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 house mouse (Mus musculus) 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 12F2 (58.0 cM)
RTPr
++
 J1 BALB/c V00762 [13] 405-496 V00759 [3] 162-214 *
JH1 129/Sv AJ851868 [18] 1207514-1207605
AKR X63165 [23] 11-63 *
BALB/c J00440 [1-5,7-9,13-15,19,24] (1) 980-1071
BALB/c X53774 [11] 1-53 *
BALB/c X63166 [23] 10-62 *
BALB/cJ BK063713✤ [12] 3906634-3906725
C58 X63168 [23] 9-61 *
CBA X63169 [23] 10-62 *
CE X63170 [23] 10-62 *
DBA/2 X63171 [23] 10-62 *
DBA/2J BK063714✤ [12] 3283678-3283769
NZB X63172 [23] 10-62 *
RF X63173 [23] 10-62 *
RIII X63174 [23] 10-62 *
IGHJ1 IGHJ1*02 F 12F2 (58.0 cM)
RTPr
++
 J1 V00770 [20] 27-117
IGHJ1 IGHJ1*03 F 12F2 (58.0 cM)
RTPr
++
 J1 A/J X63164 [23] MAP 12-64 * C57BL/6J AC073553 [22] ° 133051-133142
CM001005.2 C57BL/6J BK063712✤ [12] 2590080-2590171
C57BL/10 X63167 [23] 10-62 *
NOD/SCID IMGT000188 [21] 2591263-2591353
SJL X63175 [23] 10-62 *
IGHJ2 IGHJ2*01 F 12F2 (58.0 cM)
RTPr
++
 J2 V00770 [20] MAP 344-430 JH2 129/Sv AJ851868 [18] 1207871-1207918 *
A/J X63164 [23] 291-377
AKR X63165 [23] 290-376
BALB/c J00440 [1-5,7-9,13-15,19,24] (1) 1298-1384
BALB/c V00759 [3] 480-527 *
BALB/c V00762 [13] 723-809
BALB/c X63166 [23] 289-375
BALB/cJ BK063713✤ [12] 3906952-3907038
C57BL/6J AC073553 [22] ° 133369-133455
CM001005.2 C57BL/6J BK063712✤ [12] 2590398-2590484
C57BL/10 X63167 [23] 289-375
C58 X63168 [23] 288-374
CBA X63169 [23] 289-375
CE X63170 [23] 289-375
DBA/2 X63171 [23] 289-375
DBA/2J BK063714✤ [12] 3283996-3284082
NOD/SCID IMGT000188 [21] 2591580-2591666
NZB X63172 [23] 289-375
RF X63173 [23] 289-375
RIII X63174 [23] 289-375
SJL X63175 [23] 289-375
IGHJ2 IGHJ2*02 F 12F2 (58.0 cM)
RTPr
?+
 JH2 S73821 [25] (2) 228-314
IGHJ2 IGHJ2*03 F 12F2 (58.0 cM)
RTPr
++
 JH2 S77041 [17] (3) 1-46 *
IGHJ3 IGHJ3*01 F 12F2 (58.0 cM)
RTPr
++
 J3 V00770 [20] MAP 727-813 M17064 [6] 298-384
M17065 [6] 299-385
M17066 [6] 298-384
S73819 [25] (4) 288-335 *
S77027 [17] (4) 2-49 *
S77041 [17] (4) 343-429
JH3 129/Sv AJ851868 [18] 1208215-1208301
A/J X63164 [23] 674-760
AKR X63165 [23] 673-759
BALB/c J00440 [1-5,7-9,13-15,19,24] (1) 1681-1767
BALB/c M28190 [10] 3-89
BALB/c V00762 [13] 1106-1192
BALB/c X53774 [11] 663-749
BALB/c X63166 [23] 672-758
BALB/cJ BK063713✤ [12] 3907335-3907421
C57BL/6J AC073553 [22] ° 133752-133838
CM001005.2 C57BL/6J BK063712✤ [12] 2590781-2590867
C57BL/10 X63167 [23] 672-758
C58 X63168 [23] 671-757
CBA X63169 [23] 672-758
CE X63170 [23] 672-758
DBA/2 X63171 [23] 672-758
DBA/2J BK063714✤ [12] 3284379-3284465
NOD/SCID IMGT000188 [21] 2591963-2592049
NZB X63172 [23] 672-758
RF X63173 [23] 672-758
RIII X63174 [23] 672-758
SJL X63175 [23] 672-758
IGHJ3 IGHJ3*02 P (6) 12F2 (58.0 cM)
RTPr
++
 JH3 S73821 [25] (5) 611-697
IGHJ4 IGHJ4*01 F 12F2 (58.0 cM)
RTPr
++
 J4 V00770 [20] MAP 1295-1386 S77027 [17] (4) 530-621
V00769 [20] 11-64 *
JH4 129/Sv AJ851868 [18] 1208820-1208873 *
A/J X63164 [23] 1280-1333 *
AKR X63165 [23] 1239-1331
BALB/c J00440 [1-5,7-9,13-15,19,24] (1) 2248-2340
BALB/c X53774 [11] 1229-1321
BALB/c X63166 [23] 1238-1330
BALB/cJ BK063713✤ [12] 3907902-3907993
C57BL/6 M64567 [16] 199-252 *
C57BL/6J AC073553 [22] ° 134318-134409
CM001005.2 C57BL/6J BK063712✤ [12] 2591347-2591438
C57BL/10 X63167 [23] 1237-1329
C58 X63168 [23] 1237-1329
CBA X63169 [23] 1277-1330 *
CE X63170 [23] 1277-1330 *
DBA/2 X63171 [23] 1277-1330 *
DBA/2J BK063714✤ [12] 3284946-3285037
NOD/SCID IMGT000188 [21] 2592529-2592620
NZB X63172 [23] 1277-1330 *
RF X63173 [23] 1277-1330 *
RIII X63174 [23] 1277-1330 *
SJL X63175 [23] 1276-1329 *

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

IMGT notes: ↑
  1. This sequence has been artificially constructed by junction of the sequences from 19 overlapping clones.
  2. The one nucleotide difference most probably derive from hypersomatic mutation [11], as this IGHJ2 germline segment is downstream of a IGH V-D-J1 rearrangement. This accession number is therefore not included in Table of alleles and Alignments of alleles.
  3. Partial J-REGION: two nucleotides missing in 5'.
  4. Mus sp. species sequence.
  5. The two nucleotide differences most probably derive from hypersomatic mutations [11], as this IGHJ3 germline segment is downstream of a IGH V-D-J1 rearrangement. This accession number is therefore not included in Table of alleles and Alignments of alleles.
  6. Pseudogene due to a STOP-CODON.
IMGT references: ↑
  1. Banerji J. et al., A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes, Cell, vol. 33, no. 3, 1983, pp. 729-740. DOI: 10.1016/0092-8674(83)90015-6
  2. Davis M.M. et al., DNA sequences mediating class switching in alpha-immunoglobulins, Science, vol. 209, no. 4463, 1980, pp. 1360-1365. DOI: 10.1126/science.6774415
  3. Early P. et al., An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH, Cell, vol. 19, no. 4, 1980, pp. 981-992. DOI: 10.1016/0092-8674(80)90089-6
  4. Gilliam A.C. et al., Illegitimate recombination generates a class switch from C mu to C delta in an IgD-secreting plasmacytoma, Proc. Natl. Acad. Sci. U.S.A, vol. 81, no. 13, 1984, pp. 4164-4168. PUBMED: 6429663
  5. Gillies S.D. et al., A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene, Cell, vol. 33, no. 3, 1983, pp. 717-728. DOI: 10.1016/0092-8674(83)90014-4
  6. Gilmore G.L. et al., Absence of somatic mutation in the variable region of MPC 11 variants expressing a different heavy chain isotype, J. Immunol, vol. 139, no. 2, 1987, pp. 619-624. PUBMED: 3110275
  7. Gough N.M. et al., Sequences of the joining region genes for immunoglobulin heavy chains and their role in generation of antibody diversity, Proc. Natl. Acad. Sci. U.S.A, vol. 78, no. 1, 1981, pp. 509-513. PUBMED: 6787590
  8. Kallen R. et al., Unpublished.
  9. Kim S.K. et al., Antibody diversity: somatic hypermutation of rearranged VH genes, Cell, vol. 27, no. 3 Pt 2, 1981, pp. 573-581. DOI: 10.1016/0092-8674(81)90399-8
  10. Komori T. et al., A novel VHDJH to JH joining that induces H chain production in an Ig-null immature B cell line, J. Immunol, vol. 143, no. 3, 1989, pp. 1040-1045. PUBMED: 2501385
  11. Lebecque S.G. et al., Boundaries of somatic mutation in rearranged immunoglobulin genes: 5' boundary is near the promoter, and 3' boundary is approximately 1 kb from V(D)J gene, J. Exp. Med, vol. 172, no. 6, 1990, pp. 1717-1727. DOI: 10.1084/jem.172.6.1717
  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. Newell N. et al., J genes for heavy chain immunoglobulins of mouse, Science, vol. 209, no. 4461, 1980, pp. 1128-1132. PUBMED: 6250219
  14. Nikaido T. et al., Switch region of immunoglobulin Cmu gene is composed of simple tandem repetitive sequences, Nature, vol. 292, no. 5826, 1981, pp. 845-848. DOI: 10.1038/292845a0
  15. Obata M. et al., Structure of a rearranged gamma 1 chain gene and its implication to immunoglobulin class-switch mechanism, Proc. Natl. Acad. Sci. U.S.A, vol. 78, no. 4, 1981, pp. 2437-2441. DOI: 10.1073/pnas.78.4.2437
  16. Owens J.D.Jr. et al., Nonhomologous recombination at sites within the mouse JH-C delta locus accompanies C mu deletion and switch to immunoglobulin D secretion, Mol. Cell. Biol, vol. 11, no. 11, 1991, pp. 5660-5670. PUBMED: 1922069
  17. Portanova J.P. et al., An early post-mutational selection event directs expansion of autoreactive B cells in murine lupus, Mol. Immunol, vol. 32, no. 2, 1995, pp. 117-135. DOI: 10.1016/0161-5890(94)00129-O
  18. Retter I. et al., Sequence and characterization of the Ig heavy chain constant and partial variable region of the mouse strain 129S1, J. Immunol, vol. 179, no. 4, 2007, pp. 2419-2427. PUBMED: 17675503
  19. Sakano H. et al., Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes, Nature, vol. 290, no. 5807, 1981, pp. 562-565. DOI: 10.1038/290562a0
  20. Sakano H. et al., Two types of somatic recombination are necessary for the generation of complete immunoglobulin heavy-chain genes, Nature, vol. 286, no. 5774, 1980, pp. 676-683. DOI: 10.1038/286676a0
  21. Schmid-Siegert E. et al., Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models, Unpublished.
  22. Smith D.R. et al., Genome Therapeutics Corporation Sequencing Center: Mouse Genome Sequence Data, Unpublished.
  23. Solin M.L. et al., Allelic polymorphism of mouse Igh-J locus, which encodes immunoglobulin heavy chain joining (JH) segments, Immunogenetics, vol. 36, no. 5, 1992, pp. 306-313. DOI: 10.1007/BF00215659
  24. Takahashi N. et al., Nucleotide sequences of class-switch recombination region of the mouse immunoglobulin gamma 2b-chain gene, Gene, vol. 11, no. 1-2, 1980, pp. 117-127. DOI: 10.1016/0378-1119(80)90092-X
  25. Weber J.S. et al., Mutations in Ig V(D)J genes are distributed asymmetrically and independently of the position of V(D)J, J. Immunol, vol. 153, no. 8, 1994, pp. 3594-3602. PUBMED: 7930582