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TRA (T cell Receptor Alpha)

Identity

Other namesTRA@ (T cell Receptor Alpha)
HGNC (Hugo) TRA
LocusID (NCBI) 6955
Location -
Location_base_pair Starts at 22111109 and ends at 22111806 bp from pter
 
  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.

DNA/RNA

 
  TRA/TRD
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
Description
  • 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

    Description
  • 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
      

    Breakpoints

     

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

    Leukemias t0817q24q22ID1494 t1119q23p13ID1540 t614p25q32IRF4IGHID1175 t1213p13q14ID1323 t1117q23q12AF17ID1027
    t1117p15p13ID2134 t1114ID1070 dic920ID1143 dic0709p11p12ID1554

    External links

    Nomenclature
    HGNC (Hugo)TRA   12027
    Cards
    AtlasTCRAID39
    Entrez_Gene (NCBI)TRA  6955  T cell receptor alpha locus
    GeneCards (Weizmann)TRA
    Ensembl (Hinxton) [Gene_View]  chr14:22111109-22111806 [Contig_View]  TRA [Vega]
    cBioPortalTRA
    AceView (NCBI)TRA
    Genatlas (Paris)TRA
    WikiGenes6955
    SOURCE (Princeton)
    Genomic and cartography
    GoldenPath (UCSC)TRA  -     chr14:22111109-22111806 14q11.2  hg19-Feb_2009   [Description]    ()
    EnsemblTRA - hg19-Feb_2009 [CytoView]
    Mapping of homologs : NCBITRA [Mapview]
    OMIM186880   
    Gene and transcription
    Genbank (Entrez)-
    RefSeq transcript (Entrez)
    RefSeq genomic (Entrez)AC_000146 NC_000014 NC_018925 NG_001332 NT_026437 NW_001838110 NW_004929393
    Consensus coding sequences : CCDS (NCBI)TRA
    Alternative Splicing : Fast-db (Paris)GSHG0032565
    Gene ExpressionTRA [ NCBI-GEO ]     TRA [ SEEK ]   TRA [ MEM ]
    Protein : pattern, domain, 3D structure
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    DMDM Disease mutations6955
    Protein Interaction databases
    BioGRIDTRA
    IntegromeDBTRA
    STRING (EMBL)TRA
    Ontologies - Pathways
    Ontology : AmiGO
    Ontology : EGO-EBI
    Protein Interaction DatabaseTRA
    Wikipedia pathwaysTRA
    Gene fusion - rearrangments
    Polymorphisms : SNP, mutations, diseases
    SNP Single Nucleotide Polymorphism (NCBI)TRA
    snp3D : Map Gene to Disease6955
    SNP (GeneSNP Utah)TRA
    SNP : HGBaseTRA
    Genetic variants : HAPMAPTRA
    Exome VariantTRA
    1000_GenomesTRA 
    Mutations and Diseases : HGMDTRA
    Genomic VariantsTRA  TRA [DGVbeta]
    dbVarTRA
    ClinVarTRA
    Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
    Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
    Diseases
    OMIM186880   
    MedgenTRA
    GENETestsTRA
    Disease Genetic AssociationTRA
    Huge Navigator TRA [HugePedia]  TRA [HugeCancerGEM]
    General knowledge
    Homologs : HomoloGeneTRA
    Homology/Alignments : Family Browser (UCSC)TRA
    Phylogenetic Trees/Animal Genes : TreeFamTRA
    Chemical/Protein Interactions : CTD6955
    Chemical/Pharm GKB GenePA36704
    Clinical trialTRA
    Other databases
    Other databaseTRA@ - IMGT
    Probes
    ProbeCancer Cytogenetics (Bari)
    Litterature
    PubMed90 Pubmed reference(s) in Entrez
    CoreMineTRA
    iHOPTRA

    Bibliography

    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

    Contributor(s)

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

    Citation

    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 online version   Free pdf version   [Bibliographic record ]
    History of this paper:
    Lefranc, MP. TRA (T cell receptor alpha). Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):245-248.
    http://documents.irevues.inist.fr/bitstream/2042/38016/1/09-2003-TCRAID39.pdf
    URL : http://AtlasGeneticsOncology.org/Genes/TCRAID39.html

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Fri Jul 11 16:58:48 CEST 2014

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