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"+" 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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The Bos taurus IGH locus is localized on chromosome 21.
Localization on chromosome 21q24 for the sequences other than KT723008 needs to be confirmed as their allele assignment is only based on sequence alignment of the D-REGION with those of KT723008.
The hits to sequences other than KT723008 are given for completeness but information on the positions in the contig and chromosomal localization of these sequences should be taken with great caution owing to the uncertainties regarding the genome assembly, and to the difficulty of assigning genes due to the duplications in the IGH locus.
Several pairs of genes have high percentage of identity of their D-REGION, reaching 100% of identity for the functional IGHD3-1*01, IGHD3-3*01 and IGHD3-4*01 genes, IGHD5-3*01 and IGHD5-4*01, and IGHD6-3*01 and IGHD6-4*01. Arbitrarily these sequences are assigned to the gene with the smallest number.

Bos taurus IGHD genes owing to their organization, different from that of Homo sapiens IGHD genes, are designated by a number for the subgroup (1 to 9), followed by an hyphen and a number for the cluster (1 to 4) from 5' to 3' in the locus.

IMGT subgroup IMGT gene name IMGT allele name Fct Chromosomal
localization		 R T Pr IMGT/LIGM-DB locus reference sequences IMGT/LIGM-DB sequences from the literature
Breed Clone names Accession numbers Positions in the sequence
(D-GENE-UNIT)		 Secondary accession numbers Breed Clone names Accession numbers Positions in the sequence
(D-GENE-UNIT)
IGHD1 IGHD1-1 IGHD1-1*01 F 21q24 + + Holstein KT723008 [1] MAP 284856..284942 Hereford BosTau_1_chr21 (4) complement(125560..125646)
IGHD1-2 IGHD1-2*01 ORF (1) 21q24 + + Holstein KT723008 [1] MAP 369474..369560
IGHD1-3 IGHD1-3*01 ORF (2) 21q24 + + Holstein KT723008 [1] MAP 422613..422787
IGHD1-4 IGHD1-4*01 F 21q24 Holstein KT723008 [1] MAP 476206..476292
IGHD2 IGHD2-1 IGHD2-1*01 F 21q24 + + Holstein KT723008 [1] MAP 286100..286171 Hereford BosTau_1_chr21 (4) complement(124331..124402)
IGHD2-2 IGHD2-2*01 F 21q24 Holstein KT723008 [1] MAP 370692..370763
IGHD2-3 IGHD2-3*01 F 21q24 Holstein KT723008 [1] MAP 423840..423911
IGHD2-4 IGHD2-4*01 F 21q24 Holstein KT723008 [1] MAP 477433..477504
IGHD3 IGHD3-1 IGHD3-1*01 F 21q24 + + Holstein KT723008 [1] MAP 287243..287334 Hereford BosTau_1_chr21 (4) complement(123179..123270)
Holstein HM543732 [3] (4) 2..93
HM543737 [3] (4) 2..93
IGHD3-3 IGHD3-3*01 F 21q24 Holstein KT723008 [1] MAP 424980..425071
IGHD3-4 IGHD3-4*01 F 21q24 Holstein KT723008 [1] MAP 478574..478665
IGHD4 IGHD4-1 IGHD4-1*01 F 21q24 + + Holstein KT723008 [1] MAP 287686..287784 Hereford BosTau_1_chr21 (4) complement(122729..122827)
Holstein HM543736 [3] (4) 2..100
IGHD5 IGHD5-2 IGHD5-2*01 F 21q24 + + Holstein KT723008 [1] MAP 371829..371926 AY559838 [4] (4) 2..99
IGHD5-3 IGHD5-3*01 F 21q24 + + Holstein KT723008 [1] MAP 425887..425984 Holstein HM543734 [3] (4) 2..99
IGHD5-4 IGHD5-4*01 F 21q24 Holstein KT723008 [1] MAP 479486..479583
IGHD6 IGHD6-2 IGHD6-2*01 F 21q24 + + Holstein KT723008 [1] MAP 372840..372953 AY559840 [4] (4) 2..115
IGHD6-3 IGHD6-3*01 F 21q24 + + Holstein KT723008 [1] MAP 426339..426452 Holstein HM543735 [3] (4) 2..115
IGHD6-4 IGHD6-4*01 F 21q24 Holstein KT723008 [1] MAP 479938..480051
IGHD7 IGHD7-3 IGHD7-3*01 F 21q24 + + Holstein KT723008 [1] MAP 425411..425533 Holstein HM543733 [3] (4) 2..124
IGHD7-4 IGHD7-4*01 F 21q24 + + Holstein KT723008 [1] MAP 479005..479133
IGHD8 IGHD8-2 IGHD8-2*01 F 21q24 + + Holstein KT723008 [1] MAP 372282..372485 AY559839 [4] (4) 2..205
IGHD9 IGHD9-1 IGHD9-1*01 F 21q24 + + Holstein KT723008 [1] MAP 319619..319688 Hereford NW_001494075 (4) complement(40319..40388)
AY149283 [2] (3,4) 85..154
IGHD9-4 IGHD9-4*01 F 21q24 Holstein KT723008 [1] MAP 504099..504168

MAP: Mapped reference sequences.

IMGT notes:
  1. (1) noncanonical 5'D-HEPTAMER: caccctg instead of cactgtg
  2. (2) noncanonical 3'D-HEPTAMER: caaggtg instead of cacagtg, noncanonical 3'D-NONAMER: actcgggac instead of acaaaaacc
  3. (3) Functionality different from the reference sequence: ORF because noncanonical 3'D-HEPTAMER: cacaaaa instead of cacagtg
  4. (4) See caution note above the Gene table
IMGT references:
  1. [1] Ma L. et al. J Immunol. 2016 May 15;196(10):4358-66. doi: 10.4049/jimmunol.1600158. Epub 2016 Apr 6. PMID:27053761
  2. [2] Hosseini A. et al. Int Immunol. 2004 Jun;16(6):843-52. Epub 2004 May 4. PMID:15126417
  3. [3] Koti M. et al. Mol Immunol. 2010 Jul;47(11-12):2119-28. doi: 10.1016/j.molimm.2010.02.014. PMID:20435350
  4. [4] Shojaei F. et al. Mol Immunol. 2003 Sep;40(1):61-7. PMID:12909131
Created:
25/10/2017
Last updated:
22/09/2023
Authors:
Perrine Pégorier