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

Gene ID: 6955, updated on 23-Nov-2023

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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. upon ligation of the T-cell antigen receptor (TCR), the TCR associates with and transactivates CXCR4 via phosphorylation of S339-CXCR4 in order to activate a PREX1-Rac1-signaling pathway that stabilizes interleukin-2(IL-2), IL-4, and IL-10 messenger RNA (mRNA) transcripts.
    Title: TCR-CXCR4 signaling stabilizes cytokine mRNA transcripts via a PREX1-Rac1 pathway: implications for CTCL.
Submit: New GeneRIF Correction See all GeneRIFs (87)

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
Miscellaneous