PTCRA Gene (Protein Coding)

Pre T Cell Antigen Receptor Alpha

GC06P042915
GIFtS:
38
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] See more...

Aliases for PTCRA Gene

Aliases for PTCRA Gene

  • Pre T Cell Antigen Receptor Alpha 2 3 5
  • Pre T-Cell Antigen Receptor Alpha 2 3 4
  • PT-Alpha-TCR 3 4
  • PT-ALPHA 2 3
  • PTA 2 3
  • Pre-T-Cell Receptor Alpha Chain 3
  • PT-Alpha 4
  • PTCRA 5
  • PTa 4

External Ids for PTCRA Gene

Previous GeneCards Identifiers for PTCRA Gene

  • GC06P042885
  • GC06P042931
  • GC06P042932
  • GC06P042992
  • GC06P042883
  • GC06P042601

Summaries for PTCRA Gene

Entrez Gene Summary for PTCRA Gene

  • 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]

GeneCards Summary for PTCRA Gene

PTCRA (Pre T Cell Antigen Receptor Alpha) is a Protein Coding gene. Diseases associated with PTCRA include Palmoplantar Keratoderma And Congenital Alopecia 2 and Immunodeficiency 19. Among its related pathways are Notch Signaling Pathway (WikiPathways) and Transcriptional misregulation in cancer.

UniProtKB/Swiss-Prot Summary for PTCRA Gene

  • The pre-T-cell receptor complex (composed of PTCRA, TCRB and the CD3 complex) regulates early T-cell development.

Additional gene information for PTCRA Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTCRA Gene

Genomics for PTCRA Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PTCRA Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH06J042916 Promoter/Enhancer 0.7 EPDnew dbSUPER 250.7 +0.4 437 0.1 TCF12 RUNX3 PTCRA ENSG00000231113 PPP2R5D RPL7L1 C6orf226 PEX6 KLHDC3 MEA1 CUL9 RNU6-890P
GH06J042910 Promoter/Enhancer 1.1 ENCODE CraniofacialAtlas dbSUPER 0.7 -4.0 -4009 1.8 CTCF SIN3A SAP130 GABPB1 RBPJ TFAP4 EGR1 U2AF2 ZNF143 POLR2A PEX6 RPL7L1 ABCC10 ZNF318 GTPBP2 CUL7 RPS2P29 POLH POLR1C ENSG00000231113
GH06J042901 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 0.4 -12.5 -12475 3.2 MXD4 CEBPA ZFP64 CTCF BHLHE40 NONO THAP11 ARNT REST CUX1 ENSG00000288010 LOC105375063 piR-30350-054 RPL7L1 PEX6 CNPY3 ENSG00000231113 PPP2R5D KLC4 RN7SL403P
GH06J042919 Enhancer 0.6 Ensembl 0.7 +4.3 4304 0.2 SMAD4 SAP130 RARA TEAD3 BCL6 ZBTB33 ZNF48 BHLHE40 HHEX NR2F6 RPL7L1 ENSG00000231113 PPP2R5D C6orf226 PEX6 KLHDC3 MEA1 CUL9 RNU6-890P PTCRA
GH06J042894 Promoter 0.9 Ensembl 0.3 -21.7 -21696 0.2 IKZF1 NBN SAP130 KMT2B NCOR1 SKIL BHLHE40 SMARCA4 HDAC2 FOXM1 HE855979 lnc-RPL7L1-2 piR-30350-053 RPL7L1 CNPY3 ENSG00000231113 RNU6-890P PPP2R5D KLHDC3 MEA1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTCRA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTCRA

Top Transcription factor binding sites by QIAGEN in the PTCRA gene promoter:
  • AML1a
  • AP-4
  • AREB6
  • Brachyury
  • CP2
  • HEN1
  • HOXA9
  • HOXA9B
  • p53
  • SRY

Genomic Locations for PTCRA Gene

Latest Assembly
chr6:42,915,597-42,925,838
(GRCh38/hg38)
Size:
10,242 bases
Orientation:
Plus strand

Previous Assembly
chr6:42,883,791-42,893,576
(GRCh37/hg19 by Entrez Gene)
Size:
9,786 bases
Orientation:
Plus strand

chr6:42,883,727-42,893,573
(GRCh37/hg19 by Ensembl)
Size:
9,847 bases
Orientation:
Plus strand

Genomic View for PTCRA Gene

Genes around PTCRA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCRA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCRA Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PTCRA Gene

Proteins for PTCRA Gene

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  3. Assay products for research

  • Protein details for PTCRA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ISU1-PTCRA_HUMAN
    Recommended name:
    Pre T-cell antigen receptor alpha
    Protein Accession:
    Q6ISU1
    Secondary Accessions:
    • Q5TFZ7

    Protein attributes for PTCRA Gene

    Size:
    281 amino acids
    Molecular mass:
    29266 Da
    Quaternary structure:
    • Heterodimer with TCRB; disulfide linked. This heterodimer assembles with CD3 proteins into a signaling-competent pre-T-cell receptor complex. Interacts with RHBDD1.

    Three dimensional structures from OCA and Proteopedia for PTCRA Gene

    Alternative splice isoforms for PTCRA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTCRA Gene

Protein Expression for PTCRA Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PTCRA Gene

  • Glycosylation at Asn67
  • Modification sites at PhosphoSitePlus

Other Protein References for PTCRA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PTCRA Gene

Domains & Families for PTCRA Gene

Gene Families for PTCRA Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PTCRA Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PTCRA Gene

GenScript: Design optimal peptide antigens:
  • pT-alpha-TCR (PTCRA_HUMAN)
genes like me logo Genes that share domains with PTCRA: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PTCRA Gene

Function for PTCRA Gene

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  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for PTCRA Gene

UniProtKB/Swiss-Prot Function:
The pre-T-cell receptor complex (composed of PTCRA, TCRB and the CD3 complex) regulates early T-cell development.
GENATLAS Biochemistry:
pre-T-cell receptor alpha chain,invariant,heterodimerizing with TCRbeta chain receptor in immature thymocyte

Phenotypes From GWAS Catalog for PTCRA Gene

Gene Ontology (GO) - Molecular Function for PTCRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22795130
genes like me logo Genes that share ontologies with PTCRA: view
genes like me logo Genes that share phenotypes with PTCRA: view

Animal Models for PTCRA Gene

MGI Knock Outs for PTCRA:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCRA

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PTCRA Gene

Localization for PTCRA Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCRA Gene

Membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTCRA gene
Compartment Confidence
plasma membrane 4
extracellular 3
nucleus 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PTCRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PTCRA: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PTCRA Gene

Pathways & Interactions for PTCRA Gene

genes like me logo Genes that share pathways with PTCRA: view

SIGNOR curated interactions for PTCRA Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for PTCRA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070244 negative regulation of thymocyte apoptotic process IBA 21873635
genes like me logo Genes that share ontologies with PTCRA: view

Drugs & Compounds for PTCRA Gene

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(2) Drugs for PTCRA Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PTCRA: view

Transcripts for PTCRA Gene

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mRNA/cDNA for PTCRA Gene

4 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCRA

Alternative Splicing Database (ASD) splice patterns (SP) for PTCRA Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d
SP1: - -
SP2: - -
SP3: -
SP4: - -
SP5: - - - -

Relevant External Links for PTCRA Gene

GeneLoc Exon Structure for
PTCRA

Expression for PTCRA Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTCRA Gene

mRNA expression in normal human tissues for PTCRA Gene
mRNA expression by BioGPS for PTCRA GenemRNA expression by GTEx for PTCRA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PTCRA Gene

This gene is overexpressed in Whole Blood (x34.1) and Spleen (x8.4).

Protein differential expression in normal tissues from HIPED for PTCRA Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTCRA Gene



Protein tissue co-expression partners for PTCRA Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTCRA

SOURCE GeneReport for Unigene cluster for PTCRA Gene:

Hs.169002

mRNA Expression by UniProt/SwissProt for PTCRA Gene:

Q6ISU1-PTCRA_HUMAN
Tissue specificity: Expressed in immature but not mature T-cells. Also found in CD34+ cells from peripheral blood, CD34+ precursors from umbilical cord blood and adult bone marrow.

Evidence on tissue expression from TISSUES for PTCRA Gene

  • Blood(4.5)
  • Spleen(2.2)
  • Lymph node(2.1)
genes like me logo Genes that share expression patterns with PTCRA: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCRA Gene

Orthologs for PTCRA Gene

This gene was present in the common ancestor of mammals.

Orthologs for PTCRA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PTCRA 30 31
  • 98.7 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PTCRA 30 31
  • 85.78 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PTCRA 30 31
  • 84.14 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Ptcra 30 17 31
  • 81.35 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ptcra 30
  • 78.91 (n)
Species where no ortholog for PTCRA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for PTCRA Gene

ENSEMBL:
Gene Tree for PTCRA (if available)
TreeFam:
Gene Tree for PTCRA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTCRA: view image

Paralogs for PTCRA Gene

No data available for Paralogs for PTCRA Gene

Variants for PTCRA Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTCRA Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs146531157 Benign: not provided 42,925,516(+) G/A
NM_138296.3(PTCRA):c.680G>A (p.Arg227Gln) 		MISSENSE
rs36111725 - p.Ala183Thr
rs9471966 - p.Val106Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PTCRA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PTCRA Gene

Variant ID Type Subtype PubMed ID
esv1622905 CNV insertion 17803354
esv3576145 CNV gain 25503493
esv3608807 CNV loss 21293372
nsv1017398 CNV gain 25217958
nsv830651 CNV loss 17160897

Variation tolerance for PTCRA Gene

Residual Variation Intolerance Score: 74.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.99; 89.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTCRA Gene

Human Gene Mutation Database (HGMD)
PTCRA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTCRA

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTCRA Gene

Disorders for PTCRA Gene

MalaCards: The human disease database

(5) MalaCards diseases for PTCRA Gene - From: COP

Disorder Aliases PubMed IDs
palmoplantar keratoderma and congenital alopecia 2
  • ppkca2
immunodeficiency 19
  • imd19
t-cell lymphoblastic leukemia/lymphoma
  • t-cell leukemia
coronary aneurysm
  • aneurysm of coronary vessels
heart aneurysm
  • cardiac aneurysm
- elite association - COSMIC cancer census association via MalaCards
Search PTCRA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PTCRA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PTCRA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTCRA Gene

Publications for PTCRA Gene

  1. Genomic structure of the human pre-T cell receptor alpha chain and expression of two mRNA isoforms. (PMID: 9842925) Saint-Ruf C … von Boehmer H (European journal of immunology 1998) 2 3 4 23
  2. Cloning and comparative analysis of the human pre-T-cell receptor alpha-chain gene. (PMID: 8618853) Del Porto P … Saint-Ruf C (Proceedings of the National Academy of Sciences of the United States of America 1995) 2 3 4 23
  3. Ubiquitin-dependent intramembrane rhomboid protease promotes ERAD of membrane proteins. (PMID: 22795130) Fleig L … Lemberg MK (Molecular cell 2012) 3 4
  4. Differential subcellular localization regulates c-Cbl E3 ligase activity upon Notch3 protein in T-cell leukemia. (PMID: 19966856) Checquolo S … Screpanti I (Oncogene 2010) 3 23
  5. Spontaneous preterm birth in African Americans is associated with infection and inflammatory response gene variants. (PMID: 19019335) Velez DR … Menon R (American journal of obstetrics and gynecology 2009) 3 41

ExternalLinks

View latest publications for PTCRA gene in Mastermind

Products for PTCRA Gene

Sources for PTCRA Gene