U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    PTCRA pre T cell antigen receptor alpha [ Homo sapiens (human) ]

    Gene ID: 171558, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    PTCRAprovided by HGNC
    Official Full Name
    pre T cell antigen receptor alphaprovided by HGNC
    Primary source
    HGNC:HGNC:21290
    See related
    Ensembl:ENSG00000171611 MIM:606817; AllianceGenome:HGNC:21290
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PTA; IMD126; PT-ALPHA
    Summary
    The protein encoded by this gene is a single-pass type I membrane protein that is found in immmature but not mature T-cells. Along with TCRB and CD3 complex, the encoded protein forms the pre-T-cell receptor complex, which regulates early T-cell development. Four transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]
    Expression
    Biased expression in spleen (RPKM 1.2), lymph node (RPKM 0.8) and 5 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See PTCRA in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42916053..42925838)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42744769..42754903)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42883791..42893576)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:42846366-42847323 and GRCh37_chr6:42847324-42848280 Neighboring gene ribosomal protein L7 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24576 Neighboring gene peroxisomal biogenesis factor 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17209 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42896611-42897112 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42897113-42897614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24580 Neighboring gene CNPY3-GNMT readthrough Neighboring gene canopy FGF signaling regulator 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42906342-42906844 Neighboring gene long intergenic non-protein coding RNA 2976

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Generation of self-reactive, shared T-cell receptor α chains in the human thymus. Heikkilä N, et al. J Autoimmun, 2021 May. PMID 33652347
    2. Regulation of pre-T cell receptor (pT alpha-TCR beta) gene expression during human thymic development. Ramiro AR, et al. J Exp Med, 1996 Aug 1. PMID 8760805, Free PMC Article
    3. Genomic structure of the human pre-T cell receptor alpha chain and expression of two mRNA isoforms. Saint-Ruf C, et al. Eur J Immunol, 1998 Nov. PMID 9842925
    4. A critical role for the cytoplasmic tail of pTalpha in T lymphocyte development. Aifantis I, et al. Nat Immunol, 2002 May. PMID 11927911
    5. Extrathymic TCR gene rearrangement in human small intestine: identification of new splice forms of recombination activating gene-1 mRNA with selective tissue expression. Bas A, et al. J Immunol, 2003 Oct 1. PMID 14500629

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Generation of self-reactive, shared T-cell receptor alpha chains in the human thymus.
      Title: Generation of self-reactive, shared T-cell receptor α chains in the human thymus.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Racial disparity in pathophysiologic pathways of preterm birth based on genetic variants.
    3. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Preterm birth in Caucasians is associated with coagulation and inflammation pathway gene variants.
    4. identified a polyproline-arginine sequence in the pTalpha cytoplasmic tail that interacted in vitro with SH3 domains of the CIN85/CMS family of adaptors, and mediated the recruitment of multiprotein complexes involving all (CMS, CIN85, and CD2BP3) members
      Title: Identification of CMS as a cytosolic adaptor of the human pTalpha chain involved in pre-TCR function.
    5. High levels of pre-T cell receptor alpha-chain mRNA splice forms have been demonstrated in immature CD2+CD7+CD3- T cells of the jejunal mucosa, both intraepithelially and in lamina propria.
      Title: Extrathymic TCR gene rearrangement in human small intestine: identification of new splice forms of recombination activating gene-1 mRNA with selective tissue expression.
    6. Combined expression of pTalpha and Notch3 in T cell leukemia identifies the requirement of preTCR for leukemogenesis
      Title: Combined expression of pTalpha and Notch3 in T cell leukemia identifies the requirement of preTCR for leukemogenesis.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

    Go to the top of the page Help

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 envelope glycoproteins gp120 and gp160 directly and specifically impair the CD3/TcR-mediated activation of phospholipase C (PLC) via the CD4 molecule in uninfected T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of thymocyte apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    pre T-cell antigen receptor alpha
    Names
    pT-alpha-TCR
    pre-T-cell receptor alpha chain

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_029636.1 RefSeqGene

      Range
      5065..14850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243168.2 → NP_001230097.1  pre T-cell antigen receptor alpha isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK130819, AW014894, BC153829, U36759
      Consensus CDS
      CCDS75457.1
      UniProtKB/TrEMBL
      A0A087WTE9
      Related
      ENSP00000477815.1, ENST00000616441.2
      Conserved Domains (1) summary
      pfam15028
      Location:20 → 142
      PTCRA; Pre-T-cell antigen receptor

    2. NM_001243169.2 → NP_001230098.1  pre T-cell antigen receptor alpha isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses alternate in-frame splice junctions at the 5' ends of two exons and contains an alternate in-frame exon compared to variant 1. The resulting isoform (3) contains an alternate internal segment but lacks two others compared to isoform 1.
      Source sequence(s)
      AF165312, AW014894, BC153829, U36759
      Consensus CDS
      CCDS59019.1
      UniProtKB/Swiss-Prot
      Q6ISU1
      Related
      ENSP00000409550.1, ENST00000441198.4
      Conserved Domains (1) summary
      cl11960
      Location:34 → 121
      Ig; Immunoglobulin domain

    3. NM_001243170.2 → NP_001230099.1  pre T-cell antigen receptor alpha isoform 4 precursor

      See identical proteins and their annotated locations for NP_001230099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (4) lacks two internal segments compared to isoform 1.
      Source sequence(s)
      AF101436, AW014894, BC153829, U36759
      Consensus CDS
      CCDS59020.1
      UniProtKB/Swiss-Prot
      Q6ISU1
      Related
      ENSP00000392288.1, ENST00000446507.5

    4. NM_138296.3 → NP_612153.2  pre T-cell antigen receptor alpha isoform 2 precursor

      See identical proteins and their annotated locations for NP_612153.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AW014894, BC100771, U38996
      Consensus CDS
      CCDS4874.1
      UniProtKB/Swiss-Prot
      Q5TFZ7, Q6ISU1
      Related
      ENSP00000304447.2, ENST00000304672.6
      Conserved Domains (1) summary
      pfam15028
      Location:20 → 146
      PTCRA; Pre-T-cell antigen receptor

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      42916053..42925838
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446344.2 → XP_024302112.1  pre T-cell antigen receptor alpha isoform X2

    2. XM_024446346.2 → XP_024302114.1  pre T-cell antigen receptor alpha isoform X4

    3. XM_024446342.1 → XP_024302110.1  pre T-cell antigen receptor alpha isoform X1

      Conserved Domains (1) summary
      pfam15028
      Location:1 → 113
      PTCRA; Pre-T-cell antigen receptor

    4. XM_024446345.1 → XP_024302113.1  pre T-cell antigen receptor alpha isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      42744769..42754903
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354403.1 → XP_054210378.1  pre T-cell antigen receptor alpha isoform X2

    2. XM_054354405.1 → XP_054210380.1  pre T-cell antigen receptor alpha isoform X4

    3. XM_054354402.1 → XP_054210377.1  pre T-cell antigen receptor alpha isoform X1

    4. XM_054354404.1 → XP_054210379.1  pre T-cell antigen receptor alpha isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ISU1.1 GenPept UniProtKB/Swiss-Prot:Q6ISU1

    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
    Tools
    Miscellaneous