IMGT Repertoire (IG and TR)


Gene table: house mouse (Mus musculus) IGHD

"+" 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 between 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.
Functionality is shown between brackets, [F] and [P], when the accession number refers to genomic DNA, but not known as being germline or rearranged.

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IMGT subgroup IMGT gene name IMGT allele name Fct Chromosomal localization R T Pr Positions in the locus IMGT/LIGM-DB reference sequences IMGT/LIGM-DB sequences from the literature
Strain Clone names Accession numbers Positions in the sequence Secondary accession numbers Strain Clone names Accession numbers Positions in the sequence
IGHD1 IGHD1-1 IGHD1-1*01 F 12 (58.0 cM) + + BALB/c DFL16.1 MAP J00434 [3] C57BL/6J DFL16.1 AF018146 [19]
AC073553 [11] 80731-80753
BALB/c DFL16.1 MAP J00434 [3] 129/Sv DFL16.1 AJ851868 [18] 1145622-1145644
C57BL/6J IMGT000065 MAP 2537760-2537782
IGHD1-1*02 F 12 (58.0 cM) + + A/J DFL16.1e MAP M35332 [4]
IGHD1-2 IGHD1-2*01 F 12 (58.0 cM) + + BALB/c DFL16.2 MAP J00436 [3]
BALB/c DFL16.2 MAP J00436 [3] 129/Sv DFL16.2 AJ851868 [18] 1160902-1160918
IGHD1-3 IGHD1-3*01 F 12 (58.0 cM) 129/Sv DFL16.3 MAP AJ851868 [18] 1093409-1093431 C57BL/6J IMGT000065 MAP 2491898-2491920
IGHD2 IGHD2-1 IGHD2-1*01 F 12 (58.0 cM) + 129/Sv DSP2.5 MAP AJ851868 [18] 1165535-1165551 BALB/c DSP2.1 J00497 [2] (4)
CB.20 DSP2.1 M60955 [7] (4)
IGHD2-2 IGHD2-2*01 F 12 (58.0 cM) + + BALB/c DSP2.4 MAP J00437 [3] 129/Sv DSP2.3 AJ851868 [18] 1156802-1156818
IGHD2-3 IGHD2-3*01 F 12 (58.0 cM) + + BALB/c D-SP2.9 MAP D13199 [10] (2) CB.20 DSP2.9 M60962 [7] (4)
BALB/c DSP2.9 [15] (8)
C57BL/6J D-SP2.9 AC073553 [11] 87507-87523
129/Sv DSP2.9 AJ851868 [18] 1152483-1152499
C57BL/6J IMGT000065 2544536-2544552
IGHD2-4 IGHD2-4*01 F 12 (58.0 cM) + + BALB/c DSP2.2 MAP J00431 [2] CB.20 DSP2.2 M60956 [7] (4)
C57BL/6J DSP2.2 AC073553 [11] 92213-92229
129/Sv DSP2.2 AJ851868 [18] 1170183-1170199
C57BL/6J IMGT000065 MAP 2549242-2549258
IGHD2-5 IGHD2-5*01 F 12 (58.0 cM) + CB.20 DSP2.x MAP M60961 [7] (4) C57BL/6J DSP2.x AC073553 [11] 96880-96896
IMGT000065 MAP 2553909-2553925
IGHD2-6 IGHD2-6*01 F 12 (58.0 cM) C57BL/6J DSP2.x MAP AC073553 [11] 101538-101554 C57BL/6J IMGT000065 MAP 2558567-2558583
IGHD2-7 IGHD2-7*01 F 12 (58.0 cM) + + BALB/c DSP2.3 MAP J00435 [3] CB.20 DSP2.3 M60957 [7] (4)
C57BL/6J DSP2.3 AC073553 [11] 106187-106203
IMGT000065 MAP 2563216-2563232
IGHD2-8 IGHD2-8*01 F 12 (58.0 cM) + + BALB/c DSP2.5 MAP J00432 [3] CB.20 DSP2.5 M60958 [7] (4)
C57BL/6J D-SP2.5 AC073553 [11] 112056-112072
IMGT000065 MAP 2569085-2569101
IGHD2-9 IGHD2-9*01 F 12 (58.0 cM) + + BALB/c DSP2.6 MAP J00433 [3]
IGHD2-9*02 F 12 (58.0 cM) 129/Sv DSP2.2 MAP AJ851868 [18] 1179853-1179869
IGHD2-10 IGHD2-10*01 F 12 (58.0 cM) + + BALB/c DSP2.7 MAP J00438 [3] CB.20 DSP2.7 M60959 [7] (4)
IGHD2-10*02 F 12 (58.0 cM) 129/Sv DSP2.8 MAP AJ851868 [18] 1184513-1184529
IGHD2-11 IGHD2-11*01 F 12 (58.0 cM) + + BALB/c DSP2.8 MAP J00439 [3] CB.20 DSP2.8 M60960 [7] (4)
IGHD2-11*02 F 12 (58.0 cM) 129/Sv DSP2.7 MAP AJ851868 [18] 1189645-1189661
IGHD2-12 IGHD2-12*01 F 12 (58.0 cM) MRL/Mp-lpr DSP2.12 MAP AF428079 [12]
IGHD2-13 IGHD2-13*01 F 12 (58.0 cM) MRL/Mp-lpr DSP2.13 MAP AF428080 [12]
IGHD2-14 IGHD2-14*01 F 12 (58.0 cM) 129/Sv DSP2.11 MAP AJ851868 [18] 1174861-1174877 BALB/c DSP2.10 AF144976 [17] (11) #c
[13] (8)
IGHD3 IGHD3-1 IGHD3-1*01 F 12 (58.0 cM) + + C57BL/6J DST4.2 MAP AC073553 [11] 37594-37610 129/Sv DST4.2 AJ851868 [18] 1096108-1096124
C57BL/6J IMGT000065 2494623-2494639
IGHD3-2 IGHD3-2*01 F (1) 12 (58.0 cM) + + BALB/c DST4 MAP M23243 [5] (12) BALB/c DSP2.11 M76416 [16] #c
129/Sv DST4 AJ851868 [18] 1192320-1192335
IGHD3-2*02 F 12 (58.0 cM) C57BL/6J DST4 MAP AC073553 [11] 114694-114709 C57BL/6J IMGT000065 MAP 2571723-2571738
IGHD3-3 IGHD3-3*01 F 12 (58.0 cM) 129/Sv DST4.3 MAP AJ851868 [18] 1159345-1159361
IGHD4 IGHD4-1 IGHD4-1*01 F 12 (58.0 cM) + + BALB/c DQ52 MAP L32868 [6] C57BL/6J DQ52 AC073553 [11] 132385-132395
129/Sv DQ52 AJ851868 [18] 1206848-1206858
C57BL/6J IMGT000065 MAP 2589414-2589424
IGHD4-1*02 F 12 (58.0 cM) + + BALB/c DQ52 MAP J00440 [9]
IGHD5 IGHD5-1 IGHD5-1*01 P (13) 12 (58.0 cM) C57BL/6J P1 MAP AC073553 [11] 36114-36123 IMGT000065 MAP 2493143-2493152
IGHD5-1-1 IGHD5-1-1*01 ORF (15) 12 (58.0 cM) C57BL/6J MAP IMGT000065 2539563-2539572
IGHD5-2 IGHD5-2*01 ORF (10) 12 (58.0 cM) C57BL/6J P2 MAP AC073553 [11] 93488-93497 C57BL/6J IMGT000065 MAP 2550517-2550526
IGHD5-3 IGHD5-3*01 ORF (10) 12 (58.0 cM) C57BL/6J P3 MAP AC073553 [11] 98153-98162 C57BL/6J IMGT000065 MAP 2555182-2555191
IGHD5-4 IGHD5-4*01 ORF (10) 12 (58.0 cM) C57BL/6J P4 MAP AC073553 [11] 102813-102822 C57BL/6J IMGT000065 MAP 2559842-2559851
IGHD5-5 IGHD5-5*01 ORF (10) 12 (58.0 cM) C57BL/6J P5 MAP AC073553 [11] 107972-107981 C57BL/6J IMGT000065 MAP 2565001-2565010
IGHD5-6 IGHD5-6*01 ORF (10) 12 (58.0 cM) C57BL/6J P6 MAP AC073553 [11] 113326-113335 C57BL/6J IMGT000065 MAP 2570355-2570364
IGHD6 IGHD6-1 IGHD6-1*01 F 12 (58.0 cM) - - C57BL/6J AC073553 [11] 82752-82780 IMGT000065 MAP 2539781-2539809
IGHD6-1*02 F 12 (58.0 cM) - - BALB/c PseudoD1 MAP M26508 [8] BALB/c PseudoD1 D13197 [10] (2,5)
IGHD6-2 IGHD6-2*01 F 12 (58.0 cM) - - C57BL/6J AC073553 [11] 88020-88048 BALB/c PseudoD2 MAP D13198 [10] (2,7,14)
C57BL/6J IMGT000065 MAP 2545049-2545077
IGHD6-2-1 IGHD6-2-1*01 F 12 (58.0 cM) C57BL/6J IMGT000065 MAP 2550735-2550763
IGHD6-3 IGHD6-3*01 F 12 (58.0 cM) C57BL/6J P7, IGHD5-7 MAP AC073553 [11] 98371-98399 C57BL/6J IMGT000065 MAP 2555400-2555428
IGHD6-4 IGHD6-4*01 F 12 (58.0 cM) C57BL/6J P8, IGHD5-8 MAP AC073553 [11] 103031-103059 C57BL/6J IMGT000065 MAP 2560060-2560088
IGHD6-5 IGHD6-5*01 ORF (16) 12 (58.0 cM) C57BL/6J IMGT000065 MAP 2565217-2565245

#c: rearranged cDNA.
MAP: Mapped sequences.

IMGT notes:
  1. (1) IGHD3-2 was described as a pseudogene by Gerondakis S. et al. [5], because this D-GENE lacked the appropriate 3'D-RS. Despite this apparent lack of 3'D-RS Fenney A.J. and Riblet R. [1] demonstrated that this D-GENE can rearrange and therefore is functional.
  2. (2) Circular clones.
  3. (3) Defective 3'D-RS.
  4. (4) DH-JH joint, only the D-REGION and 5'UTR are present.
  5. (5) D-GENE is partial: no 3'D-RS, no D-REGION.
  6. (6) Defective 5'D-RS.
  7. (7) DH-JH joint.
  8. (8) No accession number.
  9. (9) CB.20 is a congenic line with the IGH locus of C57BL/Ka (IgHb) on BALB/c (IgHa) background (Bosma and Bosma, 1974).
  10. (10) Potential D-GENEs.
  11. (11) The nucleotide at the 5' end deleted in this rearranged sequence has been proposed to be t in [14] and c in [12].
  12. (12) Except for the 5' nucleotide, this D was identified in rearranged sequences in [14] and refered in later publications as DSP2.11. Howewer the rearranged DSP2.11 clone sequence has three nucleotides and five nucleotides different in 5' and 3', respectively. These differences probably correspond to N-Diversity.
  13. (13) Defective 5'D-NONAMER.
  14. (14) D13199 (BALB/c) [10] contains part of the 5'UTR of IGHD6-2 (2,5)
  15. (15) Noncanonical 3'D-NONAMER
  16. (16) noncanonical 3'D-HEPTAMER
IMGT references:
  1. [1] Feeney A.J. and Riblet R., Immunogenetics, 37, 217-221 (1993). PMID:8420829
  2. [2] Kurosawa Y. et al., Nature, 290, 565-570 (1981). PMID:6783962
  3. [3] Kurosawa Y. and Tonegawa S., J. Exp. Med., 155, 201-218 (1982). PMID:6798155
  4. [4] Landolfi N.F. et al., J. Immunol., 137, 362-365 (1986). PMID:3011910
  5. [5] Gerondakis S. et al., Immunogenetics, 28, 255-259 (1988). PMID:2843460
  6. [6] Dirkes G. et al., Immunogenetics, 40, 379 (1994). PMID:7927543
  7. [7] Gu H. et al., Cell, 65, 47-54 (1991). PMID:2013094
  8. [8] Lennon G.G. and Perry R.P., Immunogenetics, 30, 383-386 (1989). PMID:2509341
  9. [9] Gillian A.C., Proc. Natl. Acad. Sci. USA., 81, 4164-4168 (1984). PMID:6429663
  10. [10] Shimizu T. and Yamagishi H., EMBO J., 11, 4869-4875 (1992). PMID:1464314
  11. [11] Smith D.R., Unpublished.
  12. [12] Kompfner E. et al., J. Immunol., 167, 6933-6938 (2001). PMID:11739512
  13. [13] Chang Y. et al., EMBO J., 11, 1891-1899 (1992). PMID:1582417
  14. [14] Feeney A.J. et al., J. Exp. Med., 172, 1377-1390 (1990). PMID:1700054
  15. [15] Lawler A.M. et al., Proc. Natl. Acad. Sci. USA., 84, 2454-2458 (1987). PMID:3104915
  16. [16] Deng Y.J. et al., Mol. Immunol., 29, 847-856 (1992). PMID:1378929
  17. [17] Benedict C.L. et al., Immunity, 10, 607-617 (1999). PMID:10367906
  18. [18] Retter I. et al., Unpublished.
  19. [19] Ichihara Y. et al., Eur. J. Immunol., 19, 1849-1854(1989). PMID:2583225
Created:
09/03/2000
Last updated:
22/09/2023
Authors:
Géraldine Folch, Anna Tran