IMGT Repertoire (IG and TR)


Gene table: bovine (Bos taurus) IGHJ

"+" 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 J-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.

Bos taurus IGHJ genes owing to their organization, different from that of Homo sapiens IGHJ genes, are designated by a number for the cluster (1 or 2), followed by an hyphen and a number for the localization (1 to 6) from 5' to 3' in each cluster.

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
(J-GENE-UNIT)		 Secondary accession numbers Breed Clone names Accession numbers Positions in the sequence
(J-GENE-UNIT)
IGHJ1-1 IGHJ1-1*01 ORF (1) 21q24 Holstein KT723008 [1] MAP 320097..320187
IGHJ1-1*02 ORF (1) 21q24 AY149283 [2] (6) 564..655
IGHJ1-1*03 ORF (2) 21q24 Hereford NW_001494075 (6) complement(39812..39911)
IGHJ1-2 IGHJ1-2*01 ORF (3) 21q24 Holstein KT723008 [1] MAP 320277..320370
IGHJ1-2*02 ORF (3) 21q24 AY149283 [2] (6) 745..838
IGHJ1-2*03 ORF (3) 21q24 Hereford NW_001494075 (6) complement(39638..39731)
IGHJ1-3 IGHJ1-3*01 ORF (3) 21q24 Holstein KT723008 [1] MAP 320625..320713 Hereford NW_001494075 (6) complement(39295..39383)
IGHJ1-3*02 ORF (3) 21q24 AY149283 [2] (6) 1093..1181
IGHJ1-4 IGHJ1-4*01 F 21q24 Holstein KT723008 [1] MAP 320938..321023 AY149283 [2] (6) 1406..1491
IGHJ1-4*02 F 21q24 Hereford NW_001494075 (6) complement(38985..39070)
IGHJ1-5 IGHJ1-5*01 P (4) 21q24 Holstein KT723008 [1] MAP 321342..321391 (7) AY149283 [2] (6) 1810..1859 (7)
Hereford NW_001494075 (6) complement(38617..38666) (7)
IGHJ1-6 IGHJ1-6*01 F 21q24 + + Holstein KT723008 [1] MAP 321851..321942 AY149283 [2] (6) 2319..2410
DQ497629 [3] (6) 16..107
DQ497630 [3] (6) 16..107
Hereford NW_001494075 (6) complement(38066..38157)
IGHJ2-1 IGHJ2-1*01 ORF (2) 21q24 Holstein KT723008 [1] MAP 508911..509010 AY158087 [4,5] (6) 171..270
IGHJ2-2 IGHJ2-2*01 ORF (3) 21q24 Holstein KT723008 [1] MAP 509091..509184 AY158087 [4,5] (6) 351..444
IGHJ2-3 IGHJ2-3*01 ORF (3) 21q24 Holstein KT723008 [1] MAP 509437..509525 AY158087 [4,5] (6) 697..785
IGHJ2-4 IGHJ2-4*01 F 21q24 + + Holstein KT723008 [1] MAP 509717..509803 AF411242 [4] (6) <1..30 (7)
AY158087 [4,5] (6) 977..1063
IGHJ2-5 IGHJ2-5*01 P (4) 21q24 Holstein KT723008 [1] MAP 510144..510193 (7) AF411242 [4] (6) 365..414 (7)
AY158087 [4,5] (6) 1398..1447 (7)
IGHJ2-6 IGHJ2-6*01 ORF (5) 21q24 Holstein KT723008 [1] MAP 510631..510722 AF411242 [4] (6) 852..943
AY158087 [4,5] (6) 1885..1976

MAP: Mapped reference sequences.

IMGT notes:
  1. (1) non conserved consensus sequence, WGXG is replaced by WSXA
  2. (2) non conserved consensus sequence, WGXG is replaced by CGXA, unexpected DONOR-SPLICE position
  3. (3) non conserved consensus sequence, WGXG is replaced by WGXR
  4. (4) no DONOR-SPLICE
  5. (5) non conserved consensus sequence, WGXG is replaced by CGXG
  6. (6) See caution note above the Gene table
  7. (7) Positions of J-REGION
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] Li M. et al. Unpublished.
  4. [4] Zhao Y. et al. J Immunol. 2002 Oct 15;169(8):4408-16. PMID:12370374
  5. [5] Zhao Y. et al. J Biol Chem. 2003 Sep 12;278(37):35024-32. Epub 2003 Jun 26. PMID:12829708
Created:
26/10/2017
Last updated:
22/09/2023
Authors:
Perrine Pégorier