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

Gene ID: 171558, updated on 5-Mar-2024

Summary

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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; 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
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Genomic context

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See PTCRA in Genome Data Viewer
Location:
6p21.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42916053..42925838)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42744769..42754903)
105.20220307 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 chromosome 6 open reading frame 226 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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. 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
  3. 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
  4. 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
  5. A critical role for the cytoplasmic tail of pTalpha in T lymphocyte development. Aifantis I, et al. Nat Immunol, 2002 May. PMID 11927911

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

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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

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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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

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

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Preferred Names
pre T-cell antigen receptor alpha
Names
pT-alpha-TCR
pre-T-cell receptor alpha chain

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_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_2023_10

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

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