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Citing IMGT/GENE-DB:
Giudicelli, V. et al. Nucleic Acids Res., 33:D256-D261 (2005). PMID: 15608191
IMGT/GENE-DB program version:
3.1.17 (2017-07-26)
IMGT/GENE-DB data updates

Introduction

IMGT/GENE-DB is part of IMGT®, the international ImMunoGeneTics information system®, the high-quality integrated knowledge resource specializing in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species, proteins of the immunoglobulin superfamily (IgSF) and MH superfamily (MhSF), related proteins of the immune systems (RPI) of vertebrates and invertebrates, therapeutic monoclonal antibodies (mAb), and fusion proteins for immune applications (FPIA), created in 1989 by Marie-Paule Lefranc (LIGM, Université Montpellier 2, CNRS).

IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates, on the Web since February 2003.
IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps). IMGT/GENE-DB includes links to the IMGT Repertoire standardized resources (Chromosomal localization, Locus representation, Tables of alleles, Alignments of alleles, IMGT Protein displays, IMGT Colliers de Perles, etc.), to the IMGT/LIGM-DB and IMGT/3Dstructure-DB structures and IMGT/2Dstructure-DB IMGT databases.

IMGT/GENE-DB is the official repository of all of the IG and TR genes and alleles approved by the World Health Organization (WHO)/International Union of Immunological Societies (IUIS) Nomenclature Subcommittee for IG and TR (Lefranc 2007, 2008a). Reciprocal links exist between IMGT/GENE-DB and the Human Genome Nomenclature Committee (HGNC) database, NCBI Gene at the National Center for Biotechnology Information (NCBI) and Vega Genome Browser (Wellcome Trust Sanger Institute).

IMGT/GENE-DB Query page

The IMGT/GENE-DB Query page shows, on the top right, the status of the database (current date, number of genes, number of alleles and number of species).

Search according to the concepts of IMGT-ONTOLOGY

Searches in IMGT/GENE-DB are performed according to the concepts of IDENTIFICATION, LOCALIZATION and CLASSIFICATION of IMGT-ONTOLOGY.

IDENTIFICATION

Species:
only species for which genes have been entered in IMGT/GENE-DB are available.
MolecularComponent:
IG or TR.
GeneType:
allows the selection on one of the gene types.
Functionality:
allows the selection on IG and TR functionality.
Clone name:
enter a clone name or the first letters of a clone name. Clone names are those of the "Reference sequences" and "Sequences from the literature" columns in Genes tables.

LOCALIZATION

Locus:
allows the selection on IG and TR loci (includes main loci and chromosomal orphon sets).
Main Locus:
allows the selection on a main IG or TR locus.
Chromosomal orphon set:
allows the selection on IG or TR genes which are outside the main loci or Chromosomal orphon set.
As Main Locus may contain RPI genes, a selection on 'Molecular component' 'IG' or 'TR' prior to the request will allow to only retrieve IG or TR genes.

CLASSIFICATION

IMGT group:
allows the selection on IMGT groups.
IMGT subgroup:
allows the selection on IMGT subgroups.
IMGT gene:
enter an IMGT gene name, for example IGHV1-2 (List of human genes according to the IMGT nomenclature).
Note that the search is case sensitive and that UPPERcase is the rule.

You can also enter only the first letters of the IMGT gene name: for example the selection of IGHV will list in the next page all genes which have an IMGT gene name beginning with IGHV.

You can consult the Correspondence between nomenclatures.

Selection of genes which have been found:
Allows the selection of genes which have been found rearranged and/or, transcribed, for at least one allele.

LOCALIZATION IN GENOME ASSEMBLIES

Species:
only species for which the gene localization in genomes assemblies are managed in IMGT/GENE-DB are available.
Locus:
only locus for which the gene localization in genomes assemblies are managed in IMGT/GENE-DB are available.
Assembly :
allows to select the assembly.
Assembly unit:
allows to select the assembly unit, for example "Primary Assembly".
Designation:
allows to select the Designation for example "Full chromosome 14" (for Homo sapiens).

IMGT/GENE-DB direct links

Provides a set of direct links to query IMGT/GENE-DB according to an IMGT gene name, an IMGT group or to get the links to IMGT/GENE-DB and generalist genomic databases.

RESULTS OF YOUR SEARCH

Depending on the number of resulting genes, you will see:

List of resulting genes

At the top of the page, the selected criteria are indicated with the number of resulting genes and the number of resulting alleles.

The list of resulting genes is a table with the following columns:

First column: select

Allows to select the genes and then Choose your display
In the example, Homo sapiens TRAV8-3 et TRAV8-4 have been selected.

IMGT gene names

Provides the gene names in the IMGT gene nomenclature (List of human genes).

Functionality

Provides the IMGT gene functionality according to the IMGT definition.

F: Functional
ORF: Open Reading Frame
P: Pseudogene

The Functionality may be shown between parentheses or between brackets: corresponding rules are available here

When more then one functionality is indicated for a gene (for example F, [F]), this means that the gene shows several alleles with distinct functionalities.

IMGT gene definition

Provides the gene definition according to the IMGT gene nomenclature.

Number of alleles

Provides, per gene, the number of alleles currently identified in IMGT.

Chromosomal localization

IMGT/LIGM-DB reference sequence for allele *01

Provides, for the allele *01, the IMGT/LIGM-DB accession number(s) of the corresponding reference sequence(s).

Molecular component

Provides the molecular component for the gene.

Choose your display

Three choices of display are provided:

"Complete IMGT/GENE-DB entries" is selected by default. It displays the detailed results for the selected genes (see IMGT/GENE-DB DETAILED RESULTS).

"IMGT/GENE-DB reference sequences in FASTA format" for the selected genes corresponds to :

The FASTA header of IMGT/GENE-DB reference sequences in FASTA format is standardized. See FASTA format of IMGT/GENE-DB reference sequences.

"IMGT label extraction from IMGT/LIGM-DB reference sequences" allows to extract, from the IMGT/LIGM-DB reference sequences, and for each allele of the selected gene(s), the sequences corresponding to one or several IMGT labels and/or artificially spliced exons.

The list of IMGT/LIGM-DB labels is available here.

IMGT/GENE-DB DETAILED RESULTS

The IMGT/GENE-DB DETAILED RESULTS page provides the IMGT/GENE-DB entry (ies). The top of this page reminds you the gene(s) you have selected. You can click on each of them to view the corresponding IMGT/GENE-DB entry.

Content of an IMGT/GENE-DB entry :

IMGT gene name and definition

Provides the IMGT gene name (species and symbol in the IMGT gene nomenclature) and the IMGT definition (full name) of the gene.

Chromosomal localization

Provides the name of the locus (main locus or chromosomal orphon set), the chromosome number and the cytogenetic localization on the chromosome when known.

Localizations in genome assemblies

Provides the localizations of the gene and IMGT labels in the genome assemblies, if managed in IMGT/GENE-DB :

Number of alleles

Provides the number of alleles which have been currently identified in IMGT.

IMGT reference alleles

Provides a table in which are listed all identified alleles. For each allele are indicated:

Below the IMGT reference alleles table, a second table provides links to display the IMGT/GENE-DB reference sequences in FASTA format .

IMGT/GENE-DB reference sequences in FASTA format

The IMGT/GENE-DB reference sequences in FASTA format are provided according to the gene type.

The FASTA header is standardized according to FASTA format of IMGT/GENE-DB reference sequences.

Other sequences from the literature (compiled in IMGT gene tables, IMGT Repertoire)

Provides for a given reference allele, the other sequences from the literature corresponding to that allele. For each allele of the gene is indicated the IMGT/LIGM-DB reference sequence with the clone name (if known), the accession number, the molecule type (DNA or cDNA).
The specificity of cDNA sequences is indicated in the last column on the right when known.

IMGT Repertoire links

Provides additional IMGT Web resources concerning the gene in relation with its locus and group available in IMGT Repertoire.

Annotated IMGT/LIGM-DB cDNA sequences

Provides:
- the number of annotated IMGT/LIGM-DB cDNA sequences for the selected gene.
- a link to a table of annotated IMGT/LIGM-DB cDNA sequences with the accession number, the IMGT allele name, the sequence length, the sequence functionality, the sequence definition and the specificity.

Annotated IMGT/LIGM-DB rearranged genomic DNA sequences

Provides:
- the number of annotated IMGT/LIGM-DB rearranged genomic DNA sequences for the selected gene.
- a link to a table of annotated IMGT/LIGM-DB rearranged genomic DNA sequences with the accession number, the IMGT allele name, the sequence length, the sequence functionality, the sequence definition and the specificity.

Annotated IMGT/3Dstructure-DB structures

Provides:
- the number of annotated IMGT/3Dstructure-DB structures for the selected gene.
- a link to a table of annotated IMGT/3Dstructure-DB structures with the PDB code, the IMGT allele name, the IMGT protein name, the IMGT receptor type, the IMGT receptor description, the species, the chain ID.

External links

Provides external links concerning the gene to other nomenclature, genome and sequence databases.

IMGT label extraction from IMGT/LIGM-DB reference sequences

"IMGT label extraction from IMGT/LIGM-DB reference sequences" is one of the three choices of Choose your display in RESULTS OF YOUR SEARCH.
It provides, for each allele of the selected gene(s), in FASTA format, the nucleotide sequences or the amino acid sequences corresponding to the selected label(s) extracted from the IMGT/LIGM-DB reference sequences.
Nucleotide sequences are provided for F+ORF+all P alleles.
Amino acid sequences are provided for F+ORF+in-frame P alleles.

Three example are displayed below:
- Example of extraction of the FR3-IMGT label and the L-PART1+V-EXON artificially spliced label in nucleotides
- Example of extraction of the L-PART1 label in nucleotides with extension of 5 nucleotides in 5' and 30 nucleotides in 3'
- Example of extraction of the L-PART1+V-EXON artificially spliced label in amino acids

Note that the FASTA header is standardized according to FASTA format of IMGT/GENE-DB reference sequences. In addition, in case of extension with nucleotides in 5' and/or in 3', the added nucleotides in 5' and in 3' are indicated in the field 6 of the FASTA header (see example)

Example of extraction of the FR3-IMGT label and the L-PART1+V-EXON artificially spliced label in nucleotides

Example of extraction of the L-PART1 label in nucleotides with extension of 5 nucleotides in 5' and 30 nucleotides in 3' (see Choose your display)

Note that the number of added nucleotides in 5' and in 3' are indicated in the field 6 of the FASTA header.

Example of extraction of the L-PART1+V-EXON artificially spliced label in amino acids

IMGT/GENE-DB LOCALIZATION IN GENOME ASSEMBLIES

The genomic localizations of genes are provided according to the selection : Species, Locus, Assembly, Assembly unit and Designation.

The table comprises one line per localized gene including :


FASTA format of IMGT/GENE-DB reference sequences

The FASTA header of IMGT/GENE-DB reference sequences is standardized. It contains 15 fields separated by '|':

1. IMGT/LIGM-DB accession number(s)
2. IMGT gene and allele name
3. species
4. IMGT allele functionality
5. exon(s), region name(s), or extracted label(s)
6. start and end positions in the IMGT/LIGM-DB accession number(s)
7. number of nucleotides in the IMGT/LIGM-DB accession number(s)
8. codon start, or 'NR' (not relevant) for non coding labels
9. +n: number of nucleotides (nt) added in 5' compared to the corresponding label extracted from IMGT/LIGM-DB
10. +n or -n: number of nucleotides (nt) added or removed in 3' compared to the corresponding label extracted from IMGT/LIGM-DB
11. +n, -n, and/or nS: number of added, deleted, and/or substituted nucleotides to correct sequencing errors, or 'not corrected' if non corrected sequencing errors
12. number of amino acids (AA): this field indicates that the sequence is in amino acids
13. number of characters in the sequence: nt (or AA)+IMGT gaps=total
14. partial (if it is)
15. reverse complementary (if it is)

Note that the field 6. may be modified if:

Four examples are displayed below:
- Nucleotide sequences with IMGT gaps
- Amino acid sequences with IMGT gaps
- Nucleotide sequences (without gaps)
- Amino acid sequences (without gaps)

Created: 31/01/2003
Last updated: 30/06/2016

Authors: Hugo Duvergey, Denis Moreno, Mansour Saljoqi, Véronique Giudicelli and Marie-Paule Lefranc

IMGT/GENE-DB scientific responsibles: Véronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) and Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr)


-> IMGT/GENE-DB Documentation
-> IMGT/GENE-DB Query page
-> IMGT/GENE-DB direct links
-> IMGT/GENE-DB statistics
-> IMGT/GENE-DB program versions
-> IMGT/GENE-DB data updates

Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text, Lefranc, M.-P. et al., Nucleic Acids Research 2009 37(Database issue): D1006-D1012; doi:10.1093/nar/gkn838 Full text.
For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

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