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IMGT prototypes table



Definition

An IMGT prototype is the graphical representation of an entity with IMGT® standardized labels (capital letters, no plural) [1, 2]. IMGT prototypes are defined for molecular entities in IMGT® databases and tools.


Relation with IMGT-ONTOLOGY

An IMGT prototype for a molecular entity (in databases and tools) corresponds to a leafconcept of the 'Molecular_EntityPrototype' (in IMGT-ONTOLOGY) [1].
In the table, the 32 'Molecule_EntityType' leafconcepts are shown with the leafconcepts of 'GeneType', 'ConfigurationType', and 'MoleculeType' that define them.
The three leafconcepts of 'MoleculeUnit' are based on 'MoleculeType' only [1].

(*) An asterisk indicates the 8 leafconcepts that are the most classical representatives of IG and TR identification.
Each "Molecule_EntityType" leafconcept is linked to a "Molecule_EntityPrototype" leafconcept.

Clicking on the links in the table gives access to the IMGT prototypes.




'Molecule_EntityPrototype' leafconcepts and related concepts

IDENTIFICATION DESCRIPTION
MoleculeUnit
leafconcepts
Molecule_EntityType
leafconcepts
GeneType
leafconcepts
ConfigurationType
leafconcepts
MoleculeType
leafconcepts
Molecule_EntityPrototype
leafconcepts
gene
V-gene* V germline gDNA V-GENE
D-gene* D D-GENE
J-gene* J J-GENE
J-C-gene J, C J-C-GENE
C-gene* C undefined C-GENE
L-conventional-gene conventional L-CONVENTIONAL-GENE
V-D-gene V, D partially_rearranged V-D-GENE
D-J-gene D, J D-J-GENE
V-J-gene* V, J rearranged V-J-GENE
V-D-J-gene* V, D, J V-D-J-GENE
transcript
L-V-transcript V germline mRNA L-V-TRANSCRIPT
D-transcript D D-TRANSCRIPT
J-transcript J J-TRANSCRIPT
J-C-transcript J, C J-C-TRANSCRIPT
C-transcript C undefined C-TRANSCRIPT
L-nt-transcript conventional L-NT-TRANSCRIPT
nt-transcript conventional NT-TRANSCRIPT
L-V-D-transcript V, D partially_rearranged L-V-D-TRANSCRIPT
D-J-C-transcript D, J, C D-J-C-TRANSCRIPT
L-V-J-C-transcript V, J, C rearranged L-V-J-C-TRANSCRIPT
L-V-D-J-C-transcript V, D, J, C L-V-D-J-C-TRANSCRIPT
sequence
L-V-sequence V germline cDNA L-V-SEQUENCE
D-sequence D D-SEQUENCE
J-sequence J J-SEQUENCE
J-C-sequence J, C J-C-SEQUENCE
C-sequence C undefined C-SEQUENCE
L-nt-sequence conventional L-nt-SEQUENCE
nt-sequence conventional NT-SEQUENCE
L-V-D-sequence V, D partially_rearranged L-V-D-SEQUENCE
D-J-C-sequence D, J, C D-J-C-SEQUENCE
L-V-J-C-sequence* V, J, C rearranged L-V-J-C-SEQUENCE
L-V-D-J-C-sequence* V, D, J, C L-V-D-J-C-SEQUENCE


References:
[1] Giudicelli, V. and Lefranc, M.-P., "IMGT-ONTOLOGY 2012" Frontiers in Bioinformatics and Computational Biology Online access. Front. Genet. 2012; 3:79. Epub 2012 May 23. PMID: 22654892 LIGM: 401
[2] Lefranc, M.-P., "From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures" Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.ip83. doi: 10.1101/pdb.ip83. PMID: 21632791 LIGM: 384
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.
[3] Lefranc, M.-P., "From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT Standardized Keywords: For Immunoglobulins (IG), T Cell Receptors (TR), and Conventional Genes" Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.ip82. doi: 10.1101/pdb.ip82. PMID: 21632792 LIGM: 383
IMGT booklet high resolutionpdficon lower resolutionpdficon 'With generous provision from Cold Spring Harbor (CSH) Protocols'.

IMGT index:
Created:
16/04/2013
Last updated:
Thursday, 26-May-2016 21:00:48 CEST
Authors:
Souphatta Sasorith and Marie-Paule Lefranc
Editor:
Chantal Ginestoux
Scientific officer:
Marie-Paule Lefranc