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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome
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Don't let the Atlas imminent demise
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TRA (T cell Receptor Alpha)


Other namesTRA@ (T cell Receptor Alpha)
LocusID (NCBI) 6955
Location -
  for complete Figure, see: chromosome 14, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2003 IMGT, IMGT is a CNRS trademark
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
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 1995-2003 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 t(1;14)(p32;q11); involve TAL1 in 1p32
    Prognosis median survival > 5 yrs in children
    Entity t(8;14)(q24;q11); involve MYC in 8q24
    Disease T-cell acute lymphocytic leukemia (ALL); rare
    Entity t(10;14)(q24;q11); involve HOX11 in 10q24
    Disease T- cell acute lymphoblastic leukemia (ALL) and non-Hodgkin lymphoma (NHL)
    Prognosis not unfavourable
    Entity t(11;14)(p13;q11); involve RBTN2 in 11p13
    Disease T-cell acute lymphocytic leukemia (ALL)
    Entity t(14;14)(q11;q32), inv(14)(q11q32); involve TCL1 in 14q32
    Disease T-cell prolymphocytic leukemia (T-PLL) and adult T cell leukemia/lymphoma
    Prognosis poor
    Entity t(14;21)(q11;q22); involve OLIG2 in 21q22
    Disease T-cell acute lymphoblastic leukemia (ALL)
    Prognosis unknown



    Other Leukemias implicated (Data extracted from papers in the Atlas)

    Leukemias 11q23ChildAMLID1615 11q23ID1030 11q23secondLeukID1131 t1119ELLID1029 t0812q24q22ID2057
    t0814ID1050 8p11inMPDID1091 inv8p11q13ID1189 PrimarCutanALCLID2118

    External links

    HGNC (Hugo)TRA   12027
    Entrez_Gene (NCBI)TRA  6955  T cell receptor alpha locus
    GeneCards (Weizmann)TRA
    Ensembl hg19 (Hinxton) [Gene_View]  - [Contig_View]  TRA [Vega]
    Ensembl hg38 (Hinxton) [Gene_View]  - [Contig_View]  TRA [Vega]
    AceView (NCBI)TRA
    Genatlas (Paris)TRA
    SOURCE (Princeton)TRA
    Genomic and cartography
    GoldenPath hg19 (UCSC)TRA  -  
    GoldenPath hg38 (UCSC)TRA  -  
    EnsemblTRA - [CytoView hg19]  TRA - [CytoView hg38]
    Mapping of homologs : NCBITRA [Mapview hg19]  TRA [Mapview hg38]
    OMIM186880   615387   
    Gene and transcription
    Genbank (Entrez)-
    RefSeq transcript (Entrez)
    RefSeq genomic (Entrez)NC_000014 NC_018925 NG_001332 NT_026437 NW_004929393
    Consensus coding sequences : CCDS (NCBI)TRA
    Alternative Splicing : Fast-db (Paris)GSHG0032565
    Gene ExpressionTRA [ NCBI-GEO ]     TRA [ SEEK ]   TRA [ MEM ]
    SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    Protein : pattern, domain, 3D structure
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    DMDM Disease mutations6955
    Protein Interaction databases
    Ontologies - Pathways
    PubMed101 Pubmed reference(s) in Entrez


    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
    Nomenclature of the human T cell Receptor genes (Review)
    Lefranc MP
    Current Protocols in Immunology. 2000.
    The T cell Receptor FactsBook (Review)
    Lefranc MP and Lefranc G
    Academic Press, London, UK (. 1939.
    Locus Map and Genomic repertoire of the Human Immunoglobulin Genes (Review)
    Lefranc MP
    The immunologist,. 2000.
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI


    Written07-2000Marie-Paule Lefranc
    Updated09-2003Marie-Paule Lefranc


    This paper should be referenced as such :
    Lefranc, MP
    TRA (T cell receptor alpha)
    Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):245-248.
    Free journal version : [ pdf ]   [ DOI ]
    History of this paper:
    Lefranc, MP. TRA (T cell receptor alpha). Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):245-248.
    URL :

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    indexed on : Sat Mar 28 12:26:27 CET 2015

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