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PCA3 prostate cancer associated 3 [ Homo sapiens (human) ]

Gene ID: 50652, updated on 17-Sep-2024

Summary

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Official Symbol
PCA3provided by HGNC
Official Full Name
prostate cancer associated 3provided by HGNC
Primary source
HGNC:HGNC:8637
See related
Ensembl:ENSG00000225937 MIM:604845; AllianceGenome:HGNC:8637
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DD3; PCAT3; NCRNA00019; PRUNE2-AS1
Summary
This gene produces a spliced, long non-coding RNA that is highly overexpressed in most types of prostate cancer cells and is used as a specific biomarker for this type of cancer. This gene is embedded in an intronic region of the prune2 gene on the opposite DNA strand. The transcript regulates prune2 levels through formation of a double-stranded RNA that undergoes adenosine deaminase acting on RNA-dependent adenosine-to-inosine RNA editing. In prostate cancer derived cells, overexpression of PCA induced downregulation of prune2, leading to decreased cell proliferation. Conversely, silencing in prostate cancer cells resulted in increased proliferation. Regulation of this gene appears to be sensitive to androgen-receptor activation, a molecular signature of prostate cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2017]
Expression
Restricted expression toward prostate (RPKM 4.9) See more
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Genomic context

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See PCA3 in Genome Data Viewer
Location:
9q21.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (76764436..76787569)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (88920862..88944017)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79379352..79402485)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19963 Neighboring gene uncharacterized LOC105376095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28480 Neighboring gene prune homolog 2 with BCH domain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:79284679-79285292 Neighboring gene NANOG hESC enhancer GRCh37_chr9:79303428-79303929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28482 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:79398353-79399552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79402243-79402744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79402745-79403244 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:79502679-79503275 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:79512967-79513466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19964 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:79571299-79571800 Neighboring gene LYPLA2 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79626622-79627122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79627123-79627623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79629105-79629618 Neighboring gene forkhead box B2

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 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. Clinical judgment versus biomarker prostate cancer gene 3: which is best when determining the need for repeat prostate biopsy? Tombal B, et al. Urology, 2013 May. PMID 23523291
  2. The relationship between Prostate CAncer gene 3 (PCA3) and prostate cancer significance. van Poppel H, et al. BJU Int, 2012 Feb. PMID 21883822
  3. Utility of PCA3 in patients undergoing repeat biopsy for prostate cancer. Wu AK, et al. Prostate Cancer Prostatic Dis, 2012 Mar. PMID 22042252
  4. Molecular study of the PCA3 gene: genotypic analysis of PCA3 polymorphism -845G>A and metastatic prostate cancer. Fontenete S, et al. Genet Test Mol Biomarkers, 2012 May. PMID 22288776
  5. Relationship between prostate cancer gene 3 (PCA3) and characteristics of tumor aggressiveness. Augustin H, et al. Prostate, 2013 Jan. PMID 22782916

See all (88) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. lncRNA PCA3 Suppressed Carotid Artery Stenosis and Vascular Smooth Muscle Cell Function via Negatively Modulating the miR-124-3p/ITGB1 Axis.
    Title: lncRNA PCA3 Suppressed Carotid Artery Stenosis and Vascular Smooth Muscle Cell Function via Negatively Modulating the miR-124-3p/ITGB1 Axis.
  2. Urinary PCA3 a Superior Diagnostic Biomarker for Prostate Cancer among Ghanaian Men.
    Title: Urinary PCA3 a Superior Diagnostic Biomarker for Prostate Cancer among Ghanaian Men.
  3. PCA3 controls chromatin organization and p53 signal activation by regulating LAP2alpha-lamin A complexes.
    Title: PCA3 controls chromatin organization and p53 signal activation by regulating LAP2α-lamin A complexes.
  4. Circulating RNAs in prostate cancer patients.
    Title: Circulating RNAs in prostate cancer patients.
  5. LncRNA PCA3 promotes antimony-induced lipid metabolic disorder in prostate cancer by targeting MIR-132-3 P/SREBP1 signaling.
    Title: LncRNA PCA3 promotes antimony-induced lipid metabolic disorder in prostate cancer by targeting MIR-132-3 P/SREBP1 signaling.
  6. Promoter polymorphisms of the PCA3 gene are not associated with its overexpression in prostate cancer patients.
    Title: Promoter polymorphisms of the PCA3 gene are not associated with its overexpression in prostate cancer patients.
  7. These results show that the lncRNAs PCA3 and HAM-1 are upregulated during thyroid tumor development and progression and may function as oncogenes during tumor progression
    Title: Long Non-coding RNA Expression in Anaplastic Thyroid Carcinomas.
  8. Using information visualization methods, we could also distinguish between cell lines expressing the endogenous PCA3 long noncoding RNA (lncRNA) from cells that did not contain detectable levels of this biomarker.
    Title: Detection of the Prostate Cancer Biomarker PCA3 with Electrochemical and Impedance-Based Biosensors.
  9. PCA3 but not T2:ERG was associated with cancer reclassification in the first surveillance biopsy, but has negligible improvement over clinical variables alone in receiver operating characteristic curves or decision curve analyses. Neither marker was associated with reclassification in subsequent biopsies.
    Title: Performance of PCA3 and TMPRSS2:ERG urinary biomarkers in prediction of biopsy outcome in the Canary Prostate Active Surveillance Study (PASS).
  10. Urine prostate cancer gene 3 (PCA3) is significantly elevated in patients with prostate cancer and can be used for the diagnosis of prostate cancer, but its cutoff value is still controversial--{REVIEW}
    Title: Comparison of diagnostic efficacy by two urine PCA3 scores in prostate cancer patients undergoing repeat biopsies.
Submit: New GeneRIF Correction See all GeneRIFs (86)

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

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

General gene information

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Markers

Other Names

  • Differential Display code 3
  • PRUNE2 antisense RNA 1
  • prostate cancer antigen 3 (non-protein coding)
  • prostate cancer associated 3 (non-protein coding)
  • prostate cancer associated transcript 3 (non-protein coding)
  • prostate-specific gene DD3

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.

RNA

  1. NR_015342.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal exon compared to variant 1.
    Source sequence(s)
    AF103907, AY894120
    Related
    ENST00000645809.1

  2. NR_132312.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL359314, AL390239
    Related
    ENST00000412654.1

  3. NR_132313.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal exon and uses an alternate splice site, which results in a shorter transcript compared to variant 1.
    Source sequence(s)
    AF103907, AY894120, DQ374661

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    76764436..76787569
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    88920862..88944017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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