IMGT Scientific chart

How to qualify a gene (structure and localization)

Extraction of the List of standardized IMGT/LIGM-DB keywords

Use the following keywords as far as possible to describe your sequences when you submit them to a generalist database (EMBL-Bank, GenBank, DDBJ).

StructureType

The structure type distinguishes sequences that show a classical organisation (regular), from those which have been modified either naturally (spliced, processed...), or artificially (humanized, engineered...).

alternative splicing
Identifies the structures of gene that have characteristics for potential alternative splicing (for example, IG genes with features for potential secreted and membrane chains).
engineered
Identifies, whatever the molecule type, the sequences that have been modified by deliberate mutagenesis in vitro [1 source].
fusion
Identifies, whatever the molecule type, the sequences that do not have a classical organization and result from the fusion in vivo or in vitro of molecules from two (or more) different sources [2 (or more) sources].
immunotoxin
Identifies an IG (or antibody) or RPI protein fused or conjugated with a toxin, obtained in vitro.
linker
Identifies a short sequence used to link two other sequences.
membrane
Identifies, whatever the molecule type, the sequences that have a transmembrane exon or region allowing for a transmembrane chain.
partially-processed
Identifies the sequence of genes (usually orphons) that have lost part of their introns.
partially-spliced
Identifies the transcripts or cDNA sequences that have been submitted to partial RNA processing or splicing.
processed
Identifies the sequences of genes (usually orphons) that have lost their introns.
regular
Identifies, whatever the molecule type, the sequences that have a classical organization without in vivo or in vitro modification.
secreted
Identifies, whatever the molecule type, the sequences that have an hydrophilic C-terminal exon or region allowing for a secreted soluble chain, e.g presence of the CH-S sequence for IGHC.
spliced
Identifies the transcripts or cDNA sequences that have been submitted to complete RNA processing or splicing.
sterile transcript
Identifies the transcripts that cannot be translated in vivo, and corresponding cDNA. For example, for IG or TR, transcripts of V, D or J genes in germline configuration (also designated as "germline transcripts"), transcripts of C genes in undefined configuration, transcripts of switch regions, and corresponding cDNA, respectively.
truncated
Identifies a shortened protein (missing amino acids) owing to a premature STOP-CODON.
unspliced
Identifies the transcripts or cDNA sequences that have not been submitted to RNA processing or splicing.
unusual
Identifies an IG or TR gene with unexpected feature(s) (for instance, insertion of unknown sequences, unexpected rearrangements by inversion...).
vector
Identifies a sequence from cloning vector.

LocationType

orphon
Identifies, whatever the molecule type, a gene that is found in vivo on a different locus from the main locus (either on the same chromosome or on another chromosome).
transgene
Identifies, whatever the molecule type, a gene that is artificially introduced into a multicellular organism (mouse, plant...).
translocated
Identifies, whatever the molecule type, a gene that results from a translocation (in vivo).
transposed
Identifies, whatever the molecule type, a transgene or a retrotransposon that is permanently inserted in a chromosome.

Author:: Laëtitia Regnier
Last updated:: 30/05/2016