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.

Truncated pseudogenes not assigned to subgroups with functional genes

Gene table of house mouse (Mus musculus) IGHV (clans) IMGT group:
IMGT sub­groupIMGT 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
(L-V-GENE-UNIT)
or V-REGION (*)		Secondary
accession
numbers		Clone namesStrainAccession
numbers		Positions
in the sequence
(L-V-GENE-UNIT)
or V-REGION (*)
IGHV(I)IGHV(I)-1 IGHV(I)-1*01 P (1) 12F2 (58.0 cM) C57BL/6 BN000872 [1] MAP 657956-658423 CM001005.2 C57BL/6J BK063712✤ [2] 606829-607295
NOD/SCID IMGT000188 [4] 606820-607286
IGHV(I)IGHV(I)-2 IGHV(I)-2*01 P (2) 12F2 (58.0 cM) CM001005.2 C57BL/6J BK063712✤ [2] MAP 310878-311314 C57BL/6 BN000872 [1] 362004-362440
NOD/SCID IMGT000188 [4] 310877-311345
IGHV(I)IGHV(I)-3 IGHV(I)-3*01 P (3) 12F2 (58.0 cM) NOD/SCID IMGT000188 [4] <752098-752326 *
IGHV(II)IGHV(II)-1 IGHV(II)-1*01 P (4) 12F2 (58.0 cM) musIGHV194 129/Sv AJ851868 [3] MAP 974395-974864 BALB/cJ BK063713✤ [2] 3673235-3673704
C57BL/6 BN000872 [1] 2423350-2423819
CM001005.2 C57BL/6J BK063712✤ [2] 2372046-2372515
NOD/SCID IMGT000188 [4] 2373224-2373693
IGHV(II)IGHV(II)-2 IGHV(II)-2*01 P (5) 12F2 (58.0 cM) musIGHV200 129/Sv AJ851868 [3] MAP 919215-919651 BALB/cJ BK063713✤ [2] 3638235-3638703
C57BL/6 BN000872 [1] 2388363-2388799
NOD/SCID IMGT000188 [4] 2338234-2338702
IGHV(II)IGHV(II)-2D IGHV(II)-2D*01 P (6) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3602649-3603117
IGHV(II)IGHV(II)-3 IGHV(II)-3*01 P (7) 12F2 (58.0 cM) musIGHV431 129/Sv AJ851868 [3] 792977-793446 BALB/cJ BK063713✤ [2] 3476409-3476878
IGHV(II)IGHV(II)-4 IGHV(II)-4*01 P (5) 12F2 (58.0 cM) musIGHV200 129/Sv AJ851868 [3] 718413-718881 BALB/cJ BK063713✤ [2] 3402816-3403284
IGHV(II)IGHV(II)-5 IGHV(II)-5*01 P (4) 12F2 (58.0 cM) musIGHV415 129/Sv AJ851868 [3] 570827-571294 BALB/cJ BK063713✤ [2] 3254989-3255456
IGHV(II)IGHV(II)-6 IGHV(II)-6*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] <3512045-3512236 *
IGHV(III)IGHV(III)-1 IGHV(III)-1*01 P (9) 12F2 (58.0 cM) C57BL/6 AC160985 [5] MAP complement(62006-62592) C57BL/6 BN000872 [1] 2345849-2346435
CM001005.2 C57BL/6J BK063712✤ [2] 2294649-2295235
NOD/SCID IMGT000188 [4] 2295700-2296286
IGHV(III)IGHV(III)-1 IGHV(III)-1*03 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3557328->3557617 *
IGHV(III)IGHV(III)-2 IGHV(III)-2*01 P (10) 12F2 (58.0 cM) musIGHV419 129/Sv AJ851868 [3] 654557-655146
IGHV(III)IGHV(III)-3 IGHV(III)-3*01 P (4) 12F2 (58.0 cM) musIGHV412 129/Sv AJ851868 [3] 522643-523233 BALB/cJ BK063713✤ [2] 3208237-3208681
IGHV(III)IGHV(III)-4 IGHV(III)-4*01 P (4) 12F2 (58.0 cM) musIGHV410 129/Sv AJ851868 [3] MAP 486899-487391
IGHV(III)IGHV(III)-4 IGHV(III)-4*02 P (11) 12F2 (58.0 cM) C57BL/6J BK063712✤ [2] 2216629-2216979 C57BL/6 AC160985 [5] complement(140303-140601) *
C57BL/6 BN000872 [1] 2267837-2268137 *
NOD/SCID IMGT000188 [4] 2217677-2217977 *
IGHV(III)IGHV(III)-4 IGHV(III)-4*03 P (8) 12F2 (58.0 cM) DBA/2J BK063714✤ [2] 3021573-3022065
IGHV(III)IGHV(III)-5 IGHV(III)-5*01 P (12) 12F2 (58.0 cM) musIGHV423 129/Sv AJ851868 [3] 310751-311088
IGHV(III)IGHV(III)-5 IGHV(III)-5*02 P (13) 12F2 (58.0 cM) CM001005.2 C57BL/6J BK063712✤ [2] MAP 2051101-2051439 C57BL/6 BN000872 [1] 2102312-2102600 *
NOD/SCID IMGT000188 [4] 2051897-2052185 *
IGHV(III)IGHV(III)-6 IGHV(III)-6*01 P (14) 12F2 (58.0 cM) musIGHV409 129/Sv AJ851868 [3] 248755-249042 *
IGHV(III)IGHV(III)-6 IGHV(III)-6*02 P (13) 12F2 (58.0 cM) CM001005.2 C57BL/6J BK063712✤ [2] MAP 1981696-1982034 C57BL/6 BN000872 [1] 2032867-2033155 *
NOD/SCID IMGT000188 [4] 1982475-1982763 *
IGHV(III)IGHV(III)-7 IGHV(III)-7*01 P (4) 12F2 (58.0 cM) musIGHV408 129/Sv AJ851868 [3] 224597-224824 *
IGHV(III)IGHV(III)-7 IGHV(III)-7*02 P (15) 12F2 (58.0 cM) CM001005.2 C57BL/6J BK063712✤ [2] MAP 1957887-1958114 * C57BL/6 BN000872 [1] 2009047-2009274 *
NOD/SCID IMGT000188 [4] 1958653->1958880 *
IGHV(III)IGHV(III)-8 IGHV(III)-8*01 P (16) 12F2 (58.0 cM) C57BL/6 AC160985 [5] MAP complement(56169->56333) * C57BL/6 BN000872 [1] 2352108-2352272 *
CM001005.2 C57BL/6J BK063712✤ [2] 2300908->2301072 *
NOD/SCID IMGT000188 [4] 2301967-2302131 *
IGHV(III)IGHV(III)-8 IGHV(III)-8*02 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3566363->3566662 *
IGHV(III)IGHV(III)-9 IGHV(III)-9*01 P (17) 12F2 (58.0 cM) C57BL/6 AC160985 [5] MAP complement(105027-105509) C57BL/6 BN000872 [1] 2302928-2303449
CM001005.2 C57BL/6J BK063712✤ [2] 2251912-2252214 *
NOD/SCID IMGT000188 [4] 2252963-2253265 *
IGHV(III)IGHV(III)-10 IGHV(III)-10*01 P (18) 12F2 (58.0 cM) C57BL/6 AC160985 [5] MAP complement(118632-119217) C57BL/6 BN000872 [1] 2289220-2289805
CM001005.2 C57BL/6J BK063712✤ [2] 2238024-2238609
NOD/SCID IMGT000188 [4] 2239075-2239660
IGHV(III)IGHV(III)-11 IGHV(III)-11*01 P (17) 12F2 (58.0 cM) C57BL/6 AC160985 [5] MAP complement(131304-131827) C57BL/6 BN000872 [1] 2276611-2277134
CM001005.2 C57BL/6J BK063712✤ [2] 2225594-2225898 *
NOD/SCID IMGT000188 [4] 2226453-2226976
IGHV(III)IGHV(III)-12 IGHV(III)-12*01 P (19) 12F2 (58.0 cM) C57BL/6 BN000872 [1] MAP 2298802-2299104 * CM001005.2 C57BL/6J BK063712✤ [2] 2247606-2247908 *
IGHV(III)IGHV(III)-13 IGHV(III)-13*01 P (20) 12F2 (58.0 cM) C57BL/6 BN000872 [1] MAP 1785968-1786453 CM001005.2 C57BL/6J BK063712✤ [2] 1734810-1735295
NOD/SCID IMGT000188 [4] 1735560-1736046
IGHV(III)IGHV(III)-14 IGHV(III)-14*01 P (21) 12F2 (58.0 cM) CM001005.2 C57BL/6J BK063712✤ [2] MAP <2248396->2248521 * C57BL/6 BN000872 [1] 2299592-2299717 *
NOD/SCID IMGT000188 [4] <2249447-2249572 *
IGHV(III)IGHV(III)-15 IGHV(III)-15*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3535629->3535802 *
IGHV(III)IGHV(III)-16 IGHV(III)-16*01 P (22) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3452537->3452711 *
IGHV(III)IGHV(III)-17 IGHV(III)-17*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3430307-3430456 *
IGHV(III)IGHV(III)-18 IGHV(III)-18*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3358791-3359069 *
IGHV(III)IGHV(III)-19 IGHV(III)-19*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3269046->3269330 *
IGHV(III)IGHV(III)-20 IGHV(III)-20*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3234514->3234687 *
IGHV(III)IGHV(III)-21 IGHV(III)-21*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] 3217856->3218029 *
IGHV(III)IGHV(III)-22 IGHV(III)-22*01 P (8) 12F2 (58.0 cM) BALB/cJ BK063713✤ [2] <2665780->2666073 *
IGHV(III)IGHV(III)-22 IGHV(III)-22*02 P (8) 12F2 (58.0 cM) DBA/2J BK063714✤ [2] <2317840->2318127 *
IGHV(III)IGHV(III)-23 IGHV(III)-23*01 P (23) 12F2 (58.0 cM) DBA/2J BK063714✤ [2] 3030632->3030935 *
IGHV(III)IGHV(III)-24 IGHV(III)-24*01 P (24) 12F2 (58.0 cM) DBA/2J BK063714✤ [2] 2609800-2610087 *

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

IMGT notes: ↑
  1. degenerated pseudogene not assigned to subgroups with functional genes
  2. frameshifts in V-REGION: several insertions and deletions, no V-NONAMER
  3. no L-PART1, no L-PART2, truncated pseudogene not assigned to subgroups with functional genes
  4. frameshifts in V-REGION, not assigned to subgroups with functional genes
  5. frameshift in L-PART1, frameshifts in V-REGION, not assigned to subgroups with functional genes
  6. frameshift in L-PART1, degenerated pseudogene not assigned to subgroups with functional genes
  7. frameshifts in L-PART1, frameshifts in V-REGION, not assigned to subgroups with functional genes
  8. truncated pseudogene not assigned to subgroups with functional genes
  9. no INIT-CODON: Ile instead of Met, frameshifts in V-REGION: several deletions
  10. in frame STOP-CODON in L-PART1, frameshifts in V-REGION, not assigned to subgroups with functional genes
  11. no L-PART1, several STOP-CODON in V-REGION, no CONSERVED-TRP: STOP-CODON instead of Trp
  12. no L-PART1, frameshifts in V-REGION, not assigned to subgroups with functional genes
  13. no L-PART1, frameshifts in V-REGION: several insertions and deletions
  14. no L-PART1, frameshifts in V-REGION, no V-RS in 3'UTR, not assigned to subgroups with functional genes
  15. no DONOR-SPLICE, frameshifts in V-REGION: several insertions and deletions, no V-RS
  16. frameshifts in V-REGION: several insertions and deletions, no V-RS
  17. in frame STOP-CODON in L-PART1 and frameshifts in V-REGION
  18. several STOP-CODON in V-REGION, frameshift in V-REGION: deletion of 7 nt in FR3-IMGT
  19. no L-PART1, frameshifts in V-REGION: several insertions and deletions, no V-RS
  20. no INIT-CODON: Cys instead of Met, frameshift in L-PART2, frameshifts in V-REGION: several insertions and deletions
  21. no L-PART1, no L-PART2, frameshifts in V-REGION: several insertions and deletions, no V-RS
  22. no INIT-CODON: Val instead of Met, truncated pseudogene not assigned to subgroups with functional genes
  23. STOP-CODON in L-PART1, truncated pseudogene not assigned to subgroups with functional genes
  24. no L-PART1, degenerated pseudogene not assigned to subgroups with functional genes
IMGT references: ↑
  1. Johnston C.M. et al., Complete sequence assembly and characterization of the C57BL/6 mouse Ig heavy chain V region, J. Immunol, vol. 176, no. 7, 2006, pp. 4221-4234. PUBMED: 16547259
  2. 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
  3. 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
  4. Schmid-Siegert E. et al., Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models, Unpublished.
  5. Zheng X. et al., The sequence of Mus musculus BAC clone RP23-333D9, Unpublished.