IMGT Repertoire (IG and TR)


Gene table: Atlantic salmon (Salmo salar) IGHC

"+" or "-" indicates if the gene sequences have been found (+) or not been found (-) 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 gene name IMGT allele name Fct T Pr Positions in the locus IMGT/LIGM-DB reference sequences IMGT/LIGM-DB sequences from the literature
Breed Clone names Exons Accession numbers Positions in the sequence Secondary accession numbers Breed Clone names Accession numbers Positions in the sequence
IGHT1 IGHT1*01 P (1) CH4 (including CHS) GU129139 [5] 236073..236409
IGHT1D IGHT1D*01 P (2) CH1 GU129139 [5] 350789..351088
CH2 GU129139 [5] 351285..351561
CH3 GU129139 [5] 351692..352009
CH4 (including CHS) GU129139 [5] 352531..352882
M1 GU129139 [5] 353701..353855
M2 GU129139 [5] 354193..354201
IGHT2 IGHT2*01 P (3) CH1 GU129139 [5] 335321..335621
CH2 GU129139 [5] 335807..336091
CH3 GU129139 [5] 336219..>336259
IGHT2D IGHT2D*01 F CH1 GU129139 [5] 530902..531201
CH2 GU129139 [5] 531398..531682
CH3 GU129139 [5] 531813..532130
CH4 (including CHS) GU129139 [5] 532650..533002
M1 GU129139 [5] 533787..533941
M2 GU129139 [5] 534279..534287
IGHT3 IGHT3*01 P (3) CH1 GU129139 [5] 406793..407085
CH2 GU129139 [5] 407268..407552
CH3 GU129139 [5] 407678..407995
CH4 (including CHS) GU129139 [5] 408334..408671
IGHT3D IGHT3D*01 P (4) CH2 GU129139 [5] <819753..820016
CH3 GU129139 [5] 820141..820457
CH4 (including CHS) GU129139 [5] 820796..821133
IGHT4 IGHT4*01 F CH1 GU129139 [5] complement(658900..659199)
CH2 GU129139 [5] complement(658430..658714)
CH3 GU129139 [5] complement(657984..658301)
CH4 (including CHS) GU129139 [5] complement(657308..657645)
M1 GU129139 [5] complement(656311..656465)
M2 GU129139 [5] complement(655972..655980)
IGHT5 IGHT5*01 P (5) CH1 GU129139 [5] 712256..712555
CH2 GU129139 [5] 712746..713030
CH3 GU129139 [5] 713159..713476
CH4 (including CHS) GU129139 [5] 713815..714152
M1 GU129139 [5] 714945..715099
M2 GU129139 [5] 715258..715266
IGHM IGHM*01 F + CH1 GU129139 [5] 793917..794213
CH2 GU129139 [5] 795330..795671
CH3 GU129139 [5] 795972..796274
CH4-CHS GU129139 [5] 796683..797083
M1 GU129139 [5] 798850..798986
M2 GU129139 [5] 799820..799825
IGHM*02 F + g6.3, IGHM1 CH1 Y12391 [1] 8544..8840
CH2 Y12391 [1] 9959..10300
CH3 (6) Y12391 [1] 10601..10903
CH4-CHS (6) Y12391 [1] 11311..11711
M1 (6) Y12391 [1] 13310..13446
M2 Y12391 [1] 14280..14285
IGHM*03 (F) + c7.3, IGHM1 CH1 Y12456 [1] c(s) 127..423
CH2 Y12456 [1] c(s) 424..765
CH3 (6) Y12456 [1] c(s) 766..1068
CH4-CHS (6) Y12456 [1] c(s) 1069..1470
IGHMD IGHMD*01 F + CH1 GU129140 [5] 969244..969540 g5.1, IGHM2 Y12392 [1] 2653..2949
CH2 GU129140 [5] 970661..971002 g5.1, IGHM2 Y12392 [1] 4064..4405
CH3 (6) GU129140 [5] 971303..971605 g5.1, IGHM2 Y12392 [1] 4706..5008
CH4-CHS (6) GU129140 [5] 972014..972357 g5.1, IGHM2 Y12392 [1] 5416..5816
M1 (6) GU129140 [5] 974074..974210 g5.1, IGHM2 Y12392 [1] 7475..7611
M2 GU129140 [5] 975054..975059 g5.1, IGHM2 Y12392 [1] 8455..8460
IGHMD*02 (F) + c7.2, IGHM2 CH1 Y12457 [1] c(m) 190..486
CH2 Y12457 [1] c(m) 487..828
CH3 (6) Y12457 [1] c(m) 829..1131
M (6) Y12457 [1] c(m) 1132..1275
IGHD IGHD*01 F CH1 GU129139 [5] 800916..801254
CH2 GU129139 [5] 801369..801668
CH3 GU129139 [5] 801837..802151
CH4 GU129139 [5] 802308..802601
CH2D GU129139 [5] 802738..803037
CH3D GU129139 [5] 803206..803520
CH4D GU129139 [5] 803677..803970
CH2D2 GU129139 [5] 804107..804406
CH3D2 GU129139 [5] 804575..804889
CH4D2 GU129139 [5] 805046..805375
CH5 GU129139 [5] 805514..805840
CH6 GU129139 [5] 806037..806357
CH7-CHS GU129139 [5] 814226..814548
M1 GU129139 [5] 814681..814832
M2 GU129139 [5] 815205..815210
IGHD*02 F IgD-A, IGHD1 CH1 AF278717 [3] 1017..1355
CH2 AF278717 [3] 1470..1769
CH3 AF278717 [3] 1938..2252
CH4 AF278717 [3] 2409..2702
CH2D2 AF278717 [3] 2839..3138
CH3D2 AF278717 [3] 3307..3621
CH4D2 AF278717 [3] 3778..4107
CH5 AF278717 [3] 4246..4572
CH6 AF278717 [3] 4769..5089
CH7-CHS AF278717 [3] 7938..8225
M1 AF278717 [3] 8393..8544
M2 AF278717 [3] 8917..8922
IGHD*03 (F) 13(A), IGHD1 CH4 AF141607 [4] (7) c(m) <1..90
CH2D2 AF141607 [4] c(m) CH2D
CH3D2 AF141607 [4] c(m) 391..705
CH4D2 AF141607 [4] c(m) 706..1035
CH5 AF141607 [4] c(m) 1036..1362
CH6 AF141607 [4] c(m) 1363..1683
CH7-CHS AF141607 [4] c(m) 1684..1971
M1 AF141607 [4] c(m) 1972..2124
M2 AF141607 [4] c(m) 2125..2130
IGHDD IGHDD*01 F CH1 GU129140 [5] 976152..976490
CH2 GU129140 [5] 976605..976904
CH3 GU129140 [5] 977073..977387
CH4 GU129140 [5] 977544..977837
CH2D GU129140 [5] 977974..978273
CH3D GU129140 [5] 978442..978756
CH4D GU129140 [5] 978913..979206
CH2D2 GU129140 [5] 979343..979642
CH3D2 GU129140 [5] 979811..980125
CH4D2 GU129140 [5] 980282..980575
CH2D3 GU129140 [5] 980712..981011
CH3D3 GU129140 [5] 981180..981494
CH4D3 GU129140 [5] 981651..981944
CH5 GU129140 [5] 982046..982372
CH6 GU129140 [5] 982542..982862
CH7-CHS GU129140 [5] 985095..985417
M1 GU129140 [5] 985550..985701
M2 GU129140 [5] 986115..986120
IGHDD*02 F IgD-B, IGHD2 CH1 AF141605 [4] 1019..1357
CH2 AF141605 [4] 1472..1771
CH3 AF141605 [4] 1937..2251
CH4 AF141605 [4] 2408..2701
CH2D3 AF141605 [4] 2838..3137
CH3D3 AF141605 [4] 3304..3618
CH4D3 AF141605 [4] 3775..4068
CH5 AF141605 [4] 4170..4496
CH6 AF141605 [4] 4665..4985
CH7-CHS AF141605 [4] 7228..7515
M1 AF141605 [4] 7683..7834
M2 AF141605 [4] 8248..8253

MAP: Mapped reference sequences.
c: cDNA sequence.
(s): transcript of secreted chain.

IMGT notes:
  1. (1) Frameshift in CH4-CHS
  2. (2) Frameshift in CH2 and in CH4
  3. (3) Frameshift in CH1
  4. (4) STOP-CODON in CH2, frameshift in CH3
  5. (5) STOP-CODON in CH3
  6. (6) CH3 is spliced to CH4 in secretory mu cDNA, whereas it is spliced to the M1 exon in membrane mu cDNA (see [2]).
  7. (7) Partial C-REGION: CH4 partial in 5'
IMGT references:
  1. [1] Hordvik I. et al., Mol. Immunol., 34, 631-639 (1997). PMID:9393966
  2. [2] Hordvik I. et al., Eur. J. Immunol., 22, 2957-2962 (1992). PMID:1425919
  3. [3] Hordvik I., Mol. Immunol., 39, 85-91 (2002). PMID:12213331
  4. [4] Hordvik I. et al., Scand. J. Immunol., 50, 202-210 (1999). PMID:10447926
  5. [5] Yasuike M. et al. BMC Genomics 11:486-486 (2010). doi: 10.1186/1471-2164-11-486. PMID:20813058
Created:
06/01/1999
Last updated:
22/09/2023
Authors:
Sylvaine Artero, Nathalie Bosc, Saida Hadi-Saljoqi