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 dea... See more...

Aliases for PCA3 Gene

Data sources for PCA3 Gene:

RNA type for PCA3 Gene


Aliases for PCA3 Gene

External Ids for PCA3 Gene

Previous GeneCards Identifiers for PCA3 Gene

  • GC09U990136
  • GC09P079379
  • GC09P049208
  • GC09P076764

Summaries for PCA3 Gene

Entrez Gene Summary for PCA3 Gene

  • 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]

GeneCards Summary for PCA3 Gene

PCA3 (Prostate Cancer Associated 3) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with PCA3 include Prostate Disease and Prostate Cancer.

Gene Wiki entry for PCA3 Gene

Rfam classification for PCA3 Gene

  • Prostate cancer antigen RNA 3 conserved region 2

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary and piRNA Summary for PCA3 Gene

Genomics for PCA3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCA3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J076691 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +0.3 307 1.7 SIN3A YY1 SPI1 RAD51 TAF1 TOE1 ZFP69B TRIM28 ZNF366 L3MBTL2 PCA3 PRUNE2 piR-50437-667 GCNT1
GH09J076700 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 250.4 +8.9 8921 8.6 ZNF654 CTCF REST MAFF RAD21 SMC3 ZNF316 MAFK ZNF24 MAFG PCA3 PRUNE2 piR-50437-667 ENSG00000274326 GCNT1
GH09J076764 Promoter 0.3 EPDnew 250.2 +72.4 72439 0.1 PCA3 ENSG00000274326 piR-50437-667 PRUNE2 GCNT1
GH09J076689 Enhancer 0.2 ENCODE 250.7 -1.9 -1922 0.9 PCA3 PRUNE2 piR-55361-570 GCNT1
GH09J076687 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 0.7 -3.8 -3826 2.2 CEBPA THAP11 RXRA SMAD4 ETV4 MIER3 RARA GABPB1 FOXP1 BCL6 PRUNE2 GCNT1 PCA3 piR-55361-570
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCA3 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the PCA3 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • NF-Y
  • NF-YA
  • NF-YB
  • POU2F1
  • POU2F1a
  • Spz1

Genomic Locations for PCA3 Gene

Latest Assembly
171,328 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
23,134 bases
Plus strand

(GRCh37/hg19 by Ensembl)
23,134 bases
Plus strand

Genomic View for PCA3 Gene

Genes around PCA3 on UCSC Golden Path with GeneCards custom track
PCA3 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
PCA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCA3 Gene

Proteins for PCA3 Gene

Post-translational modifications for PCA3 Gene

No Post-translational modifications

No data available for DME Specific Peptides for PCA3 Gene

Domains & Families for PCA3 Gene

Gene Families for PCA3 Gene

genes like me logo Genes that share domains with PCA3: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCA3 Gene

Function for PCA3 Gene

Phenotypes From GWAS Catalog for PCA3 Gene

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCA3 Gene

Localization for PCA3 Gene

Subcellular locations from

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 PCA3 gene
Compartment Confidence
plasma membrane 2
extracellular 2
nucleus 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for PCA3 Gene

Pathways & Interactions for PCA3 Gene

PathCards logo

SuperPathways for PCA3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCA3 Gene


No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for PCA3 Gene

Drugs & Compounds for PCA3 Gene

No Compound Related Data Available

Transcripts for PCA3 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for PCA3 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS0000075E3C_9606 lncRNA 3922 4

RefSeq: NR_132312,

Ensembl: ENST00000412654 (view in UCSC) ,

LNCipedia: lnc-FOXB2-9:1,


URS000075CA8F_9606 lncRNA 3738 3

Ensembl: ENST00000645809 (view in UCSC) ,

LNCipedia: lnc-FOXB2-9:4,


URS00004C2861_9606 lncRNA 322 3

Ensembl: ENST00000647409 (view in UCSC) ,

LNCipedia: lnc-FOXB2-9:6,

ENA: DQ374660.1:1..322:misc_RNA,

URS00008E3A1F_9606 lncRNA 3760 2

RefSeq: NR_015342,

LNCipedia: lnc-FOXB2-9:3,

URS0000D628FB_9606 lncRNA 3670 2

Ensembl: ENST00000646947 (view in UCSC) ,

LNCipedia: PCA3:6,

PCA3 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for PCA3 Gene

4 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for PCA3 Gene

No ASD Table

Relevant External Links for PCA3 Gene

GeneLoc Exon Structure for

Expression for PCA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCA3 Gene

mRNA differential expression in normal tissues according to GTEx for PCA3 Gene

This gene is overexpressed in Prostate (x28.6).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCA3

SOURCE GeneReport for Unigene cluster for PCA3 Gene:


Evidence on tissue expression from TISSUES for PCA3 Gene

  • Urine(2.8)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with PCA3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCA3 Gene

Orthologs for PCA3 Gene

Evolution for PCA3 Gene

Gene Tree for PCA3 (if available)
Gene Tree for PCA3 (if available)
Alliance of Genome Resources:
Additional Orthologs for PCA3

No data available for Orthologs for PCA3 Gene

Paralogs for PCA3 Gene

No data available for Paralogs for PCA3 Gene

Variants for PCA3 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCA3 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 PCA3 Gene

Variant ID Type Subtype PubMed ID
dgv1484e214 CNV gain 21293372
esv2663601 CNV deletion 23128226
esv2738601 CNV deletion 23290073
esv2759697 CNV loss 17122850
esv3620746 CNV loss 21293372
nsv1040363 CNV gain 25217958
nsv824952 CNV loss 20364138

Additional Variant Information for PCA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for PCA3 Gene

Disorders for PCA3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PCA3 Gene - From: LNC, COP, and GCD

Disorder Aliases PubMed IDs
prostate disease
  • prostate diseases
prostate cancer
  • prostate cancer, somatic
ovarian epithelial cancer
  • eoc
parkinson disease, late-onset
  • pd
- elite association - COSMIC cancer census association via MalaCards
Search PCA3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCA3

genes like me logo Genes that share disorders with PCA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCA3 Gene

Publications for PCA3 Gene

  1. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. (PMID: 10606244) Bussemakers MJ … Isaacs WB (Cancer research 1999) 2 3 22 72
  2. PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3. (PMID: 26080435) Salameh A … Arap W (Proceedings of the National Academy of Sciences of the United States of America 2015) 2 3 72
  3. PCA3 noncoding RNA is involved in the control of prostate-cancer cell survival and modulates androgen receptor signaling. (PMID: 23130941) Ferreira LB … Gimba ER (BMC cancer 2012) 2 3 72
  4. New genomic structure for prostate cancer specific gene PCA3 within BMCC1: implications for prostate cancer detection and progression. (PMID: 19319183) Clarke RA … Gardiner RA (PloS one 2009) 3 22 72
  5. Clinical utility of the PCA3 urine assay in European men scheduled for repeat biopsy. (PMID: 18602209) Haese A … Schalken JA (European urology 2008) 3 22 72

Products for PCA3 Gene

Sources for PCA3 Gene