To propose new IG or TR genes to IMGT, the genomic sequence should be publicly available (in generalist databases or in genome assembly).
Information to be provided
The information to be provided comprises, for each gene:
1) the public accession number of the clone from which the sequence was extracted (or of the NCBI assembly positions and version), with the proposed gene name (provisional), positions start and end in that accession number,
2) the corresponding sequence in FASTA format:
- for V genes: from the beginning of the L-PART1 (atg) to the 3'end of the V-RS
- for D genes: from the 5' end of the 5'D-RS to the 3' end of the 3'D-RS
- for J genes: from the 5' end of the J-RS to the 3'end of the J-REGION
- for C genes: from the 5' end of the first exon to the 3' end (stop codon) of the last exon.
3) the proposed functionality (F, ORF, P), and comments (any comment which can be useful, for example, why a gene is considered 'ORF' or 'P')
4) additionally, for V genes,
- the CDR-IMGT lengths (the germline CDR3-IMGT includes, if present, the one or two nucleotides upstream of the V-HEPTAMER)
- the closest human V-REGION gene and allele with score, percentage of identity and alignment length ratio, as provided by IMGT/V-QUEST.
For pseudogenes, the above information obtained using the option 'Search for insertions and deletions in V-REGION', with summary of the out-of-frame defects (for example, '1 del (1), 2 ins (1,2)' for one deletion of 1 nucleotide (nt), 2 insertions of 1 nt and 2nt).
IG and TR subgroup numbers
The IG and TR subgroup numbers are assigned, whenever it is possible, by comparison to the Homo sapiens subgroups (V-REGION nucleotide sequence identity >75% for functional and ORF genes and, for information, CDR-IMGT lengths). This means that some Homo sapiens subgroup numbers may not be represented in some species or conversely that new numbers may be added for subgroups not represented in Homo sapiens.
IG and TR gene numbers.
Lefranc M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447