IMGT Scientific chart

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).

ChainType

The chain type identifies the nature of the peptidic chain potentially encoded by IG, TR, MH and RPI genes.

IG-Heavy
Identifies an Immunoglobulin Heavy IGH (locus,gene or chain).
IG-Heavy-Alpha
Identifies an Immunoglobulin Heavy Alpha (gene or chain).
IG-Heavy-Alpha-1-IGHA1
Identifies an Immunoglobulin Heavy Alpha-1 IGHA1 (gene or chain).
IG-Heavy-Alpha-2-IGHA2
Identifies an Immunoglobulin Heavy Alpha-2 IGHA2 (gene or chain).
IG-Heavy-Alpha-IGHA
Identifies an Immunoglobulin Heavy Alpha (gene or chain).
IG-Heavy-Delta
Identifies an Immunoglobulin Heavy Delta (gene or chain).
IG-Heavy-Epsilon
Identifies an Immunoglobulin Heavy Epsilon (gene or chain).
IG-Heavy-Gamma
Identifies an Immunoglobulin Heavy Gamma (gene or chain).
IG-Heavy-Gamma-1-a-IGHG1A
Identifies an Immunoglobulin Heavy Gamma-1-a IGHG1A (gene or chain)
IG-Heavy-Gamma-1-b-IGHG1B
Identifies an Immunoglobulin Heavy Gamma-1-b IGHG1B (gene or chain)
IG-Heavy-Gamma-1-IGHG1
Identifies an Immunoglobulin Heavy Gamma-1 IGHG1 (gene or chain).
IG-Heavy-Gamma-2-a-IGHG2A
Identifies an Immunoglobulin Heavy Gamma-2-a IGHG2A (gene or chain).
IG-Heavy-Gamma-2-b-IGHG2B
Identifies an Immunoglobulin Heavy Gamma-2-b IGHG2B (gene or chain).
IG-Heavy-Gamma-2-c-IGHG2C
Identifies an Immunoglobulin Heavy Gamma-2-c IGHG2C (gene or chain).
IG-Heavy-Gamma-2-IGHG2
Identifies an Immunoglobulin Heavy Gamma-2 IGHG2 (gene or chain).
IG-Heavy-Gamma-3-IGHG3
Identifies an Immunoglobulin Heavy Gamma-3 IGHG3 (gene or chain).
IG-Heavy-Gamma-4-a-IGHG4A
Identifies an Immunoglobulin Heavy Gamma-4-a-IGHG4A (gene or chain).
IG-Heavy-Gamma-4-IGHG4
Identifies an Immunoglobulin Heavy Gamma-4 IGHG4 (gene or chain).
IG-Heavy-Gamma-5-1-IGHG5-1
Identifies an Immunoglobulin Heavy Gamma-5-1 (gene or chain).
IG-Heavy-Gamma-5-2-IGHG5-2
Identifies an Immunoglobulin Heavy Gamma-5-2 (gene or chain).
IG-Heavy-Gamma-6-1-IGHG6-1
Identifies an Immunoglobulin Heavy Gamma-6-1 (gene or chain).
IG-Heavy-Gamma-6-2-IGHG6-2
Identifies an Immunoglobulin Heavy Gamma-6-2 (gene or chain).
IG-Heavy-Mu
Identifies an Immunoglobulin Heavy Mu (gene or chain).
IG-Heavy-Nu
Identifies an Immunoglobulin Heavy Nu (gene or chain) (previously IgNAR) (nurse shark).
IG-Heavy-Omega
Identifies an Immunoglobulin Heavy Omega (gene or chain) (shark).
IG-Heavy-Omicron
Identifies an Immunoglobulin Heavy Omicron (gene or chain) of Ornithorhynchus anatinus (platypus).
IG-Heavy-Phi
Identifies an Immunoglobulin Heavy Phi constant (gene or chain) (anura amphibian).
IG-Heavy-Pi
Identifies an Immunoglobulin Heavy Pi constant (gene or chain) (caudata or urodela amphibian).
IG-Heavy-Rho
Identifies an Immunoglobulin Heavy Rho (gene or chain) (skate).
IG-Heavy-Tau
Identifies an Immunoglobulin Heavy Tau (gene or chain) (some teleostei).
IG-Heavy-Upsilon
Identifies an Immunoglobulin Heavy Upsilon (gene or chain) (frog, bird).
IG-Heavy-Xi
Identifies an Immunoglobulin Heavy Xi (gene or chain) (xenopus).
IG-Heavy-Zeta
Identifies an Immunoglobulin heavy (gene or chain), which are not IG-Heavy-Nu or IG-Heavy-Omega (teleostei).
IG-Light
Identifies an Immunoglobulin Light (locus, gene or chain).
IG-Light-Iota-IGI
Identifies an Immunoglobulin Light Iota IGI (locus, gene, or chain) (shark, teleostei).
IG-Light-Kappa-IGK
Identifies an Immunoglobulin Light Kappa IGK (locus, gene or chain).
IG-Light-Lambda-IGL
Identifies an Immunoglobulin Light Lambda IGL (locus, gene or chain).
IG-Light-Rho
Identifies an Immunoglobulin Light Rho (gene or chain) (frog).
IG-Light-Sigma
Identifies an Immunoglobulin Light Sigma (gene or chain) (frog, shark).
MH1
Identifies an MH class I (locus, gene, or chain).
MH1-Alpha
Identifies an MH class I Alpha (gene or chain).
MH1-Alpha-MH1-A
Identifies a MH class I Alpha MH1-A (gene or chain).
MH1-Alpha-MH1-B
Identifies a MH class I Alpha MH1-B (gene or chain).
MH1-Alpha-MH1-C
Identifies a MH class I Alpha MH1-C (gene or chain).
MH1-Alpha-MH1-D
Identifies a MH class I Alpha MH1-D (gene or chain).
MH2
Identifies an MH class II (locus, gene, or chain).
MH2-Alpha
Identifies an MH class II Alpha (gene or chain).
MH2-Alpha-MH2-DA
Identifies a MH class II Alpha MH2-DA (gene or chain).
MH2-Beta
Identifies an MH class II Beta (gene or chain).
MH2-Beta-MH2-DB1
Identifies a MH class II Beta MH2-DB1 (gene or chain).
MH2-Beta-MH2-DB2
Identifies a MH class II Beta MH2-DB2 (gene or chain).
RPI-Beta2microglobulin (B2M)
Identifies a RPI Beta 2 microglobulin B2M (gene or chain).
RPI-CD8
Identifies a RPI CD8 (gene or chain)
RPI-MH1Like
Identifies a RPI MH1Like (gene or chain).
RPI-MH1Like-Alpha
Identifies a RPI MH1Like Alpha (gene or chain).
RPI-PreB-Light-C
Identifies a RPI PreB receptor Light Constant (gene or chain) (previously surrogate lambda-like or lambda-5).
RPI-PreB-Light-C-1-IGLL1
Identifies a RPI PreB receptor Light Constant-1 IGLL1 (gene or chain).
RPI-PreB-Light-C-2-IGLL2
Identifies a RPI PreB receptor Light Constant-2 IGLL2 (gene or chain).
RPI-PreB-Light-C-3-IGLL3
Identifies a RPI PreB receptor Light Constant-3 IGLL3 (gene or chain).
RPI-PreB-Light-C-4-IGLL4
Identifies a RPI PreB receptor Light Constant-4 IGLL4 (gene or chain).
RPI-PreB-Light-C-5-IGLL5
Identifies a RPI PreB receptor Light Constant-5 IGLL5 (gene or chain).
RPI-PreB-Light-V
Identifies a RPI PreB receptor Light Variable (gene or chain) (previously VpreB).
RPI-PreB-Light-V-1-VPREB1
Identifies a RPI PreB receptor Light Variable-1 VPREB1 (gene or chain).
RPI-PreB-Light-V-2-VPREB2
Identifies a RPI PreB receptor Light Variable-2 VPREB2 (gene or chain).
RPI-PreT-Alpha
Identifies a RPI PreT receptor Alpha (gene or chain).
RPI-PreT-Alpha-PTCRA
Identifies a RPI PreT receptor Alpha PTCRA (gene or chain).
TR-Alpha-TRA
Identifies the T cell Receptor Alpha TRA (locus, gene, or chain).
TR-Beta-1-TRBC1
Identifies a T cell Receptor Beta-1 TRBC1 (gene or chain).
TR-Beta-2-TRBC2
Identifies a T cell Receptor Beta-2 TRBC2 (gene or chain).
TR-Beta-3-TRBC3
Identifies a T cell Receptor Beta-3 TRBC3 (gene or chain).
TR-Beta-TRB
Identifies the T cell Receptor Beta TRB (locus, gene, or chain).
TR-Delta-TRD
Identifies the T cell Receptor Delta TRD (locus, gene, or chain).
TR-Gamma-1-TRGC1
Identifies a T cell Receptor Gamma-1 TRGC1 (gene or chain).
TR-Gamma-2-TRGC2
Identifies a T cell Receptor Gamma-2 TRGC2 (gene or chain).
TR-Gamma-3-TRGC3
Identifies a T cell Receptor Gamma-3 TRGC3 (gene or chain).
TR-Gamma-4-TRGC4
Identifies a T cell Receptor Gamma-4 TRGC4 (gene or chain).
TR-Gamma-5-TRGC5
Identifies a T cell Receptor Gamma-5 TRGC5 (gene or chain).
TR-Gamma-TRG
Identifies the T cell Receptor Gamma TRG (locus, gene, or chain).

ConfigurationType

germline
Identifies, whatever the molecule type, the configuration of the IG and TR variable (V), diversity (D) and joining (J) genes before DNA rearrangements, and by extension, the configuration of the sequences that contain germline genes (with or without constant (C) genes in undefined configuration).
partially-rearranged
Identifies, whatever the molecule type, the configuration of partially rearranged IG or TR D genes, and by extension, the configuration of sequence that contain at least one partially rearranged D gene [with another D or with rearranged variable (V) or joining (J) genes (with or without constant (C) genes in undefined configuration)].
rearranged
Identifies, whatever the molecule type, the configuration of the IG and TR variable (V), diversity (D) and joining (J) genes after DNA rearrangements, and by extension, the configuration of the sequences that contain rearranged genes with, if present, completely rearranged D genes (with or without constant (C) genes in undefined configuration).
undefined
Identifies, whatever the molecule type, the configuration of the conventional genes and that of the IG and TR constant (C) genes, and by extension, the configuration of the molecules that only contain genes in undefined configuration.

FormatType

diabody
Identifies an engineered bivalent IG (or antibody) format made of two fragments (VH+VL), noncovalently linked head to foot. The domains of the same chain are connected by a too short linker to allow their own pairing.
Fab
Identifies the fragment antigen binding of an IG (or antibody) obtained by papain digestion or in vitro construct. An Fab consists of the Fd (VH+CH1) heavy chain fragment linked by a disulfide bond to the light chain (VL+CL).
Fc
Identifies the fragment crystallisable of an IG (or antibody) obtained by papain digestion or in vitro construct. An Fc consists of the two identical CH2+CH3 heavy chain fragments linked by disulfide bridges.
Fd
Identifies the fragment of a IG (or antibody) heavy chain comprising VH+CH1.
Fv
Identifies the VH and VL domains of an IG (or antibody), or the two domains of a TR, held together by strong noncovalent interactions.
scFv
Identifies a single chain Fv. A scFV is an engineered monovalent IG (or antibody) or TR made of one VH and one VL domain (VH+VL), covalently linked by a linker whose length allows the pairing of the domains.
scFv-scFv
Identifies a single chain made of two scFv in tandem with usually different specificities (di-scFV or bi-scFv).

Functionality

functional
Identifies, whatever the molecule type, the functionality of sequences in undefined or germline configuration, whose coding region has an open reading frame without stop codon, no defect in the splicing sites, recombination signals and/or regulatory elements.
ORF
Identifies, whatever the molecule type, the functionality of sequences in undefined or germline configuration, whose coding region has an open reading frame (ORF), but alterations have been described in the splicing sites, recombination signals and/or regulatory elements, and/or changes of conserved amino acids to lead to incorrect folding, and/or the entity is an orphon.
productive
Identifies, whatever the molecule type, the functionality of sequences in rearranged or partially rearranged configuration, whose coding region has an open reading frame without stop codon and without described defects in the initiation codon, splicing sites and/or regulatory elements. Furthermore, for IG and TR, there is an in-frame junction.
pseudogene
Identifies, whatever the molecule type, the functionality of sequences in undefined or germline configuration, whose coding region has stop codon(s) and/or frameshift mutation(s), and/or a mutation affects the initiation codon.
unproductive
Identifies, whatever the molecule type, the functionality of sequences in rearranged or partially rearranged configuration, whose coding region has stop codon(s) and/or frameshift mutation(s), and/or if a mutation affects the initiation codon, and/or if there are defects in the splicing sites and/or in the regulatory element(s), and/or there are unusual features (translocated, gene fusion...) and/or changes of conserved amino acids demonstrated as leading to incorrect folding. Furthermore, for IG and TR an out-of-frame junction.

General

antigen receptor
Identifies molecules with antigen-binding sites that bind non-covalently with an antigen. They comprise immunoglobulins (IG) and T cell receptors (TR).
Immunoglobulin superfamily (IgSF)
Identifies the proteins that contain at least one variable (V) domain or constant (C) domain. IgSF comprises the antigen receptors, IG and TR (with V-DOMAIN and C-DOMAIN) and any protein that contains V-LIKE-DOMAIN and/or C-LIKE-DOMAIN.
Major histocompatibility superfamily (MhSF)
Identifies the proteins that contain two groove (G) domains. MhSF comprises the major histocompatibility (MH) proteins (with G-DOMAIN) and any protein that contains two G-LIKE-DOMAIN.
Scavenger receptor superfamily (SrSF)
Identifies the proteins that contain at least one scavenger (S) domain (or S-DOMAIN).

GeneType

Four types of genes are involved in the IG and TR synthesis: the variable (V), diversity (D) and joining (J) genes which encode the part of the IG and TR chain, or variable domain, that binds the antigens (recognition function), and the constant (C) genes which encode the part of the IG or TR chain, or C region, which has effector properties in IG.

constant
Identifies a constant (C) gene, a gene that codes the constant region of an IG or of a TR chain.
conventional-with-leader
Identifies any (coding or not coding) gene other than IG or TR genes with a leader L region (or signal peptide).
conventional-without-leader
Identifies any (coding or not coding) gene other than IG or TR genes with no leader L region (or signal peptide).
diversity
Identifies a diversity (D) gene, a gene that rearranges at the DNA level and codes the diversity region of the variable domain of an IG or of a TR chain.
joining
Identifies a joining (J) gene, a gene that rearranges at the DNA level and codes the joining region of the variable domain of an IG or of a TR chain.
variable
Identifies a variable (V) gene, a gene that rearranges at the DNA level and codes the variable region of the variable domain of an IG or of a TR chain.

HealthStatus

heavy chain disease (HCD)
Defines a proliferative disorder of B cells that produce truncated monoclonal immunoglobulin heavy chains (Mu, Gamma or Alpha). Structural studies have shown various internal deletions within VH domain and extending through the CH1 domain of the constant region.
leukemia
Defines a cancer (B or T cell malignant proliferation) of the blood or bone marrow characterized by proliferation of leukocytes (white blood cells).
lymphoma
Defines a cancer (B or T cell malignant proliferation) leading to a solid tumor in secondary lymphoid organs.
myeloma
Defines a cancer of plasma cells normally responsible for the production of antibodies. It is characterized by the development of multiple osteolytic tumors by plasma cells (plasmacytomas).
normal individual
Defines a healthy or vaccinated individual
rheumatoid arthritis (RA)
Defines a chronic, systemic inflammatory disorder that may affect many tissues and organs, but principally attacks synovial joints.
rheumatoid factor (RF)
Defines an autoantibody anti-IgG. It is an antibody against the Fc part of IgG. RF and IgG form immune complexes which contribute to the process in some autoimmune diseases, such as rheumatoid arthritis.
systemic lupus erythematosus (SLE)
Defines a chronic systemic autoimmune disease that can affect any part of the body (heart, joints, skin, lungs, blood vessels, liver, kidneys, and nervous system).
tumor
Defines an abnormal mass of tissue (or neoplasm) as a result of neoplasia (abnormal proliferation of cells). Tumor is not synonymous with cancer. A tumor can be benign, pre-malignant or malignant.

IMGT_Expertise

IMGT reference sequence
Identifies a sequence used as a reference by IMGT to define each allele of a given gene.
IMGT-NC inferred allele
Identifies a sequence used to define an IMGT-NC inferred allele.
incorrect sequence
Identifies a sequence with detected errors and/or with too many uncertainties.
normal rearranged repertoire
Identifies a rearranged (productive or unproductive) IG or TR sequence from the repertoire of a normal individual (no known pathology according to publication).
partner
Identifies a sequence that belongs to an antigen receptor and comprises a V domain and for which the other sequence of the same antigen receptor and comprising the other V domain is known.
patent
Identifies a sequence protected by a patent application.
primer
Identifies a short nucleotide sequence designed in vitro and used in polymerase chain reaction (PCR) amplification or for sequencing.
repeat
Identifies a sequence with a repeat (e.g., Alu) annotated by IMGT
specificity
Identifies the nature of the antigen recognized by an antigen receptor (IG or TR). The specificity is defined for rearranged IG and TR sequences.

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.

MolecularComponent

CD3
Identifies coreceptor proteins, part of the T cell receptor (TcR) at the T cell surface. Includes CD3 gamma (CD3G), CD3 delta (CD3D), CD3 epsilon (CD3E) and CD3 zeta (CD3Z) chains.
CD79
Identifies coreceptor proteins, part of the BcR at the B cell surface (in humans, includes CD79A and CD79B).
composite protein for clinical applications (CPCA)
Identifies genetically engineered proteins other than FPIA that result from the fusion of peptide, region and/or domain of protein(s) of different sources, or from the fusion of peptide, region and/or domain of protein(s) to a chemical or biochemical agent. Fc may be present but is not used for its effector properties.
Fc receptor (FcR)
Identifies a family of membrane receptors that binds the Fc of an antibody. They are members of the IgSF superfamily except FCGRT that is a member of the MhSF superfamily. They provide a link between the innate and adaptative immune responses.
fusion protein for immune applications (FPIA)
Identifies a genetically engineered fusion protein for immune applications. FPIA are proteins that result from the fusion of peptide, region and/or domain of protein(s) of different sources with two constant domains of IG used for their effector properties (INN suffix -cept).
immunoglobulin (IG)
Identifies an antibody or antigen receptor expressed by B cells (membrane form) or plasma cells (secreted form) that specifically binds an antigen.
interleukin (IL)
Identifies a cytokine secreted by leukocytes and endothelial cells that binds to interleukin receptor on T, B and hematopoietic cells. This interaction leads to signalling that promotes cell development and differentiation.
Killer cell immunoglobulin-like receptor (KIR)
Identifies a family of membrane receptors expressed by NK cells and a subpopulation of T cells, that bind MH1 proteins. They are members of the IgSF superfamily.
Killer cell lectine-like receptor (KLR)
Identifies a family of receptor of the C type lectine superfamily. (previously NKG, Natural Killer Group)
Leucocyte immunoglobulin-like receptor (LILR)
Identifies a family of leucocyte immunoglobulin-like receptors expressed by NK cells. They belong to the IgSF superfamily.
major histocompatibility (MH)
Identifies a major histocompatibility protein presenting a peptide (or "processed antigen") to the T cell. The peptide is noncovalently bound in a groove formed by two G (groove) domains. The two domains belong either to the same chain (alpha chain of the MH1), or to two different chains (alpha and beta chains of the MH2). In the MH1, the alpha chain is associated to the RPI-Beta2microglobulin (B2M).
polymeric immunoglobulin receptor (PIGR)
Identifies a polymeric immunoglobulin (IgA and IgM) receptor.
related protein of the immune system (RPI)
Identifies a related protein of the immune system that comprises proteins of the IgSF other than IG and TR, proteins of the MhSF other than MH, and proteins involved in the immune response found in vivo.
T cell receptor (TR)
Identifies a membrane antigen receptor expressed by T cells that specifically binds a peptide (or "processed antigen") presented by a MH protein.
variable lymphocyte receptor (VLR)
Identifies a variable lymphocyte receptor in Petromyzon marinus (lamprey).

MoleculeType

cDNA
Identifies complementary DNA, a nucleotide sequence made of A, T, C and G, obtained in vitro by reverse transcription of mRNA.
gDNA
Identifies genomic DNA, a nucleotide sequence made of A, T, C and G, obtained from a genome, or by extension, synthetic DNA having the characteristics of genomic DNA.
unassigned DNA
Identifies sequences which cannot be assigned to gDNA or cDNA.

Molecule_EntityType

C-gene
Identifies, for gDNA, molecule entities with a C gene in undefined configuration. C-gene is in undefined configuration.
C-sequence
Identifies, for cDNA, molecule entities with a C region in undefined configuration. C-sequence is in undefined configuration.
conventional-gene
Identifies, for gDNA, a conventional gene without leader in undefined configuration.
D-gene
Identifies, for gDNA, molecule entities with a germline D gene. D-gene is in germline configuration.
D-J-C-sequence
Identifies, for cDNA, molecule entities with a partially rearranged D region, a rearranged J region and a C region in undefined configuration. D-J-C-sequence is in partially rearranged configuration.
D-J-gene
Identifies, for gDNA, molecule entities with a partially rearranged D gene and a rearranged J gene. D-J-gene is in partially rearranged configuration.
D-sequence
Identifies, for cDNA, molecule entities with a germline D region. D-sequence is in germline configuration.
J-C-gene
Identifies, for gDNA, processed orphon with a germline J gene and a C gene in undefined configuration. J-C-gene is in germline configuration.
J-C-sequence
Identifies, for cDNA, molecule entities with a germline J region and a C region in undefined configuration. J-C-sequence is in germline configuration.
J-gene
Identifies, for gDNA, molecule entities with a germline J gene. J-gene is in germline configuration.
J-sequence
Identifies, for cDNA, molecule entities with a germline J region. J-sequence is in germline configuration.
L-conventional-gene
Identifies, for gDNA, a conventional gene with leader in undefined configuration.
L-nt-sequence
Identifies, for cDNA, molecule entities with a leader L region and a conventional region in undefined configuration. L-nt-sequence is in undefined configuration.
L-V-D-J-C-sequence
Identifies, for cDNA, molecule entities with a leader L region, a rearranged V region, at least one rearranged D region, a rearranged J region and a C region in undefined configuration. L-V-D-J-C-sequence is in rearranged configuration.
L-V-D-sequence
Identifies, for cDNA, molecule entities with a leader L region, a rearranged V region and a partially rearranged D. L-V-D-sequence is in partially rearranged configuration.
L-V-J-C-sequence
Identifies, for cDNA, molecule entities with a leader L region, a rearranged V region, a rearranged J region and a C region in undefined configuration. L-V-J-C-sequence is in rearranged configuration.
L-V-sequence
Identifies, for cDNA, molecule entities with a leader L region and a germline V region. L-V-sequence is in germline configuration.
nt-sequence
Identifies, for cDNA, molecule entities with a conventional region in undefined configuration. Nt-sequence is in undefined configuration.
V-D-gene
Identifies, for gDNA, molecule entities with a rearranged V gene and a partially rearranged D gene. V-D-gene is in partially rearranged configuration.
V-D-J-gene
Identifies, for gDNA, molecule entities with a rearranged V gene, at least one rearranged D gene and a rearranged J gene. V-D-J-gene is in rearranged configuration.
V-gene
Identifies, for gDNA, molecule entities with a germline V gene. V-gene is in germline configuration.
V-J-gene
Identifies, for gDNA, molecule entities with a rearranged V gene and a rearranged J gene. V-J-gene is in rearranged configuration.

Obtention

contig
Identifies a contiguous sequence or map obtained by assemblage of overlapping shorter sequences or clones, respectively.
hybridoma
Identifies hybrid cell lines obtained by fusing a specific antibody-producing B cell with a myeloma (B cell cancer) cell. An antibody produced by an hybridoma is a monoclonal antibody (mAb).
transgenic repertoire
Identifies the repertoire obtained from the recipient of transgenic IG or TR DNA.

Particularities

autoantibody
Identifies an IG (or antibody), whose specificity is directed against self components of an organism and which leads to an immune response against them.
catalytic
Identifies the property of a protein that is able to perform an enzymatic reaction, e.g. to catalyze a chemical reaction.
cold agglutinin
Identifies an IG (or antibody) directed against the I antigen of the red blood cells. The hemagglutination occurs at cold temperature and leads to hemolysis.
polyreactive
Identifies a monoclonal antibody that can bind to several self or foreign antigens.

Recombinaison

3'Kde-RS
Identifies a kappa-deletion element (kappa-del) localized in 3' of the IGKC gene, in the IGK locus, the RS of which is used for recombinations leading to Trec.
5'Kde-3'Kde joint
Identifies, in the IGK locus, the joint on the chromosome resulting from a rearrangement between the 5'Kde-RS and the 3'Kde-RS.
5'Kde-RS
Identifies a kappa-deletion element (kappa-del) localized in 5' of the IGKC gene, between the IGKJ genes and the IGKC gene, in the IGK locus, the RS of which is used for recombinations leading to Krec.
deltaRec
Identifies a TRAV/DV vestigial pseudogene, located in 3' of the TRAV locus, the V-RS of which is used for recombinaisons Trec.
excision circle
Identifies a circular genomic DNA resulting from IG and TR V-(D)-J rearrangements by deletion and characterized by a signal joint, or resulting from IGH switch recombination in the IGH locus; excision circle also includes Trec (TR recombinaison excision circle) resulting from a TRAV/DV (deltaRec)-(D)-J rearrangement that deletes the TRD locus or part of it, and Krec (IGK recombinaison excision circle) resulting from a 5'Kde-3'Kde rearrangement that produces a 5'Kde-3'Kde joint and deletes the IGKC gene.
signal joint
Identifies two recombination signals joined in opposite orientation as a result of rearrangements in IG or TR loci, localized on an excision circle (rearrangement by deletion) or on the chromosome (rearrangement by inversion).
switch
Identifies a sequence of about 2 kb, composed of ~20 to 80 bp repeats, located in 5' of the IGHC genes and involved in IG class switch recombination. This process leads to a change of the IG class or subclass (by switching the IGHC region), while maintaining the same antibody specificity.
switch-like
Identifies, in invertebrates, a sequence of unknown function with a structural similarity to the vertebrate switch.

Regulation

enhancer
Defines a regulatory sequence that enhances the expression of a gene.
promoter
Defines a regulatory sequence that promotes the expression of a gene.
silencer
Defines a regulatory sequence that inhibits the expression of a gene.

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.

TaxonomyRelated

chimeric
Identifies, whatever the molecule type, the sequences that have a classical organization and result from the fusion in vivo or in vitro of molecules from two (usually) sources. For example, L-V-D-J-C-sequence of IG resulting from the fusion in vitro of the variable domain from one source (murine, rat...) with the constant region from human [2 sources].
humanized
Identifies, whatever the molecule type, the sequences that have a classical organization and have been modified in vitro with the purpose of humanization. For example, L-V-D-J-C-sequence of IG resulting from the grafting in vitro of the CDR from one source (murine, rat...) to the FR (and with the constant region) from human [2 sources].
synthetic construct
Identifies sequences which cannot be assigned to a taxon (Taxonomy), or to chimeric or humanized.

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