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Frequently asked questions

IMGT/GENE-DB


Is it possible to retrieve flanking sequence at the 5' and/or 3' ends of IMGT labels that describe IMGT/GENE-DB annotated sequences?
Yes, flanking sequences at the 5' and/or 3' ends of the IMGT labels can be retrieved, in FASTA format, by querying the IMGT/GENE-DB entry section, "Choose your display > IMGT label extraction from IMGT/LIGM-DB reference sequences". For more information: IMGT label extraction from IMGT/LIGM-DB reference sequences.
How can I retrieve the V leader sequences from IMGT reference sequences?
Step 1: Make your selection (species, group, functionality) in IMGT/GENE-DB (access from https://www.imgt.org). For a selection "Homo sapiens", "IGHV" and "functional", the results of your search will be, for example:
Gene-DB result 1

Step 2: Select all genes (click in box at the bottom of the list of resulting genes) and in the "Choose your display" "IMGT label extraction from IMGT/LIGM-DB reference sequences" section, click on "Choose label(s) for extraction" and select the IMGT label "L-PART1+L-PART2" (L-PART1 and L-PART2 being shown as artificially spliced in that query).
Gene-DB result 2
How to obtain from IMGT/GENE-DB complete amino acid sequences (artificially spliced) of a constant gene, or of a group of C genes?
  1. To get the complete amino acid sequence (artificially spliced) of a reference constant gene, the query is 13.2
    • https://www.imgt.org/genedb/GENElect?query=13.2+Genesymbol&species=Species
      with for Genesymbol, the gene name (for instance IGHG1), and for Species, the latin name of the species (for instance Homo+sapiens) https://www.imgt.org/genedb/GENElect?query=13.2+IGHG1&species=Homo+sapiens
  2. To get the artificially spliced nucleotide sequence of that gene, the query is 13.1
  3. To get the complete amino acid sequence (artificially spliced) of reference constant genes of a group, the query is 14.2
    • https://www.imgt.org/genedb/GENElect?query=14.2+Group&species=Species
      with for Group, the group name (for instance IGHC), and for Species, the latin name of the species (for instance Homo+sapiens) https://www.imgt.org/genedb/GENElect?query=14.2+IGHC&species=Homo+sapiens
  4. To get the artificially spliced nucleotide sequence of that group, the query is 14.1
The information on the direct links are available at: https://www.imgt.org/genedb/directlinks
You can access that page at the bottom of the IMGT/GENE-DB Query page.
How to download the sequences of the available IG or TR genes of a given group of a given species, for example Homo sapiens IGHV, from IMGT/GENE-DB?
For the download of sequences, you may query the database:
in the IMGT/GENE-DB Query page, IDENTIFICATION: Species= Homo sapiens, CLASSIFICATION: IMGT group= IGHV.
At the bottom of the 'RESULTS OF YOUR SEARCH PAGE', click on "Select all genes", and in the section "Choose your display" (see https://www.imgt.org/genedb/doc#h2_62) select one of the options of "IMGT/GENE-DB allele reference sequences in FASTA format".

An alternative is to use an URL with format described in the direct links (https://www.imgt.org/genedb/directlinks), for example:
https://www.imgt.org/genedb/GENElect?query=7.2+IGHV&species=Homo+sapiens
How to retrieve sequences of the alleles of the human constant genes?
You can retrieve nucleotide and amino acid sequences of the alleles of a given gene in IMGT/GENE-DB (https://www.imgt.org/genedb/), from the table 'IMGT/GENE-DB reference sequences (in FASTA format)' displayed in the 'IMGT/GENE entry' page resulting from the query (for instance, Homo sapiens IGHG1).
You can retrieve nucleotide or amino acid sequences for a given gene (e.g., IGHG1 gene) or for genes of a group (e.g., IGHC group) of a given species (e.g., Homo sapiens), using the IMGT/GENE-DB direct links (https://www.imgt.org/genedb/directlinks).
Alleles can be compared visually in 'Alignments of alleles' (https://www.imgt.org/IMGTrepertoire/Proteins/index.php#B) in IMGT Repertoire.
How to get nucleotide sequences of the human constant IG genes for primer design?
Query IMGT/GENE-DB
IDENTIFICATION:
Species: Homo sapiens
Functionality: functional
CLASSIFICATION:
IMGT Group: IGHC (for heavy), IGKC (for light kappa), IGLC (for light lambda)

Submit.
In the List of resulting genes, select the genes of interest.
In Choose your display, in the right column 'IMGT label extraction' from IMGT/LIGM-DB reference sequences (F+ORF+all P)
'Choose label(s) for extraction and/or artificially spliced exons' in the menu:
For example: 'CH1' (for heavy) or 'C-REGION' (for light kappa or lambda)
Submit.
You will get the sequences in FASTA of the CH1 or of the C-REGION of the different alleles of the selected genes.
The nucleotide sequences can be compared with the Alignments of alleles (for correspondence with IMGT unique numbering of the C-DOMAIN) https://www.imgt.org/IMGTrepertoire/Proteins/alleles/list_alleles.php?species=Homo sapiens&group=IGHC
https://www.imgt.org/IMGTrepertoire/Proteins/alleles/list_alleles.php?species=Homo sapiens&group=IGKC
https://www.imgt.org/IMGTrepertoire/Proteins/alleles/list_alleles.php?species=Homo sapiens&group=IGLC
How can I export FASTA sequences for V genes that include the L-REGION in addition to V-REGION?
Step 1: Make your selection (species, group, functionality) in IMGT/GENE-DB (access from https://www.imgt.org). For a selection Species "Macaca mulatta", Functionality "any", IMGT Group "TRAV", the results of your search will be, for example:
Gene-DB result 1

Step 2: Select all genes (click in box at the bottom of the list of resulting genes) and in the "Choose your display" "IMGT label extraction from IMGT/LIGM-DB reference sequences" section, click on "Choose label(s) for extraction" and select the IMGT label "L-PART1+V-EXON" (L-PART1 and V-EXON being shown as artificially spliced in that query).
Gene-DB result 2
How can I export FASTA sequences for L-V GENE-UNIT?
Step 1: Make your selection (species, group, functionality) in IMGT/GENE-DB (access from https://www.imgt.org). For a selection Species "Homo sapiens", Functionality "functional", IMGT Group "IGHV", the results of your search will be, for example:
Gene-DB result 1

Step 2: Select all genes (click in box at the bottom of the list of resulting genes) and in the "Choose your display" "IMGT label extraction from IMGT/LIGM-DB reference sequences" section, click on "Choose label(s) for extraction" and select the IMGT label "L-V-GENE-UNIT".
Gene-DB result 2
Be aware that only sequences annotated with the chosen label will be retrieved (partial sequences for which the label could not be assigned are missed).