Citing IMGT dynamic tools: Sanou G., Zeitoun G. et al. IMGT® at scale: FAIR, Dynamic and Automated Tools for Immune Locus Analysis, Nucleic Acids Research. 2025;,gkaf1024. doi: 10.1093/nar/gkaf1024 (Free Article) PMID: 41091930.
Program version: v. 

Add information about removed genes/alleles.
May 15th, 2025.

Add the possibility to obtain a gene table per strain (for mouse now and for other species later) and allotypes/isotypes for human.
September 25th, 2024.

Bibliographical references in alphabetic order, small design changes and addition of "NL" for non-localized gene.
June 14th, 2024.

Addition of 'Score for IMGT allele confirmation' as well as NCBI TPA accession numbers.
September 20th, 2023.

Implementation of the dynamic gene table.

Gene table legend:

"+" 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 in 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.

IMGT allele confirmation: A scoring system is employed to indicate the number of IMGT/LIGM-DB reference sequences and other sequences from the literature in which an IG or TR gene allele has been identified and annotated.

Removed genes/alleles
If a gene/allele existence or name has to be changed, the old name or gene/allele would be deleted and its name won't be reused. They are kept in the gene table for historical reasons.
A single star ()
indicates that an IG or TR gene allele is annotated in the reference sequence only.
Two stars ()
indicate that an IG or TR gene allele is annotated in its reference sequence and in one sequence from the literature.
Three stars ()
indicate that an IG or TR gene allele is annotated in its reference sequence and in at least two sequences from the literature.
In the Excel file, the stars are represented by the plus symbol (+).

Click on:
  • IMGT gene name to get the corresponding IMGT/GENE-DB entry (link).
  • IMGT allele name to see the corresponding Alignments of alleles (link).
  • Accession number to get the corresponding IMGT/LIGM-DB entry (link).
  • MAP: mapped sequences. Click to access GENE-DB «LOCALIZATION IN GENOME ASSEMBLIES» (link).
  • [number] to access the corresponding IMGT reference (popover).
  • (number) to see the corresponding IMGT note (popover).
Options:
  • You can show/hide columns (), download data () or put the table in fullscreen () using buttons.
See also (IMGT Scientific chart):
Select a species and a IMGT group to get the gene table:
Only IMGT available species/group are shown in the drop-down list.
The gene table can take several seconds to appear, please be patient.
Gene table of house mouse (Mus musculus) IGKJ IMGT group:
IMGT gene nameIMGT allele nameScore for
IMGT allele
confirmation		FctChromosomosal
localization		R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)		Secondary
accession
numbers		Clone namesStrainAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
IGKJ1 IGKJ1*01 F 6C1 (30.0 cM)
RTPr
++
 J1 V00777 [4] MAP 701-777 V00805 [8] (2) 20-57 *
X68864 [5] (3) 40->65 *
X68866 [5] 40->67 *
X68867 [5] 40->67 *
129S1/SvImJ IMGT000127 3170338-3170414
A/J M15521 [7] 85-122 *
BALB/cJ IMGT000123 3182474-3182550
CM000999.2 C57BL/6J IMGT000068 [2,3] 3176888-3178288
C58 M27036 [6] 85-122 *
DBA/2J IMGT000125 3179630-3179706
SJL M27037 [6] 85-122 *
SK M27038 [6] 85-122 *
IGKJ1 IGKJ1*02 F 6C1 (30.0 cM)
RTPr
++
 J1 C58 M15559 [1] (4) <1-37 *
IGKJ2 IGKJ2*01 F 6C1 (30.0 cM)
RTPr
++
 J2 V00777 [4] MAP 1055-1132 X68859 [5] (3) 40->67 *
129S1/SvImJ IMGT000127 3170692-3170769
BALB/cJ IMGT000123 3182828-3182905
CM000999.2 C57BL/6J IMGT000068 [2,3] 3177242-3177319
DBA/2J IMGT000125 3179984-3180061
SJL M27037 [6] 439-477 *
SK M27038 [6] 439-477 *
IGKJ2 IGKJ2*02 F 6C1 (30.0 cM) J2 C58 M15559 [1] 353-391 *
IGKJ2 IGKJ2*03 F 6C1 (30.0 cM)
RTPr
++
 J2 C58 M27036 [6] 439-477 *
IGKJ3 IGKJ3*01 ORF (1) 6C1 (30.0 cM)
RTPr
+
 J3 V00777 [4] MAP 1364-1438 129S1/SvImJ IMGT000127 3171001-3171075
BALB/cJ IMGT000123 3183137-3183211
CM000999.2 C57BL/6J IMGT000068 [2,3] (5) 3177551-3177625
C58 M15559 [1] 660-697 *
C58 M27036 [6] 746-783 *
DBA/2J IMGT000125 3180293-3180367
SK M27038 [6] 746-783 *
IGKJ3 IGKJ3*02 ORF (6) 6C1 (30.0 cM)
RTPr
+
 J3 SJL M27037 [6] 746-783 *
IGKJ4 IGKJ4*01 F 6C1 (30.0 cM)
RTPr
++
 J4 V00777 [4] MAP 1685-1762 X68854 [5] 41->67 *
X68861 [5] (3) 41->67 *
129S1/SvImJ IMGT000127 3171323-3171400
BALB/cJ IMGT000123 3183459-3183536
CM000999.2 C57BL/6J IMGT000068 [2,3] 3177873-3177950
DBA/2J IMGT000125 3180615-3180692
SJL M27037 [6] 1070-1107 *
SK M27038 [6] 1071-1108 *
IGKJ4 IGKJ4*02 F 6C1 (30.0 cM)
RTPr
++
 J4 C58 M15559 [1] 985-1022 * C58 M27036 [6] 1070-1107 *
IGKJ5 IGKJ5*01 F 6C1 (30.0 cM)
RTPr
++
 J5 V00777 [4] MAP 2024-2100 129S1/SvImJ IMGT000127 3171662-3171738
BALB/cJ IMGT000123 3183798-3183874
CM000999.2 C57BL/6J IMGT000068 [2,3] 3178212-3178288
C58 M15559 [1] 1323-1360 *
C58 M27036 [6] 1408-1445 *
DBA/2J IMGT000125 3180954-3181030
SJL M27037 [6] 1408-1445 *
SK M27038 [6] 1409-1446 *
IMGT notes: ↑
  1. non canonical DONOR_SPLICE: nct instead of ngt
  2. Partial J-GENE: no J-NONAMER.
  3. Partial J-REGION: 3 amino acids missing in 3'.
  4. Partial J-REGION: one nucleotide missing in 5'.
  5. Noncanonical J-HEPTAMER, noncanonical J-MOTIF, noncanonical DONOR-SPLICE.
  6. Noncanonical DONOR-SPLICE: nct instead of ngt.
IMGT references: ↑
  1. Boyd R.T. et al., Genetic polymorphism at the mouse immunoglobulin J kappa locus (Igk-J) as demonstrated by Southern hybridization and nucleotide sequence analysis, Immunogenetics, vol. 24, no. 3, 1986, pp. 150-157. PUBMED: 2875941
  2. Church,D.M. et al., Lineage-specific biology revealed by a finished genome assembly of the mouse, PLoS Biol (2009), PUBMED: 19468303
  3. Church,D.M. et al., Modernizing reference genome assemblies, PLoS Biol, vol. 9, no. 7, 2011, PUBMED: 21750661
  4. Max E.E. et al., The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes, J. Biol. Chem, vol. 256, no. 10, 1981, pp. 5116-5120. PUBMED: 6262318
  5. Philips R.A, Isolation of scid pre-B cells that rearrange kappa light chain genes: formation of normal signal and abnormal coding joins, EMBO J, vol. 8, no. 3, 1989, pp. 735-742. PUBMED: 2785917
  6. Ponath P.D. et al., Structural and evolutionary comparisons of four alleles of the mouse Igk-J locus which encodes immunoglobulin kappa light chain joining (J kappa) segments, Immunogenetics, vol. 29, no. 6, 1989, pp. 389-396. DOI: 10.1007/BF00375867
  7. Sanz I. and Capra J.D, V kappa and J kappa gene segments of A/J Ars-A antibodies: somatic recombination generates the essential arginine at the junction of the variable and joining regions, Proc. Natl. Acad. Sci. U.S.A, vol. 84, no. 4, 1987, pp. 1085-1089. PUBMED: 3103124
  8. Seidman J.G. et al., A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation, Nature, vol. 280, no. 5721, 1979, pp. 370-375. DOI: 10.1038/280370a0