete J-REGION.
  10. Sequenced in haplotypes b1c and c, respectively.
IMGT references: ↑
  1. Buluwela L. et al., A VH gene is located within 95 Kb of the human immunoglobulin heavy chain constant region genes, Eur. J. Immunol, vol. 18, no. 11, 1988, pp. 1843-1845. PUBMED: 3144456
  2. Buluwela L. et al., The use of chromosomal translocations to study human immunoglobulin gene organization: mapping DH segments within 35 kb of the C mu gene and identification of a new DH locus, EMBO J, vol. 7, no. 7, 1988, pp. 2003-2010. PUBMED: 3138112
  3. Flanagan J.G. et al., The sequence of a human immunoglobulin epsilon heavy chain constant region gene, and evidence for three non-allelic genes, EMBO J, vol. 1, no. 5, 1982, pp. 655-660. PUBMED: 6234164
  4. Hansen,N.F. et al., Direct Submission, Computational and Statistical Genomics Branch, NHGRI/NIH, 49 Convent Drive, Rm 4A35, Bethesda, MA 20892, USA.
  5. Hu,H. et al., Precisely Resolving Complex Structural Variations in Cancers by Whole Genome Assembly from Primary Tumor, Unpublished.
  6. Ichihara Y. et al., Organization of human immunoglobulin heavy chain diversity gene loci, EMBO J, vol. 7, no. 13, 1988, pp. 4141-4150. PUBMED: 3243276
  7. Li,H. et al., Direct Submission, Genomics Institute, UCSC Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA.
  8. Li,H. et al., Human Pangenomics Reference Consortium: Year 1 Assemblies, Unpublished.
  9. Liao,W.W. et al., A draft human pangenome reference, Nature, vol. 617, no. 7960, 2023, pp. 312-324.
  10. Liao W.W. et al., A draft human pangenome reference, Nature, vol. 617, no. 7960, 2023, pp. 312-324. PUBMED: 37165242
  11. Li H. et al., Human Pangenomics Reference Consortium: Year 1 Assemblies, Unpublished.
  12. 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
  13. Mattila P.S. et al., Extensive allelic sequence variation in the J region of the human immunoglobulin heavy chain gene locus, Eur. J. Immunol, vol. 25, no. 9, 1995, pp. 2578-2582. PUBMED: 7589129
  14. Nottenburg C. et al., Variant human JH6 gene sequence has two amino acid replacements, Unpublished.
  15. Ohm-Laursen L. et al., Identification of two new alleles, IGHV3-23*04 and IGHJ6*04, and the complete sequence of the IGHV3-h pseudogene in the human immunoglobulin locus and their prevalences in Danish Caucasians, Immunogenetics, vol. 57, no. 9, 2005, pp. 621-627. DOI: 10.1007/s00251-005-0035-8
  16. Rabbitts T.H. et al., Human immunoglobulin heavy chain genes: evolutionary comparisons of C mu, C delta and C gamma genes and associated switch sequences, Nucleic Acids Res, vol. 9, no. 18, 1981, pp. 4509-4524. DOI: 10.1093/nar/9.18.4509
  17. Rabbitts T.H. et al., The nineteenth Colworth Medal Lecture. The human immunoglobulin genes, Biochem. Soc. Trans, vol. 11, no. 2, 1983, pp. 119-126. PUBMED: 6420211
  18. Rabbitts T.H. et al., Transcription enhancer identified near the human C mu immunoglobulin heavy chain gene is unavailable to the translocated c-myc gene in a Burkitt lymphoma, Nature, vol. 306, no. 5945, 1983, pp. 806-809. DOI: 10.1038/306806a0
  19. Ravetch J.V. et al., Structure of the human immunoglobulin mu locus: characterization of embryonic and rearranged J and D genes, Cell, vol. 27, no. 3 Pt 2, 1981, pp. 583-591. DOI: 10.1016/0092-8674(81)90400-1
  20. Siebenlist U. et al., Human immunoglobulin D segments encoded in tandem multigenic families, Nature, vol. 294, no. 5842, 1981, pp. 631-635. DOI: 10.1038/294631a0
  21. Wong,K. et al., Towards a reference genome that captures global genetic diversity, Unpublished.