IMGT Repertoire (IG and TR)

Gene table: spotted ratfish (Hydrolagus colliei) IGHV

"+" 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 Spotted ratfish (Hydrolagus colliei) IGHV genes and allele have a temporary designation based on the IMGT gene name nomenclature rules for the unmapped genes, the incomplete loci, or the cDNAs in the absence of germline genes.
Spotted ratfish (Hydrolagus colliei) genes are designated by a number for the subgroup [2] followed by the letter S and a number.

IMGT subgroup IMGT gene name IMGT allele name Fct 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
IGHV1 IGHV1S1 IGHV1S1*01 (F) + + 3430 AF003853 [1] #c
IGHV1S2 IGHV1S2*01 (F) + + 20442 AF003839 [1] (2) #c
IGHV1S3 IGHV1S3*01 F 20501 AF003841 [1]
IGHV1S4 IGHV1S4*01 [P] 20420 AF003848 [1] (1) °
IGHV1S5 IGHV1S5*01 (P) 20421 AF003849 [1] (1) #c
IGHV1S6 IGHV1S6*01 (F) + + 3431 AF003854 [1] (2) #c
IGHV1S7 IGHV1S7*01 (F) + + 13432 AF003855 [1] (2) #c
IGHV1S8 IGHV1S8*01 (F) + + 3433 AF003856 [1] (2) #c
IGHV1S9 IGHV1S9*01 (F) + + 3434 AF003857 [1] #c
IGHV1S10 IGHV1S10*01 (F) + + 3435 AF003858 [1] #c
IGHV1S11 IGHV1S11*01 (F) + + 3436 AF003859 [1] (2) #c
IGHV1S12 IGHV1S12*01 (F) + + 2659 AF003860 [1] #c
IGHV1S13 IGHV1S13*01 (F) + + 20441 AF003861 [1] #c
IGHV1S14 IGHV1S14*01 (F) + + 20182 AF003946 [1] ~VDJ

#c: rearranged cDNA.
°: genomic DNA, but not known as being germline or rearranged.
~VDJ: VDJ genomic DNA rearranged in the cassette.

IMGT notes:
  1. (1) Partial sequence.
  2. (2) In the absence of genomic sequences and maps, it is not possible to know if sequences differing by a few nucleotides derive from allelic genes or from duplicated clusters. Sequences which differ by <5 nucleotides are shown below:
    IGHV gene and allele names (Accession  numbers)Nucleotide differences
    IGHV1S7*01 (AF003855)IGHV1S2*01 (AF003839)a92>g; c98>g
    IGHV1S6*01 (AF003854)IGHV1S8*01 (AF003856)g9>a; c40>t; g141>c
    IGHV1S11*01 (AF003859)IGHV1S6*01 (AF003854)t2>c; c5>t; a54>g
IMGT references:
  1. [1] Rast J.P. et al., Immunogenetics, 47, 234-245 (1998). PMID:9435342
  2. [2] Roman T. et al., Immunogenetics, 43, 325-326 (1996). PMID:9110939
Last updated:
Lorena Betancourt, Dominique Scaviner