IMGT Repertoire (IG and TR)


Gene table: rainbow trout (Oncorhynchus mykiss) 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
Strain Clone names Exons Accession numbers Positions in the sequence (exons) Secondary accession numbers Strain Clone names Accession numbers Positions in the sequence (exons)
IGHT IGHT*01 F CH1 AY872256 [1] 32069-32365
CH2 AY872256 [1] 32572-32856
CH3 AY872256 [1] 32981-33298
CH4 AY872256 [1] 33620-33957
M1 AY872256 [1] 34749-34903
M2 AY872256 [1] 35243-35251
IGHM1 IGHM1*01 F CH1 AY872256 [1] 93022-93318
CH2 AY872256 [1] 94474-94815
CH3 AY872256 [1] 95119-95418
CH4 AY872256 [1] 95827-96227
M1 AY872256 [1] 98574-98710
M2 AY872256 [1] 99573-99578
IGHM1*02 (F) + + lambda RT15 CH1 X65262 [2] (1) #c(s) 382-519 lambda RTHC1 X67713 [2] (1)
X65261 [2] (2) #c(s) 1-162 lambda RTHC1 X67713 [2] (1)
CH2 X65261 [2] #c(s) 163-504 lambda RTtm X65263 [2] (3) #c(m)
CH3 X65261 [2] (4) #c(s) 505-804 lambda RTtm X65263 [2] #c(m)
CH4 X65261 [2] (4) #c(s) 805-1206
lambda RTtm M1 X65263 [2] (4) #c(m) 356-493
M2 X65263 [2] #c(m) 494-499
IGHM1*03 (F) + + cRTVH50 CH1 S63348 [3] #c(s) 403-699 cRTVH50/CH Y08598 [4] #c(s)
CH2 S63348 [3] #c(s) 700-1041 cRTVH50/CH Y08598 [4] #c(s)
CH3 S63348 [3] (4) #c(s) 1042-1341 cRTVH50/CH Y08598 [4] #c(s)
CH4 S63348 [3] (4) #c(s) 1342-1743 cRTVH50/CH Y08598 [4] #c(s)
IGHM1*04 (F) + + RBTIGTM2 CH1 U04615 [5] #c(m) 403-699
CH2 U04615 [5] #c(m) 700-1041
CH3 U04615 [5] (4) #c(m) 1042-1344
M1 U04615 [5] (4) #c(m) 1345-1482
M2 U04615 [5] #c(m) 1483-1488
IGHM1*05 (F) + + RBTIGTM1 CH1 U04616 [5] #c(m) 406-702
CH2 U04616 [5] #c(m) 703-1044
CH3 U04616 [5] (4) #c(m) 1045-1347
M1 U04616 [5] (4) #c(m) 1348-1485
M2 U04616 [5] #c(m) 1486-1491
IGHM2 IGHM2*01 F gRTIgM CH1 X83372 [6] (2) 1-271
CH2 X83372 [6] 1429-1770
CH3 X83372 [6] 2074-2373
CH4 X83372 [6] (5) 2785-3071
IGHD IGHD*01 F CH1 AY872256 [1] 100661-100999
CH2 AY872256 [1] 101125-101424
CH3 AY872256 [1] 104153-104467
CH4 AY872256 [1] 104627-104920
CH2D AY872256 [1] 105057-105356
CH3D AY872257 [1] 844-1158
CH4D AY872257 [1] 1318-1611
CH2D2 AY872257 [1] (6) 1748-2047
CH7 AY872257 [1] 6737-7024
M1 AY872257 [1] 7191-7342
M2 AY872257 [1] 7739-7744

#c: rearranged cDNA.
(s) Trancript of a secreted chain.
(m) Trancript of a membrane chain.

IMGT notes:
  1. (1) Functional but the C-REGION is partial in 3': CH1 is partial
  2. (2) Functional but the C-REGION is partial in 5': CH1 is partial
  3. (3) Functional but the C-REGION is partial in 5': CH2 is partial
  4. (4) Functional but CH3 is spliced to CH4 in secretory mu cDNA, whereas it is spliced to the M1 exon in membrane mu cDNA (see [2]).
  5. (5) Functional but the C-REGION is partial in 3': CH4 is partial
  6. (6) Functional but the C-REGION contains repetitive regions
IMGT references:
  1. [1] Hansen J.D. et al., Proc. Natl. Acad. Sci. U.S.A., 102, 6919-6924 (2005). PMID:15863615
  2. [2] Lee M.A. et al., Mol. Immunol., 30, 641-648 (1993). PMID:8487781
  3. [3] Andersson E. and Matsunaga T., Immunogenetics, 38, 243-250 (1993). PMID:8319974
  4. [4] Andersson E. et al., Unpublished (1996).
  5. [5] Hansen J. et al., Mol. Immunol., 31, 499-501 (1994). PMID:8183286
  6. [6] Andersson E. et al., Immunogenetics, 41, 312-315 (1995). PMID:7721353
  7. [7] Roman T. et al., Immunogenetics 43, 325-326 (1996). PMID:9110939
Created:
15/12/2009
Last updated:
22/09/2023
Authors:
Sylvaine Artero, Nathalie Bosc, Géraldine Folch, Amandine Lacan