Citing IMGT databases: Manso T. et al. IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res. 2022 Jan 7;50(D1):D1262-D1272. doi: 10.1093/nar/gkab1136 PMID: 34875068 Free PMC article.
Program version: v. 

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 signify the frequency of occurrences of a specific allele within sequence data. A single star () indicates that no instances of the allele have been identified in the literature. Two stars () indicate the discovery of one literature sequence containing the allele. If more than one literature sequence is found to contain the allele, it is designated with three stars (). 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) IGLJ 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 (*)
IGLJ1 IGLJ1*01 F 16A3 (13.0 cM)
RTPr
++
 J1 BALB/c V00813 [1,7] MAP 101-166 129S1_SvImJ IMGT000124 207129-207192
BALB/c X58411 [11] (4) 5227-5292
M315J1 BALB/c X58419 [3,10] 103-168
BALB_cJ IMGT000126 207140-207203
CM001009.3 C57BL/6J IMGT000117 [5,6] 207404-207470
DBA_2J IMGT000134 207070-207135
NOD/SCID IMGT000211 [8] 207391-207457
IGLJ2 IGLJ2*01 F 16A3 (13.0 cM)
RTPr
++
 J2 BALB/c J00593 [4,7] MAP 107-172 129S1_SvImJ IMGT000124 70151-70216
BALB/c X58414 [9,11] (5) 420-485
M315J2 BALB/c X58420 [3,10] 108-173
BALB_cJ IMGT000126 70167-70232
CM001009.3 C57BL/6J IMGT000117 [5,6] 70432-70497
DBA_2J IMGT000134 70102-70167
NOD/SCID IMGT000211 [8] 70422-70487
IGLJ2P IGLJ2P*01 ORF (1) 16A3 (13.0 cM) CM001009.3 C57BL/6J IMGT000117 [5,6] MAP 71067-71135 129S1_SvImJ IMGT000124 70786-70854
BALB_cJ IMGT000126 70802-70870
DBA_2J IMGT000134 70738-70806
NOD/SCID IMGT000211 [8] 71057-71125
IGLJ3 IGLJ3*01 F 16A3 (13.0 cM)
RTPr
++
 J3 BALB/c J00583 [4,7] MAP 58-123 129S1_SvImJ IMGT000124 203311-203376
BALB/c X58411 [11] (4) 1413-1478
M315J3 BALB/c X58421 [3,10] 100-165
BALB_cJ IMGT000126 203322-203387
CM001009.3 C57BL/6J IMGT000117 [5,6] 203589-203654
DBA_2J IMGT000134 203254-203319
NOD/SCID IMGT000211 [8] 203576-203641
IGLJ3P IGLJ3P*01 P (2) 16A3 (13.0 cM) PseudoJ3 BALB/c J00584 [7] MAP 1-67 129S1_SvImJ IMGT000124 203980-204046
BALB_cJ IMGT000126 203991-204057
CM001009.3 C57BL/6J IMGT000117 [5,6] 204287-204324 *
DBA_2J IMGT000134 203923-203989
NOD/SCID IMGT000211 [8] 204245-204311
IGLJ4 IGLJ4*01 ORF (3) 16A3 (13.0 cM) PseudoJL4 BALB/c J00596 [4,7] MAP (6) 85-148 129S1_SvImJ IMGT000124 73852-73915
BALB/c X58414 [9,11] (5) 4124-4191
M315J4 BALB/c X58422 [3,10] 152-193 *
BALB_cJ IMGT000126 73868-73931
CM001009.3 C57BL/6J IMGT000117 [5,6] 74133-74196
DBA_2J IMGT000134 73804-73867
NOD/SCID IMGT000211 [8] 74123-74186
IMGT notes: ↑
  1. noncanonical DONOR-SPLICE: nat instead of ngt, noncanonical J-MOTIF: FSXN instead of FGXG, noncanonical J-HEPTAMER: cattgcc instead of cattgtg
  2. no J-HEPTAMER
  3. noncanonical DONOR-SPLICE: nat instead of ngt, noncanonical J-HEPTAMER:atcagtg instead of cacagtg
  4. X58411 contains the IGLJ1, IGLC1, IGLJ3 and IGLC3 genes from the BALB/c MOPC 315 B cell line. Originally these genes were submitted independently (X58411 being the IGLC1 accession number). Secondary accession numbers of X58411 correspond to the primary accession numbers of IGLJ1 (X58419/M28320), IGLJ3 (X58421/M28322/M28323) and IGLC3 (X58415/M28327) from MOPC 315.
  5. X58414 contains the IGLJ2, IGLC2, IGLJ4 and IGLC4 genes from the BALB/c MOPC 315 B cell line. Originally these genes were submitted independently (X58414 being the IGLC2 accession number). Secondary accession numbers of X58414 correspond to the primary accession numbers of IGLJ2 (X58420/M28321), IGLJ4 (X58422/M28324) and IGLC4 (X58416) from MOPC 315. The secondary accession number X58410/M28329 corresponds to the primary accession number of IGLC4 from BALB/c J 558 cell line, whose sequence is identical to that of MOPC 315.
  6. Note that the sequences of Mus musculus IGLJ4*01 and Mus spretus IGLJ4*01 are identical.
IMGT references: ↑
  1. Arp B. et al., Sequences of immunoglobulin lambda 1 genes in a lambda 1 defective mouse strain, Nature, vol. 298, no. 5870, 1982, pp. 184-187. DOI: 10.1038/298184a0
  2. Bernard O. et al., Sequences of mouse immunoglobulin light chain genes before and after somatic changes, Cell, vol. 15, no. 4, 1978, pp. 1133-1144. DOI: 10.1016/0092-8674(78)90041-7
  3. Blomberg B.B. et al., DNA sequences of the joining regions of mouse lambda light chain immunoglobulin genes, Proc. Natl. Acad. Sci. U.S.A, vol. 79, 1982, pp. 530-533. Patent ID: 82197527
  4. Blomberg B. et al., DNA sequences of the joining regions of mouse lambda light chain immunoglobulin genes, Proc. Natl. Acad. Sci. U.S.A, vol. 79, no. 2, 1982, pp. 530-533. PUBMED: 6804942
  5. Church,D.M. et al., Lineage-specific biology revealed by a finished genome assembly of the mouse, PLoS Biol (2009), PUBMED: 19468303
  6. Church,D.M. et al., Modernizing reference genome assemblies, PLoS Biol, vol. 9, no. 7, 2011, PUBMED: 21750661
  7. Miller J. et al., Structural alterations in J regions of mouse immunoglobulin lambda genes are associated with differential gene expression, Nature, vol. 295, no. 5848, 1982, pp. 428-430. DOI: 10.1038/295428a0
  8. Schmid-Siegert E. et al., Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models, Unpublished.
  9. Selsing E. et al., Evolution of mouse immunoglobulin lambda genes, Proc. Natl. Acad. Sci. U.S.A, vol. 79, no. 15, 1982, pp. 4681-4685. PUBMED: 6812053
  10. Weiss S. et al., Somatic point mutations in unrearranged immunoglobulin gene segments encoding the variable region of lambda light chains, EMBO J, vol. 6, 1987, pp. 927-932. Patent ID: 87246527
  11. Weiss S. et al., Somatic point mutations in unrearranged immunoglobulin gene segments encoding the variable region of lambda light chains, EMBO J, vol. 6, no. 4, 1987, pp. 927-932. PUBMED: 3109891