Atlas of Genetics and Cytogenetics in Oncology and Haematology

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TRA (T cell Receptor Alpha)

Written2000-07Marie-Paule Lefranc
IMGT, LIGM, IGH, UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France

(Note : for Links provided by Atlas : click)


Alias (NCBI)TRA@ (T cell Receptor Alpha)
HGNC Previous nameTCRA
HGNC Previous nameTCRA, TRA@
LocusID (NCBI) 6955
Atlas_Id 39
Location 14q11.2  [Link to chromosome band 14q11]
  for complete Figure, see: chromosome 14, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
  TRA (T cell Receptor Alpha) Top: Probe bA60K12 - Courtesy Mariano Rocchi; Bottom: Hybridization with Vysis TRA/D Break Apart probe (Abbott Molecular, US) showing the gene on 14q11.2 (red-green or a fused yellow signal) - Courtesy Adriana Zamecnikova.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
Note The human TRA locus is located on the chromosome 14 on the long arm at band 14q11.2. The orientation of the locus has been determined by the analysis of translocations, involving the TRA and TRD loci, in leukemia and lymphoma.


V-GENE: Green box: Functional; Red: Pseudogene.
D-GENE: Blue: Functional.
J-GENE: Yellow: Functional; Pale yellow: Open reading frame; Red: pseudogene.
C-GENE: Blue: Functional.
for complete Figure, see: locus TRA, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
  • The human TRA locus at 14q11.2 spans 1000 kilobases (kb). It consists of 54 TRAV genes belonging to 41 subgroups, 61 TRAJ segments localized on 71 kb, and a unique TRAC gene.
  • The most 5' TRAV genes occupy the most centromeric position, whereas the TRAC genes, 3' of the locus, is the most telomeric gene in the TRA locus.
  • The organization of the TRAJ segments on a large area is quite unusual and has not been observed in the other immunoglobulin or T cell receptor loci.
  • Moreover the TRD locus is nestled in the TRA locus between the TRAV and TRAJ segments. V-J-rearrangements in the TRA locus therefore result in deletion of the TRD genes localized on the same chromosome. That deletion occurs in two steps, that is a deletion of the TRD genes, involving specific sequences located upstream from TRDC (sequence pseudo J alpha) would take place before the TRAV-J rearrangement.
  • The potentiel genomic TRA repertoire comprises 45-47 functional TRAV genes belonging to 33-35 subgroups, 50 functional TRAJ segments, and the unique TRAC gene.
  • Among the variable genes are included five genes designated as TRAV/DV which belong to five different subgroups and which have been found rearranged either to TRAJ or to TRDD segments and can therefore be used in the synthesis of alpha or delta chains.
  • The total number of human TRA genes per haploid genome is 116 of which 96 to 98 genes are functional. Enhancer sequences have been characterized 4.5kb 3' from TRAC.
  • List of the human TRA genes
  • Protein

  • Proteins encoded by the TRA locus are the T cell receptor alpha chains. They result from the recombination (or rearrangement), at the DNA level, of two genes: TRAV and TRAJ, with deletion of the intermediary DNA to create a rearranged TRAV-J gene. The rearranged TRAV-J gene is transcribed with the TRAC gene and translated into an T cell receptor alpha chain.
  • Translation of the variable germline genes involved in the TRAV-J rearrangements are available at IMGT Repertoire Protein displays. TRA V-J rearrangements can be analysed using the IMGT/V-QUEST tool.
  • Mutations

    Note Mutations which correspond to allelic polymorphisms of the functional germline TRAV, TRAJ and TRAC genes are described in the IMGT database: (IMGT Repertoire>Alignments of alleles)

    Implicated in

    Entity Translocations which frequently result from errors of the recombinase enzyme complex (RAG1, RAG2, etc.), which is responsable of the Immunoglobulin and T cell receptor V-J and V-D-J rearrangements. TRAV or TRAJ recombination signals or isolated heptamer are observed at the breakpoints.
    Entity ; involve TRA - TAL1 in 1p32
    Prognosis median survival > 5 yrs in children
    Entity ; involve TRA - MYC in 8q24
    Disease T-cell acute lymphocytic leukemia (ALL); rare
    Entity ; involve TRA - HOX11 in 10q24
    Disease T- cell acute lymphoblastic leukemia (ALL) and non-Hodgkin lymphoma (NHL)
    Prognosis not unfavourable
    Entity ; involve RBTN2 in 11p13
    Disease T-cell acute lymphocytic leukemia (ALL)
    Entity ; involveTRA - TCL1 in 14q32
    Disease and adult T cell leukemia/lymphoma
    Prognosis poor
    Entity ; involve TRA - OLIG2 in 21q22
    Disease T-cell acute lymphoblastic leukemia (ALL)
    Prognosis unknown




    Crystal structure of p14TCL1, an oncogene product involved in T-cell prolymphocytic leukemia, reveals a novel beta-barrel topology.
    Hoh F, Yang YS, Guignard L, Padilla A, Stern MH, Lhoste JM, van Tilbeurgh H
    Structure (London, England : 1993). 1998 ; 6 (2) : 147-155.
    PMID 9519406
    Locus Map and Genomic repertoire of the Human Immunoglobulin Genes (Review)
    Lefranc MP
    The immunologist,. 2000.
    The T cell Receptor FactsBook (Review)
    Lefranc MP and Lefranc G
    Academic Press, London, UK (398 pages), 2001. ISBN: 124413528


    This paper should be referenced as such :
    Lefranc, MP
    TRA (T cell receptor alpha)
    Atlas Genet Cytogenet Oncol Haematol. 2000;4(3):117-118.
    Free journal version : [ pdf ]   [ DOI ]

    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 39 ]
      Hepatosplenic T-cell lymphoma (HSTCL)
    t(7;14)(q35;q32.1) TRB::TCL1A::inv(14)(q11q32.1) TRA-TRD/TCL1A::t(14;14)(q11;q32.1) TRA-TRD/TCL1A
    Pediatric T-Cell Acute Lymphoblastic Leukemia
    t(1;7)(p32;q34) TRB::TAL1::t(1;14)(p32;q11) TRA/TAL1::1p32 rearrangements
    t(6;14)(p25.3;q11.2) TRA::IRF4
    t(7;12)(q34;p13) TRB::CCND2::t(12;14)(p13;q11) TRA or TRD/CCND2
    t(2;7)(p11;q21) IGK::CDK6::t(7;14)(q21;q32) IGH/CDK6::t(7;22)(q21;q11) IGL/CDK6::t(7;14)(q21;q11) TRA/CDK6
    t(7;14)(q34;q11) TRA::TRB
    t(7;14)(q34;q11) TRA::TRB
    t(8;14)(q24;q11) TRA::MYC
    t(11;14)(p13;q11) TRD::LMO2::t(7;11)(q35;p13) TRB/LMO2
    t(7;11)(q34;p15) TRB::LMO1::t(11;14)(p15;q11) TRD/LMO1
    t(14;14)(q11;q32) CEBPE::IGH::inv(14)(q11q32) CEBPE/IGH
    t(14;19)(q11;q13) TRA::NECTIN2
    t(14;21)(q11;q22) TRA::OLIG2
    t(20;21)(q13.2;q22.12) ZFP64::RUNX1
    TAL1 (1p32) deletion in lymphoid malignancies
    T-lineage acute lymphoblastic leukemia (T-ALL)
    Classification of T-Cell disorders
    T-cell large granular lymphocyte leukaemia
    t(1;14)(p33;q11) TAL1::TRA
    t(2;14)(p21;q11) ZFP36L2::TRA
    t(6;14)(q22;q11) TRA::CEP85L
    t(9;14)(p21;q11) CDKN2A::TRA
    t(9;14)(p21;q11) TRA::CDKN2A
    t(9;14)(q34;q11) TRA::NOTCH1
    t(10;14)(q24;q11) TLX1::TRA
    t(11;14)(p13;q11) TRA::LMO2
    t(11;14)(p15;q11) LMO1::TRA
    t(14;14)(q11;q13) NKX2-1::TRA
    t(14;14)(q11;q13) TRA::NKX2-1
    inv(14)(q11q32):t(14;14)(q11;q32) IGH::TRA
    t(14;14)(q11;q32) TRA::TCL1A
    t(14;16)(q11;p13) USP7::TRA
    t(X;14)(q28;q11) TRA::MTCP1
    T-cell prolymphocytic leukemia (T-PLL)
    t(X;14)(q28;q11.2) TRA-TRD::MTCP1::t(X;7)(q28;q34) TRB/MTCP1

    External links


    HGNC (Hugo)TRA   12027
    Entrez_Gene (NCBI)TRA    T cell receptor alpha locus
    AliasesIMD7; TCRA; TRA@
    GeneCards (Weizmann)TRA
    Ensembl hg19 (Hinxton) [Gene_View]
    Ensembl hg38 (Hinxton) [Gene_View]   [Sequence]  - [Contig_View]  TRA [Vega]
    TCGA cBioPortalTRA
    AceView (NCBI)TRA
    Genatlas (Paris)TRA
    SOURCE (Princeton)TRA
    Genetics Home Reference (NIH)TRA
    Genomic and cartography
    GoldenPath hg38 (UCSC)TRA  -  
    GoldenPath hg19 (UCSC)TRA  -  
    GoldenPathTRA - [CytoView hg19]  TRA - [CytoView hg38]
    Genome Data Viewer NCBITRA [Mapview hg19]  
    Gene and transcription
    Genbank (Entrez)-
    RefSeq transcript (Entrez)
    Consensus coding sequences : CCDS (NCBI)TRA
    Gene ExpressionTRA [ NCBI-GEO ]   TRA [ EBI - ARRAY_EXPRESS ]   TRA [ SEEK ]   TRA [ MEM ]
    Gene Expression Viewer (FireBrowse)TRA [ Firebrowse - Broad ]
    GenevisibleExpression of TRA in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)6955
    GTEX Portal (Tissue expression)TRA
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtP0DSE1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtP0DSE1  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProP0DSE1
    Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)   
    Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig_sub    Ig_V-set    TCR_alpha_C   
    Domain families : Pfam (Sanger)DUF1968 (PF09291)    V-set (PF07686)   
    Domain families : Pfam (NCBI)pfam09291    pfam07686   
    Domain families : Smart (EMBL)IG (SM00409)  IGv (SM00406)  
    Conserved Domain (NCBI)TRA
    PDB (RSDB)1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    PDB Europe1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    PDB (PDBSum)1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    PDB (IMB)1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    Structural Biology KnowledgeBase1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    SCOP (Structural Classification of Proteins)1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    CATH (Classification of proteins structures)1OGA    2VLJ    2VLK    2VLR    5HHM    5HHO   
    AlphaFold pdb e-kbP0DSE1   
    Protein Interaction databases
    IntAct (EBI)P0DSE1
    Ontologies - Pathways
    Ontology : AmiGOdetection of tumor cell  T cell mediated cytotoxicity directed against tumor cell target  integral component of membrane  signaling receptor activity  alpha-beta T cell receptor complex  
    Ontology : EGO-EBIdetection of tumor cell  T cell mediated cytotoxicity directed against tumor cell target  integral component of membrane  signaling receptor activity  alpha-beta T cell receptor complex  
    NDEx NetworkTRA
    Atlas of Cancer Signalling NetworkTRA
    Wikipedia pathwaysTRA
    Orthology - Evolution
    Phylogenetic Trees/Animal Genes : TreeFamTRA
    Homologs : HomoloGeneTRA
    Homology/Alignments : Family Browser (UCSC)TRA
    Gene fusions - Rearrangements
    Fusion : MitelmanIGH::TRA [14q32.33/-]  
    Fusion : MitelmanTRA::CDKN2A [-/9p21.3]  
    Fusion : MitelmanTRA::IRF4 [-/6p25.3]  
    Fusion : MitelmanTRA::MTCP1 [-/Xq28]  
    Fusion : MitelmanTRA::MYC [-/8q24.21]  
    Fusion : MitelmanTRA::NOTCH1 [-/9q34.3]  
    Fusion : MitelmanTRA::OLIG2 [-/21q22.11]  
    Fusion : MitelmanTRA::PVRL2 [-/19q13.32]  
    Fusion : MitelmanTRA::TCL1A [-/14q32.13]  
    Fusion : MitelmanTRA::TRB [-/-]  
    Fusion : QuiverTRA
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerTRA [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)TRA
    Exome Variant ServerTRA
    Varsome BrowserTRA
    ACMGTRA variants
    Genomic Variants (DGV)TRA [DGVbeta]
    DECIPHERTRA [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisTRA 
    ICGC Data PortalTRA 
    TCGA Data PortalTRA 
    Broad Tumor PortalTRA
    OASIS PortalTRA [ Somatic mutations - Copy number]
    Cancer Gene: CensusTRA 
    Mutations and Diseases : HGMDTRA
    LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
    DgiDB (Drug Gene Interaction Database)TRA
    DoCM (Curated mutations)TRA
    CIViC (Clinical Interpretations of Variants in Cancer)TRA
    NCG (London)TRA
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Genetic Testing Registry TRA
    NextProtP0DSE1 [Medical]
    Target ValidationTRA
    Huge Navigator TRA [HugePedia]
    Clinical trials, drugs, therapy
    Protein Interactions : CTDTRA
    Pharm GKB GenePA36704
    Clinical trialTRA
    canSAR (ICR)TRA
    DataMed IndexTRA
    Other databaseTRA@ - IMGT
    PubMed123 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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    indexed on : Fri Oct 8 21:29:11 CEST 2021

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