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TRB (T cell Receptor Beta)

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)

Identity

Alias (NCBI)TRB@ (T cell Receptor Beta)
HGNC (Hugo) TRB
HGNC Alias nameT-cell antigen receptor, beta polypeptide, T-cell receptor, beta cluster
HGNC Previous nameTCRB
 TRB@
HGNC Previous nameTCRB, TRB@
LocusID (NCBI) 6957
Atlas_Id 24
Location 7q34  [Link to chromosome band 7q34]
 
  for complete Figure, see: chromosome 7, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
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 TRB locus is located on chromosome 7 on the long arm, at band 7q35. The orientation of the locus has been determined by the analysis of translocations, involving the TRB locus, in leukemia and lymphoma

DNA/RNA

 
  TRB
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 TRB, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark TRB
V-GENE: Green box: Functional; Yellow box: Open reading frame; Red: Pseudogene.
D-GENE: Blue: Functional.
J-GENE: Grey: Functional .
C-GENE: Blue: Functional.
GENES NOT RELATED: Purple: Functional; Purple open box: Pseudogene.
for complete Figure, see: locus TRB, IGMT (The international ImMunoGeneTics information system) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
Description
  • The human TRB locus at 7q35 spans 620 kb. It consists of 64-67 TRBV genes belonging to 32 subgroups.
  • Except for TRBV30, localized downstream of the TRBC2 gene, in inverted orientation of transcription, all the other TRBV genes are located upstream of a duplicated D-J-C-cluster, which comprises, for the first part one TRBD, six TRBJ, and the TRBC1 gene, and for the second part, one TRBD, eight TRBJ, and the TRBC2 gene.
  • The most 5' TRBV genes occupy the most centromeric position, whereas the TRBV30 gene, 3' of the locus, is the most telomeric gene in the TRB locus.
  • The potentiel repertoire consists of 39-46 functional TRBV genes belonging to 21-23 subgroups, the two TRBD, thirteen TRBJ (6 from the first cluster and 7 from the second cluster), and the two TRBC genes.
  • Six TRBV orphons have been localized on chromosome 9 at 9p21. Enhancer sequences have been characterized 5.5kb 3' from TRBC2.
  • List of the human TRB genes

    • Protein

    Description
  • Proteins encoded by the TRB locus are the T cell receptor beta chains. They result from the recombination (or rearrangement), at the DNA level, of three genes: TRBV, TRBD and TRBJ, with deletion of the intermediary DNA to create a rearranged TRBV-D-J gene. The rearranged TRBV-D-J gene is transcribed with one of the two TRBC genes and translated into a T cell receptor beta chain.
  • Translation of the variable germline genes involved in the TRBV-D-J rearrangements are available at IMGT Repertoire Protein displays. TRB V-D-J rearrangements can be analysed using the IMGT/V-QUEST tool.

    • Mutations

    Note Mutations which correspond to allelic polymorphisms of the functional germline TRBV, TRBD, TRBJ and TRBC genes are described in the IMGT database: (IMGT Repertoire>Alignments of alleles)

    Implicated in

    Note
      
    Entity Translocations which frequently result from errors of the recombinase enzyme complexe (RAG1, RAG2, etc.), responsable of the Immunoglobulin and T cell receptor V-J and V-D-J rearrangements. TRBV, TRBD or TRBJ recombination signals or isolated heptamer are frequently observed at the breakpoints
      
      
    Entity t(1;7)(p34;q35); involve TRB - LCK in 1p34
    Disease T-cell acute lymphocytic leukemia (ALL)
      
      
    Entity t(1;7)(p32;q35); involve TRB - TAL1 in 1p32
    Disease T-cell acute lymphocytic leukemia (ALL)
    Prognosis median survival > 5 yrs in children
      
      
    Entity t(7;9)(q35;q32); involve TRB - TAL2 in 9q32
    Disease T-cell acute lymphocytic leukemia (ALL)
      
      
    Entity t(7;9)(q35;q34); involve TRB - TAN1 in 9q34
    Disease T-cell acute lymphocytic leukemia (ALL)
      
      
    Entity t(7;10)(q35;q24); involve TRB - HOX11 in 10q24
    Disease T- cell acute lymphoblastic leukemia (ALL) and non-Hodgkin lymphoma (NHL)
    Prognosis not unfavourable
      
      
    Entity t(7;11)(q35;p13); involve TRB - RBTN2 in 11p13
    Disease T-cell acute lymphocytic leukemia (ALL)
      
      
    Entity t(7;14)(q35;q32); involve TRB - TCL1 in 14q32
    Disease T-cell lymphoproliferations
      
      
    Entity t(7;19)(q35;p13); involve TRB - LYL1 in 19p13
    Disease T-cell acute lymphoblastic leukemia (ALL)
      

    Breakpoints

     

    Bibliography

    The T cell Receptor FactsBook (Review)
    Lefranc M-P and Lefranc G
    Academic Press, London, UK (398 pages), 2001. ISBN: 124413528
     
    Locus Map and Genomic repertoire of the Human Immunoglobulin Genes (Review)
    Lefranc MP
    The immunologist,. 2000.
     

    Citation

    This paper should be referenced as such :
    Lefranc, MP
    TRB (T cell receptor beta)
    Atlas Genet Cytogenet Oncol Haematol. 2000;4(3):119-120.
    Free journal version : [ pdf ]   [ DOI ]

    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 34 ]
      t(10;14)(q24;q11) TLX1/TRD::t(7;10)(q34;q24) TRB/HOX11
    Breast implant-associated anaplastic large cell lymphoma
    Hepatosplenic T-cell lymphoma (HSTCL)
    Intestinal T-cell lymphoma
    Pediatric T-Cell Acute Lymphoblastic Leukemia
    t(1;7)(p34;q34) TRB/LCK
    t(1;7)(p32;q34) TRB/TAL1::t(1;14)(p32;q11) TRA/TAL1::1p32 rearrangements
    t(6;7)(q23;q34) TRB/MYB and AHI1
    inv(7)(p15q34) TRB/HOXA10::t(7;7)(p15;q34) TRB/HOXA10
    t(7;9)(q34;q32) TRB/TAL2
    t(7;9)(q34;q34) TRB/NOTCH1
    t(7;12)(q34;p13) TRB/CCND2::t(12;14)(p13;q11) TRA or TRD/CCND2
    t(7;14)(p15;q11) TRD/HOXA10
    t(7;14)(p15;q32)
    t(7;14)(q34;q11) TRA/TRB
    t(7;14)(q34;q11) TRA/TRB
    t(7;19)(q34;p13) TRB/LYL1
    t(X;7)(q22;q34) IRS4/TRB
    t(11;14)(p13;q11) TRD/LMO2::t(7;11)(q35;p13) TRB/LMO2
    t(20;21)(q13.2;q22.12) ZFP64/RUNX1
    TAL1 (1p32) deletion in lymphoid malignancies
    T-lineage acute lymphoblastic leukemia (T-ALL)
    T-cell large granular lymphocyte leukaemia
    ins(3;7)(q26;q34q22) TRB/MECOM
    inv(7)(p14q34) TRB/TRG
    inv(7)(p14q34) TRG/TRB
    inv(7)(p15q34)ort(7;7)(p15;q34) TRB/HOXA11
    t(7;7)(p15;q34) TRB/HOXA9
    t(7;10)(q34;q24) TLX1/TRB
    t(7;11)(q34;p15) RIC3/TRB
    t(7;20)(q34;q11) KIF3B/TRB
    t(7;22)(q34;q12) TRB/IL2RB
    t(X;7)(q22;q34) TRB/IRS4
    t(X;14)(q28;q11.2) TRA-TRD/MTCP1::t(X;7)(q28;q34) TRB/MTCP1

    External links

    Nomenclature
    HGNC (Hugo)TRB   12155
    Cards
    AtlasTCRBID24
    Entrez_Gene (NCBI)TRB    T cell receptor beta locus
    AliasesTCRB; TRB@
    GeneCards (Weizmann)TRB
    Ensembl hg19 (Hinxton) [Gene_View]
    Ensembl hg38 (Hinxton) [Gene_View]   [Sequence]  - [Contig_View]  TRB [Vega]
    TCGA cBioPortalTRB
    AceView (NCBI)TRB
    Genatlas (Paris)TRB
    SOURCE (Princeton)TRB
    Genetics Home Reference (NIH)TRB
    Genomic and cartography
    GoldenPath hg38 (UCSC)TRB  -  
    GoldenPath hg19 (UCSC)TRB  -  
    GoldenPathTRB - [CytoView hg19]  TRB - [CytoView hg38]
    genome Data Viewer NCBITRB [Mapview hg19]  
    Gene and transcription
    Genbank (Entrez)-
    RefSeq transcript (Entrez)
    RefSeq genomic (Entrez)NC_000007 NG_001333 NT_187562
    Consensus coding sequences : CCDS (NCBI)TRB
    Gene ExpressionTRB [ NCBI-GEO ]   TRB [ EBI - ARRAY_EXPRESS ]   TRB [ SEEK ]   TRB [ MEM ]
    Gene Expression Viewer (FireBrowse)TRB [ Firebrowse - Broad ]
    GenevisibleExpression of TRB in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)6957
    GTEX Portal (Tissue expression)TRB
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtP0DSE2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtP0DSE2  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProP0DSE2
    Splice isoforms : SwissVarP0DSE2
    PhosPhoSitePlusP0DSE2
    Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig_C1-set    Ig_sub    Ig_V-set   
    Domain families : Pfam (Sanger)C1-set (PF07654)    V-set (PF07686)   
    Domain families : Pfam (NCBI)pfam07654    pfam07686   
    Domain families : Smart (EMBL)IG (SM00409)  IGc1 (SM00407)  IGv (SM00406)  
    Conserved Domain (NCBI)TRB
    Blocks (Seattle)TRB
    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   
    SuperfamilyP0DSE2
    Peptide AtlasP0DSE2
    Protein Interaction databases
    DIP (DOE-UCLA)P0DSE2
    IntAct (EBI)P0DSE2
    BioGRIDTRB
    STRING (EMBL)TRB
    ZODIACTRB
    Ontologies - Pathways
    QuickGOP0DSE2
    Ontology : AmiGO
    Ontology : EGO-EBI
    NDEx NetworkTRB
    Atlas of Cancer Signalling NetworkTRB
    Wikipedia pathwaysTRB
    Orthology - Evolution
    OrthoDB6957
    Phylogenetic Trees/Animal Genes : TreeFamTRB
    HOGENOMP0DSE2
    Homologs : HomoloGeneTRB
    Homology/Alignments : Family Browser (UCSC)TRB
    Gene fusions - Rearrangements
    Fusion : MitelmanTRA/TRB [-/-]  
    Fusion : MitelmanTRB/CCND2 [-/12p13.32]  
    Fusion : MitelmanTRB/HOXA10 [-/7p15.2]  
    Fusion : MitelmanTRB/HOXA11 [-/7p15.2]  
    Fusion : MitelmanTRB/HOXA@ [-/-]  
    Fusion : MitelmanTRB/IRS4 [-/Xq22.3]  
    Fusion : MitelmanTRB/LCK [-/1p35.1]  
    Fusion : MitelmanTRB/LMO1 [-/11p15.4]  
    Fusion : MitelmanTRB/LYL1 [-/19p13.2]  
    Fusion : MitelmanTRB/MECOM [-/3q26.2]  
    Fusion : MitelmanTRB/MYB [-/6q23.3]  
    Fusion : MitelmanTRB/NOTCH1 [-/9q34.3]  
    Fusion : MitelmanTRB/TAL2 [-/9q31.2]  
    Fusion : MitelmanTRB/TLX1 [-/10q24.31]  
    Fusion : Fusion_HubTRB--BV03S1J2.2    TRB--NOTCH1    TRB--TCRVB   
    Fusion : QuiverTRB
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerTRB [hg38]
    dbVarTRB
    ClinVarTRB
    MonarchTRB
    1000_GenomesTRB 
    Exome Variant ServerTRB
    Varsome BrowserTRB
    Genomic Variants (DGV)TRB [DGVbeta]
    DECIPHERTRB [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisTRB 
    Mutations
    ICGC Data PortalTRB 
    TCGA Data PortalTRB 
    Broad Tumor PortalTRB
    OASIS PortalTRB [ Somatic mutations - Copy number]
    Cancer Gene: CensusTRB 
    Mutations and Diseases : HGMDTRB
    BioMutasearch TRB
    DgiDB (Drug Gene Interaction Database)TRB
    DoCM (Curated mutations)TRB (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)TRB (select a term)
    intoGenTRB
    OncoKBTRB
    NCG6 (London) select TRB
    Cancer3DTRB(select the gene name)
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM
    Orphanet14434   
    DisGeNETTRB
    MedgenTRB
    Genetic Testing Registry TRB
    NextProtP0DSE2 [Medical]
    GENETestsTRB
    Target ValidationTRB
    Huge Navigator TRB [HugePedia]
    ClinGenTRB
    Clinical trials, drugs, therapy
    MyCancerGenomeTRB
    Protein Interactions : CTD
    Pharm GKB GenePA36837
    PharosP0DSE2
    Clinical trialTRB
    Miscellaneous
    canSAR (ICR)TRB (select the gene name)
    HarmonizomeTRB
    DataMed IndexTRB
    Other databaseTRB@ - IMGT
    Probes
    Litterature
    PubMed115 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    EVEXTRB
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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    indexed on : Fri Jan 1 19:02:37 CET 2021
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