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    Tcra T cell receptor alpha chain [ Mus musculus (house mouse) ]

    Gene ID: 21473, updated on 26-Nov-2024

    Summary

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    Official Symbol
    Tcraprovided by MGI
    Official Full Name
    T cell receptor alpha chainprovided by MGI
    Primary source
    MGI:MGI:98553
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Tcralpha
    Summary
    T cell receptors recognize foreign antigens which have been processed as small peptides and bound to major histocompatibility complex (MHC) molecules at the surface of antigen presenting cells (APC). Each T cell receptor is a dimer consisting of one alpha and one beta chain or one delta and one gamma chain. In a single cell, the T cell receptor loci are rearranged and expressed in the order delta, gamma, beta, and alpha. If both delta and gamma rearrangements produce functional chains, the cell expresses delta and gamma. If not, the cell proceeds to rearrange the beta and alpha loci. This region represents the germline organization of the T cell receptor alpha and delta loci. Both the alpha and delta loci include V (variable), J (joining), and C (constant) segments and the delta locus also includes diversity (D) segments. The delta locus is situated within the alpha locus, between the alpha variable and joining genes. During T cell development, the delta chain is synthesized by a recombination event at the DNA level joining a D segment with a J segment; a V segment is then joined to the D-J gene. The alpha chain is synthesized by recombination joining a single V segment with a J segment. For both chains, the C segment is later joined by splicing at the RNA level. Recombination of many different V segments with several J segments provides a wide range of antigen recognition. Additional diversity is attained by junctional diversity, resulting from the random additional of nucleotides by terminal deoxynucleotidyltransferase. Ten variable segments can be used in either alpha or delta chains and are described by TRAV/DV symbols. Several V and J segments of the alpha locus are known to be incapable of encoding a protein and are considered pseudogenes. [provided by RefSeq, Jul 2008]
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    Genomic context

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    See Tcra in Genome Data Viewer
    Location:
    14 C2; 14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (52665424..54461655)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (52427967..54224198)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_36706 Neighboring gene olfactory receptor family 10 subfamily G member 1B Neighboring gene olfactory receptor enhancer H Neighboring gene olfactory receptor family 10 subfamily G member 1 Neighboring gene T cell receptor alpha variable 1 Neighboring gene STARR-seq mESC enhancer starr_36708 Neighboring gene olfactory receptor family 4 subfamily E member 2 Neighboring gene predicted gene, 36382 Neighboring gene olfactory receptor family 4 subfamily E member 1 Neighboring gene STARR-seq mESC enhancer starr_36709 Neighboring gene enolase 1, alpha non-neuron pseudogene Neighboring gene predicted gene, 36448 Neighboring gene olfactory receptor family 4 subfamily E member 5 Neighboring gene ATPase, H+ transporting, lysosomal accessory protein 2 pseudogene Neighboring gene T cell receptor alpha variable 3-1 Neighboring gene STARR-seq mESC enhancer starr_36711 Neighboring gene T cell receptor alpha variable 4-1 Neighboring gene T cell receptor alpha variable 2 Neighboring gene T cell receptor alpha variable 5-1 Neighboring gene T cell receptor alpha variable 15D-1-DV6D-1 Neighboring gene T cell receptor alpha variable 6-1 Neighboring gene T cell receptor alpha variable 7D-2 Neighboring gene T cell receptor alpha variable 7-1 Neighboring gene T cell receptor alpha variable 6-2 Neighboring gene T cell receptor alpha variable 4D-2 Neighboring gene T cell receptor alpha variable 6D-3 Neighboring gene T cell receptor alpha variable 7D-3 Neighboring gene T cell receptor alpha variable 15D-2-DV6D-2 Neighboring gene T cell receptor alpha variable 6D-4 Neighboring gene T cell receptor alpha variable 7D-4 Neighboring gene T cell receptor alpha variable 8D-1 Neighboring gene T cell receptor alpha variable 9D-1 Neighboring gene T cell receptor alpha variable 6D-5 Neighboring gene T cell receptor alpha variable 12D-1 Neighboring gene T cell receptor alpha variable 6D-6 Neighboring gene T cell receptor alpha variable 13D-1 Neighboring gene T-cell receptor alpha variable region 14D-1 Neighboring gene solute carrier family 45, member 4 pseudogene Neighboring gene T cell receptor alpha variable 10D Neighboring gene T cell receptor alpha variable 7D-5 Neighboring gene T cell receptor alpha variable 11D Neighboring gene ribosomal protein S19, pseudogene 2 Neighboring gene T cell receptor alpha variable 3D-2 Neighboring gene T cell receptor alpha variable 12D-2 Neighboring gene T cell receptor alpha variable 9D-2 Neighboring gene T cell receptor alpha variable 4D-3 Neighboring gene T cell receptor alpha variable 12D-3 Neighboring gene T cell receptor alpha variable 5D-2 Neighboring gene nuclear receptor binding factor 2 pseudogene Neighboring gene T cell receptor alpha variable 9D-3 Neighboring gene T cell receptor alpha variable 13D-2 Neighboring gene T cell receptor alpha variable 14D-2 Neighboring gene T cell receptor alpha variable 5D-3 Neighboring gene STARR-seq mESC enhancer starr_36712 Neighboring gene STARR-seq mESC enhancer starr_36713 Neighboring gene T cell receptor alpha variable 16D-DV11 Neighboring gene T cell receptor alpha variable 14D-3-DV8 Neighboring gene T cell receptor alpha variable 3D-3 Neighboring gene T cell receptor alpha variable 9D-4 Neighboring gene T cell receptor alpha variable 4D-4 Neighboring gene T cell receptor alpha variable 5D-4 Neighboring gene T cell receptor alpha variable 13D-3 Neighboring gene T cell receptor alpha variable 6D-7 Neighboring gene T cell receptor alpha variable 7D-6 Neighboring gene glutamate oxaloacetate transaminase 2, mitochondrial pseudogene Neighboring gene STARR-seq mESC enhancer starr_36715 Neighboring gene T cell receptor alpha variable 8D-2 Neighboring gene T cell receptor alpha variable 13D-4 Neighboring gene T cell receptor alpha variable 15D-3 Neighboring gene predicted gene, 30214 Neighboring gene T cell receptor alpha variable 7N-4 Neighboring gene T cell receptor alpha variable 9N-1 Neighboring gene T cell receptor alpha variable 6N-5 Neighboring gene T cell receptor alpha variable 12N-1 Neighboring gene T cell receptor alpha variable 6N-6 Neighboring gene T cell receptor alpha variable 13N-1 Neighboring gene T cell receptor alpha variable 14N-1 Neighboring gene T cell receptor alpha variable 7N-5 Neighboring gene T cell receptor alpha variable 10N Neighboring gene T cell receptor alpha variable 15N-1 Neighboring gene T cell receptor alpha variable 11N Neighboring gene ribosomal protein S19, pseudogene 1 Neighboring gene T cell receptor alpha variable 3N-2 Neighboring gene T cell receptor alpha variable 9N-2 Neighboring gene T cell receptor alpha variable 12N-2 Neighboring gene T cell receptor alpha variable 4N-3 Neighboring gene T cell receptor alpha variable 12N-3 Neighboring gene nuclear receptor binding factor 2 pseudogene Neighboring gene T cell receptor alpha variable 5N-2 Neighboring gene T cell receptor alpha variable 13N-2 Neighboring gene T cell receptor alpha variable 9N-3 Neighboring gene T cell receptor alpha variable 14N-2 Neighboring gene T cell receptor alpha variable 5N-3 Neighboring gene T cell receptor alpha variable 15N-2 Neighboring gene T cell receptor alpha variable 3N-3 Neighboring gene T cell receptor alpha variable 9N-4 Neighboring gene T cell receptor alpha variable 4N-4 Neighboring gene T cell receptor alpha variable 13N-3 Neighboring gene T cell receptor alpha variable 5N-4 Neighboring gene T cell receptor alpha variable 6N-7 Neighboring gene STARR-seq mESC enhancer starr_36716 Neighboring gene T cell receptor alpha variable 7N-6 Neighboring gene aspartate aminotransferase, mitochondrial, pseudogene Neighboring gene T cell receptor alpha variable 13N-4 Neighboring gene STARR-seq mESC enhancer starr_36717 Neighboring gene T cell receptor alpha variable 14N-3 Neighboring gene T cell receptor alpha variable 8n-2 Neighboring gene T cell receptor alpha variable 15N-3 Neighboring gene T cell receptor alpha variable 16n Neighboring gene T cell receptor alpha variable 15-1-DV6-1 Neighboring gene T cell receptor alpha variable 7-2 Neighboring gene T cell receptor alpha variable 4-2 Neighboring gene T cell receptor alpha variable 6-3 Neighboring gene T cell receptor alpha variable 7-3 Neighboring gene STARR-seq mESC enhancer starr_36720 Neighboring gene T cell receptor alpha variable 6-4 Neighboring gene T cell receptor alpha variable 7-4 Neighboring gene predicted gene, 18711 Neighboring gene T cell receptor alpha variable 8-1 Neighboring gene T cell receptor alpha variable 15-2-DV6-2 Neighboring gene T cell receptor alpha variable 9-1 Neighboring gene T cell receptor alpha variable 6-5 Neighboring gene T cell receptor alpha variable 12-1 Neighboring gene T cell receptor alpha variable 6-6 Neighboring gene T cell receptor alpha variable 13-1 Neighboring gene T cell receptor alpha variable 14-1 Neighboring gene T cell receptor alpha variable 7-5 Neighboring gene T cell receptor alpha variable 10 Neighboring gene T cell receptor alpha variable 11 Neighboring gene T cell receptor alpha variable 4-4-DV10 Neighboring gene T cell receptor alpha variable 12-2 Neighboring gene T cell receptor alpha variable 9-2 Neighboring gene T cell receptor alpha variable 3-2 Neighboring gene T cell receptor alpha variable 12-3 Neighboring gene T cell receptor alpha variable 4-3 Neighboring gene T cell receptor alpha variable 6-7-DV9 Neighboring gene STARR-seq mESC enhancer starr_36721 Neighboring gene T cell receptor alpha variable 13-2 Neighboring gene T cell receptor alpha variable 5-2 Neighboring gene T cell receptor alpha variable 14-2 Neighboring gene T cell receptor alpha variable 13-4-DV7 Neighboring gene glutamate oxaloacetate transaminase 2, mitochondrial pseudogene Neighboring gene T cell receptor alpha variable 3-3 Neighboring gene T cell receptor alpha variable 9-4 Neighboring gene T cell receptor alpha variable 13-3 Neighboring gene T cell receptor alpha variable 5-4 Neighboring gene T cell receptor alpha variable 7-6 Neighboring gene T cell receptor alpha variable 14-3 Neighboring gene T-cell receptor alpha variable 8-2 Neighboring gene T cell receptor alpha variable 15-3 Neighboring gene T cell receptor alpha variable 12-4 Neighboring gene T cell receptor alpha variable 16 Neighboring gene T cell receptor alpha variable 13-5 Neighboring gene T cell receptor alpha variable 21-DV12 Neighboring gene T cell receptor alpha variable 3-4 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 T cell receptor alpha variable 20 Neighboring gene predicted gene, 30392 Neighboring gene STARR-positive B cell enhancer ABC_E3113 Neighboring gene T cell receptor delta variable 1 Neighboring gene T cell receptor delta variable 2-1 Neighboring gene T cell receptor alpha variable 22 Neighboring gene T cell receptor delta variable 2-2 Neighboring gene STARR-seq mESC enhancer starr_36723 Neighboring gene T cell receptor alpha variable 23 Neighboring gene T cell receptor delta chain Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:54784778-54784961 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:54804154-54804337 Neighboring gene T cell receptor delta variable 3 Neighboring gene predicted gene, 30275 Neighboring gene STARR-positive B cell enhancer ABC_E7311 Neighboring gene STARR-positive B cell enhancer ABC_E1168 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:54852981-54853251 Neighboring gene STARR-positive B cell enhancer ABC_E5435 Neighboring gene CapStarr-seq enhancers MGSCv37_chr14:54846812-54847013 and MGSCv37_chr14:54847102-54847395 Neighboring gene T cell receptor delta variable 4 Neighboring gene T cell receptor delta diversity 1 Neighboring gene T cell receptor delta joining 1 Neighboring gene T cell receptor delta diversity 2 Neighboring gene T cell receptor alpha joining 59 Neighboring gene T cell receptor alpha joining 60 Neighboring gene T cell receptor alpha joining 61 Neighboring gene T cell receptor alpha joining 58 Neighboring gene T cell receptor alpha joining 57 Neighboring gene T cell receptor alpha joining 56 Neighboring gene T cell receptor alpha joining 55 Neighboring gene T cell receptor alpha joining 53 Neighboring gene T cell receptor alpha joining 52 Neighboring gene T cell receptor alpha joining 54 Neighboring gene T cell receptor delta joining 2 Neighboring gene T cell receptor alpha joining 51 Neighboring gene T cell receptor alpha joining 49 Neighboring gene T cell receptor alpha joining 50 Neighboring gene T cell receptor alpha joining 48 Neighboring gene T cell receptor alpha joining 47 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 45 Neighboring gene T cell receptor alpha joining 44 Neighboring gene T cell receptor delta variable 5 Neighboring gene T cell receptor alpha joining 46 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 33 Neighboring gene T cell receptor alpha joining 31 Neighboring gene T cell receptor alpha joining 32 Neighboring gene T cell receptor alpha joining 34 Neighboring gene T cell receptor alpha joining 35 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 T cell receptor delta, constant region Neighboring gene T cell receptor alpha joining 22 Neighboring gene T cell receptor alpha joining 26 Neighboring gene T cell receptor alpha joining 25 Neighboring gene T cell receptor alpha joining 24 Neighboring gene T cell receptor alpha joining 23 Neighboring gene T cell receptor alpha joining 19 Neighboring gene T cell receptor alpha joining 18 Neighboring gene T cell receptor alpha joining 17 Neighboring gene T cell receptor alpha joining 16 Neighboring gene T cell receptor alpha joining 20 Neighboring gene T cell receptor alpha joining 21 Neighboring gene T cell receptor alpha joining 15 Neighboring gene T cell receptor alpha joining 14 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 6 Neighboring gene T cell receptor alpha joining 5 Neighboring gene T cell receptor alpha joining 7 Neighboring gene T cell receptor alpha joining 8 Neighboring gene T cell receptor alpha joining 9 Neighboring gene T cell receptor alpha joining 3 Neighboring gene T cell receptor alpha joining 2 Neighboring gene T cell receptor alpha joining 1 Neighboring gene T cell receptor alpha joining 4 Neighboring gene abhydrolase domain containing 4 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. Valpha gene replacement in a TCRalpha knock-in mouse. Golub R, et al. Eur J Immunol, 2001 Oct. PMID 11592067
    2. The shaping of the T cell repertoire. Correia-Neves M, et al. Immunity, 2001 Jan. PMID 11163227
    3. Autoreactive isotype-specific T cells determine B cell frequency. Granucci F, et al. Eur J Immunol, 2001 Jan. PMID 11265637
    4. Evaluation of the percentage of peripheral T cells with two different T cell receptor alpha-chains and of their potential role in autoimmunity. Corthay A, et al. J Autoimmun, 2001 Jun. PMID 11437490
    5. Shortening of complementarity determining region 3 of the T cell receptor α chain during thymocyte development. Matsutani T, et al. Mol Immunol, 2011 Jan. PMID 21126768

    See all (857) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Three-way contact analysis characterizes the higher order organization of the Tcra locus.
      Title: Three-way contact analysis characterizes the higher order organization of the Tcra locus.
    2. Differently Regulated Gene-Specific Activity of Enhancers Located at the Boundary of Subtopologically Associated Domains: TCRalpha Enhancer.
      Title: Differently Regulated Gene-Specific Activity of Enhancers Located at the Boundary of Subtopologically Associated Domains: TCRα Enhancer.
    3. TCRalpha reporter mice reveal contribution of dual TCRalpha expression to T cell repertoire and function.
      Title: TCRα reporter mice reveal contribution of dual TCRα expression to T cell repertoire and function.
    4. Lck bound to coreceptor is less active than free Lck.
      Title: Lck bound to coreceptor is less active than free Lck.
    5. About 10% of peripheral T cells express 2 functional TCR alphabeta heterodimers. Lack of dual TCR expression resulted in reduced lymphopenia-induced proliferation. Dual TCR expression enhances T cell homeostasis via increased reactivity against self-peptide:MHC (pMHC) ligands.
      Title: Endogenous co-expression of two T cell receptors promotes lymphopenia-induced proliferation via increased affinity for self-antigen.
    6. The authors show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor alpha and beta chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 complementary determining loop of the T cell receptor alpha chain.
      Title: The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor.
    7. miR-181a/b-1-deficient mice expressing elevated levels of a Valpha14Jalpha18 TCRalpha chain, were examined.
      Title: Overexpression of Vα14Jα18 TCR promotes development of iNKT cells in the absence of miR-181a/b-1.
    8. pharmacological inhibition of RORgamma skews TCRalpha gene rearrangement, limits T cell repertoire diversity, and inhibits development of autoimmune encephalomyelitis.targeting RORgammaT not only inhibits Th17 cell development and function but also fundamentally alters thymic-emigrant recognition of self and foreign antigens.
      Title: Inhibition of RORγT Skews TCRα Gene Rearrangement and Limits T Cell Repertoire Diversity.
    9. We found that the lack of dual TCRalpha expression skewed the insulin-specific thymocyte population toward greater regulatory T (Treg) cell commitment, resulting in a more tolerogenic Treg to conventional T cell ratio and protection from diabetes.
      Title: Cutting Edge: Dual TCRα Expression Poses an Autoimmune Hazard by Limiting Regulatory T Cell Generation.
    10. Diets enriched primarily in saturated fatty acids increased TCR nanoscale clustering to a level usually seen only on activated cells.
      Title: A high fat diet containing saturated but not unsaturated fatty acids enhances T cell receptor clustering on the nanoscale.
    Submit: New GeneRIF Correction See all GeneRIFs (90)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • Tcr alpha

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within T cell lineage commitment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein homotetramerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of T cell receptor complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of alpha-beta T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Names
    T cell receptor alpha chain
    Tcr alpha

    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_007044.1 

      Range
      501..1796732
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000080.7 Reference GRCm39 C57BL/6J

      Range
      52665424..54461655
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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