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    TRA T cell receptor alpha locus [ Homo sapiens (human) ]

    Gene ID: 6955, updated on 7-Jul-2024

    Summary

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    Official Symbol
    TRAprovided by HGNC
    Official Full Name
    T cell receptor alpha locusprovided by HGNC
    Primary source
    HGNC:HGNC:12027
    See related
    AllianceGenome:HGNC:12027
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IMD7; TCRA; TRA@
    Summary
    Enables signaling receptor activity. Involved in T cell mediated cytotoxicity directed against tumor cell target and detection of tumor cell. Part of alpha-beta T cell receptor complex. [provided by Alliance of Genome Resources, Apr 2022]
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    Genomic context

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    See TRA in Genome Data Viewer
    Location:
    14q11.2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (21621904..22552132)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (15819498..16749884)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (22090057..23021075)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:22085839-22086341 Neighboring gene olfactory receptor family 10 subfamily G member 1 pseudogene Neighboring gene ubiquitin conjugating enzyme E2 N pseudogene 1 Neighboring gene T cell receptor alpha variable 1-1 Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:22165724-22166296 Neighboring gene VISTA enhancer hs1705 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_33791 Neighboring gene T cell receptor alpha variable 1-2 Neighboring gene olfactory receptor family 10 subfamily G member 2 Neighboring gene olfactory receptor family 4 subfamily E member 2 Neighboring gene olfactory receptor family 4 subfamily E member 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:22264004-22265203 Neighboring gene T cell receptor alpha variable 2 Neighboring gene T cell receptor alpha variable 3 Neighboring gene T cell receptor alpha variable 4 Neighboring gene ribosomal protein L4 pseudogene 1 Neighboring gene T cell receptor alpha variable 5 Neighboring gene T cell receptor alpha variable 6 Neighboring gene T cell receptor alpha variable 8-1 Neighboring gene T cell receptor alpha variable 9-1 Neighboring gene T cell receptor alpha variable 7 Neighboring gene T cell receptor alpha variable 12-1 Neighboring gene T cell receptor alpha variable 10 Neighboring gene T cell receptor alpha variable 11 (pseudogene) Neighboring gene T cell receptor alpha variable 8-2 Neighboring gene T cell receptor alpha variable 8-3 Neighboring gene T cell receptor alpha variable 13-1 Neighboring gene T cell receptor alpha variable 12-2 Neighboring gene T cell receptor alpha variable 8-4 Neighboring gene T cell receptor alpha variable 14/delta variable 4 Neighboring gene T cell receptor alpha variable 13-2 Neighboring gene T cell receptor alpha variable 8-5 (pseudogene) Neighboring gene T cell receptor alpha variable 9-2 Neighboring gene spalt like transcription factor 4 pseudogene Neighboring gene T cell receptor alpha variable 12-3 Neighboring gene T cell receptor alpha variable 15 (pseudogene) Neighboring gene T cell receptor alpha variable 8-6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8112 Neighboring gene T cell receptor alpha variable 16 Neighboring gene T cell receptor alpha variable 17 Neighboring gene T cell receptor alpha variable 18 Neighboring gene T cell receptor alpha variable 19 Neighboring gene Sharpr-MPRA regulatory region 3554 Neighboring gene T cell receptor alpha variable 20 Neighboring gene T cell receptor alpha variable 23/delta variable 6 Neighboring gene T cell receptor alpha variable 21 Neighboring gene T cell receptor alpha variable 22 Neighboring gene uncharacterized LOC124903284 Neighboring gene T cell receptor alpha variable 26-1 Neighboring gene T cell receptor alpha variable 24 Neighboring gene T cell receptor delta variable 1 Neighboring gene T cell receptor alpha variable 25 Neighboring gene T cell receptor alpha variable 8-7 (pseudogene) Neighboring gene T cell receptor alpha variable 29/delta variable 5 Neighboring gene T cell receptor alpha variable 27 Neighboring gene T cell receptor alpha variable 28 (pseudogene) Neighboring gene T cell receptor alpha variable 30 Neighboring gene T cell receptor alpha variable 26-2 Neighboring gene T cell receptor alpha variable 31 (pseudogene) Neighboring gene T cell receptor alpha variable 32 (pseudogene) Neighboring gene T cell receptor alpha variable 36/delta variable 7 Neighboring gene T cell receptor alpha variable 33 (pseudogene) Neighboring gene uncharacterized LOC107984649 Neighboring gene T cell receptor alpha variable 34 Neighboring gene T cell receptor alpha variable 38-2/delta variable 8 Neighboring gene T cell receptor alpha variable 35 Neighboring gene T cell receptor alpha variable 38-1 Neighboring gene translin associated factor X pseudogene Neighboring gene T cell receptor alpha variable 37 (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8113 Neighboring gene T cell receptor alpha variable 39 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:22856413-22856913 Neighboring gene T cell receptor alpha variable 40 Neighboring gene T cell receptor alpha variable 41 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8115 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:22916943-22917478 Neighboring gene TRD antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:22931886-22933085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8116 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr14:22940183-22940684 and GRCh37_chr14:22940685-22941184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8124 Neighboring gene T cell receptor delta variable 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5585 Neighboring gene T cell receptor delta diversity 1 Neighboring gene T cell receptor delta diversity 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8126 Neighboring gene T cell receptor delta diversity 3 Neighboring gene T cell receptor delta joining 1 Neighboring gene T cell receptor delta locus Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8130 Neighboring gene T cell receptor delta joining 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8127 Neighboring gene T cell receptor delta joining 2 Neighboring gene T cell receptor delta joining 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8133 Neighboring gene uncharacterized LOC105370399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8134 Neighboring gene T cell receptor alpha joining 61 (non-functional) Neighboring gene T cell receptor alpha joining 60 (pseudogene) Neighboring gene T cell receptor alpha joining 59 (non-functional) Neighboring gene T cell receptor alpha joining 58 (non-functional) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8135 Neighboring gene T cell receptor alpha joining 57 Neighboring gene T cell receptor alpha joining 56 Neighboring gene T cell receptor delta variable 3 Neighboring gene T cell receptor alpha joining 55 (pseudogene) Neighboring gene T cell receptor alpha joining 54 Neighboring gene T cell receptor alpha joining 53 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:23057127-23057768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:23051199-23051700 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:23049159-23049321 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:23039191-23039913 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:23057769-23058410 Neighboring gene T cell receptor alpha joining 52 Neighboring gene T cell receptor alpha joining 51 (pseudogene) Neighboring gene T cell receptor alpha joining 50 Neighboring gene T cell receptor delta constant Neighboring gene T cell receptor alpha joining 49 Neighboring gene T cell receptor alpha joining 48 Neighboring gene T cell receptor alpha joining 46 Neighboring gene T cell receptor alpha joining 45 Neighboring gene T cell receptor alpha joining 47 Neighboring gene T cell receptor alpha joining 44 Neighboring gene T cell receptor alpha joining 43 Neighboring gene T cell receptor alpha joining 42 Neighboring gene T cell receptor alpha joining 41 Neighboring gene T cell receptor alpha joining 40 Neighboring gene T cell receptor alpha joining 39 Neighboring gene T cell receptor alpha joining 38 Neighboring gene T cell receptor alpha joining 37 Neighboring gene T cell receptor alpha joining 36 Neighboring gene T cell receptor alpha joining 35 (non-functional) Neighboring gene T cell receptor alpha joining 34 Neighboring gene T cell receptor alpha joining 33 Neighboring gene T cell receptor alpha joining 32 Neighboring gene T cell receptor alpha joining 31 Neighboring gene T cell receptor alpha joining 30 Neighboring gene T cell receptor alpha joining 29 Neighboring gene T cell receptor alpha joining 28 Neighboring gene T cell receptor alpha joining 27 Neighboring gene long intergenic non-protein coding RNA 2332 Neighboring gene T cell receptor alpha joining 25 (non-functional) Neighboring gene T cell receptor alpha joining 26 Neighboring gene T cell receptor alpha joining 24 Neighboring gene T cell receptor alpha joining 23 Neighboring gene T cell receptor alpha joining 22 Neighboring gene T cell receptor alpha joining 21 Neighboring gene T cell receptor alpha joining 20 Neighboring gene T cell receptor alpha joining 17 Neighboring gene T cell receptor alpha joining 19 (non-functional) Neighboring gene T cell receptor alpha joining 18 Neighboring gene T cell receptor alpha joining 14 Neighboring gene T cell receptor alpha joining 15 Neighboring gene T cell receptor alpha joining 16 Neighboring gene T cell receptor alpha joining 13 Neighboring gene T cell receptor alpha joining 12 Neighboring gene T cell receptor alpha joining 11 Neighboring gene T cell receptor alpha joining 10 Neighboring gene T cell receptor alpha joining 9 Neighboring gene T cell receptor alpha joining 7 Neighboring gene T cell receptor alpha joining 8 Neighboring gene T cell receptor alpha joining 5 Neighboring gene T cell receptor alpha joining 6 Neighboring gene T cell receptor alpha joining 4 Neighboring gene T cell receptor alpha joining 3 Neighboring gene T cell receptor alpha joining 2 (non-functional) Neighboring gene T cell receptor alpha joining 1 (non-functional) Neighboring gene T cell receptor alpha constant Neighboring gene defender against cell death 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Selective ablation of TRA-1-60(+) pluripotent stem cells suppresses tumor growth of prostate cancer. White JM, et al. Theranostics, 2023. PMID 37153742, Free PMC Article
    2. Electrostatic Complementarity of T-Cell Receptor-Alpha CDR3 Domains and Mutant Amino Acids Is Associated with Better Survival Rates for Sarcomas. Yeagley M, et al. Pediatr Hematol Oncol, 2021 Apr. PMID 33616477
    3. T-cell clonality assessment by next-generation sequencing improves detection sensitivity in mycosis fungoides. Sufficool KE, et al. J Am Acad Dermatol, 2015 Aug. PMID 26048061
    4. TCR-triggered extracellular superoxide production is not required for T-cell activation. Belikov AV, et al. Cell Commun Signal, 2014 Aug 1. PMID 25081034, Free PMC Article
    5. Down regulation of T cell receptor expression in COPD pulmonary CD8 cells. Grundy S, et al. PLoS One, 2013. PMID 23977094, Free PMC Article

    See all (129) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Type B thymomas in patients with myasthenia gravis display a distinctive pattern of alphabeta TCR and IL-7 receptor alpha expression on CD4[+]CD8[+] thymocytes.
      Title: Type B thymomas in patients with myasthenia gravis display a distinctive pattern of αβ TCR and IL-7 receptor α expression on CD4(+)CD8(+) thymocytes.
    2. Selective ablation of TRA-1-60[+] pluripotent stem cells suppresses tumor growth of prostate cancer.
      Title: Selective ablation of TRA-1-60(+) pluripotent stem cells suppresses tumor growth of prostate cancer.
    3. T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells.
      Title: T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells.
    4. Electrostatic Complementarity of T-Cell Receptor-Alpha CDR3 Domains and Mutant Amino Acids Is Associated with Better Survival Rates for Sarcomas.
      Title: Electrostatic Complementarity of T-Cell Receptor-Alpha CDR3 Domains and Mutant Amino Acids Is Associated with Better Survival Rates for Sarcomas.
    5. T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4.
      Title: T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4.
    6. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen.
      Title: Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen.
    7. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide.
      Title: The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide.
    8. T cell receptor alpha beta+/CD19+ graft depletion effectively prevents graft-versus-host disease.
      Title: Mismatched related vs matched unrelated donors in TCRαβ/CD19-depleted HSCT for primary immunodeficiencies.
    9. A conserved alpha-beta transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane.
      Title: A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane.
    10. Data (from studies using TCR-F50/GIL/HLA-A2) suggest there are multiple structurally distinct solutions to recognizing identical peptide-MHC ligand with sufficient affinity to elicit broad anti- influenza A virus response protective against viral escape/T-cell clonal loss. (TCR-F50 = GIL-specific T-cell receptor, alpha-beta; HLA-A2 major histocompatibility complex class I A; GIL = immunodominant influenza A virus epitope)
      Title: Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope.
    Submit: New GeneRIF Correction See all GeneRIFs (88)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study of recipient genotype and medium-term kidney allograft function.
    EBI GWAS Catalog
    Genome wide analysis of narcolepsy in China implicates novel immune loci and reveals changes in association prior to versus after the 2009 H1N1 influenza pandemic.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis of intraocular pressure.
    EBI GWAS Catalog
    Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy.
    EBI GWAS Catalog
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog
    Narcolepsy is strongly associated with the T-cell receptor alpha locus.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • M1-specific T cell receptor alpha chain
    • T-cell antigen receptor, alpha polypeptide
    • T-cell receptor, alpha (V,D,J,C)
    • TCRA, TRA@
    • TR alpha chain TRAV27*01J42*01C*01

    Clone Names

    • FLJ22602, MGC22624, MGC23964, MGC71411, MGC117436

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables signaling receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell mediated cytotoxicity directed against tumor cell target IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in detection of tumor cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to bacterium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of alpha-beta T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Names
    T cell receptor alpha locus
    M1-specific T cell receptor alpha chain
    T-cell antigen receptor, alpha polypeptide
    T-cell receptor, alpha (V,D,J,C)
    TCRA, TRA@
    TR alpha chain TRAV27*01J42*01C*01

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_001332.3 

      Range
      1..930229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      21621904..22552132
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      15819498..16749884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DSE1.1 GenPept UniProtKB/Swiss-Prot:P0DSE1
    P0DTU3.1 GenPept UniProtKB/Swiss-Prot:P0DTU3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials