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. 

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 bornean orangutan (Pongo pygmaeus) IGHJ IMGT group:
IMGT gene nameIMGT allele nameFctScore for
IMGT allele
confirmation		Chromosomosal
localization		R T PrIMGT/LIGM-DB reference sequencesIMGT/LIGM-DB sequences from the literature
IsolateClone namesAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)		Secondary
accession
numbers		IsolateClone namesAccession
numbers		Positions
in the sequence
(J-GENE-UNIT)
or J-REGION (*)
IGHJ1 IGHJ1*01 P (1) AG05252 IMGT000144 [1] MAP 1412984-1413069
IGHJ2 IGHJ2*01 F AG05252 IMGT000144 [1] MAP 1413201-1413290
IGHJ3 IGHJ3*01 ORF (2) AG05252 IMGT000144 [1] MAP 1413408-1413498
IGHJ4 IGHJ4*01 ORF (3) AG05252 IMGT000144 [1] MAP 1413807-1413897
IGHJ5 IGHJ5*01 F AG05252 IMGT000144 [1] MAP 1414022-1414110
IGHJ6 IGHJ6*01 F AG05252 IMGT000144 [1] MAP 1414396-1414482
IGHJ7 IGHJ7*01 ORF (4) AG05252 IMGT000144 [1] MAP 1414797-1414886
IGHJ8 IGHJ8*01 P (5) AG05252 IMGT000144 [1] MAP 1415198-1415285
IGHJ9 IGHJ9*01 ORF (6) AG05252 IMGT000144 [1] MAP 1415403-1415494
IMGT notes: ↑
  1. frameshift in J-REGION
  2. noncanonical J-HEPTAMER:ggctgtg instead of cactgtg
  3. noncanonical J-HEPTAMER:tagtgtg instead of cactgtg, noncanonical J-NONAMER:tgttcatgtinstead of ggtttttgt, noncanonical J-MOTIF:WSxG instead of WGxG, noncanonical DONOR-SPLICE:ngg instead of ngt
  4. noncanonical J-NONAMER:agttcttgc instead of ggtttttgt
  5. frameshift in J-REGION causing defectuous DONOR-SPLICE
  6. noncanonical J-MOTIF:WTxG instead of WGxG
IMGT references: ↑
  1. Koren,S. et al., Complete, haplotype-resolved assemblies of non-human primate chromosomes X and Y, Unpublished.