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

Subcategory (RNA class) for PCA3 Gene


Quality Score for this RNA gene is


Aliases for PCA3 Gene

  • Prostate Cancer Associated 3 2 3 5
  • Prostate Cancer Associated Transcript 3 (Non-Protein Coding) 2 3
  • Prostate Cancer Associated 3 (Non-Protein Coding) 2 3
  • Prostate Cancer Antigen 3 (Non-Protein Coding) 2 3
  • PRUNE2 Antisense RNA 1 2 3
  • PCA3 2 170
  • Prostate-Specific Gene DD3 3
  • Non-Protein Coding RNA 19 2
  • Prostate Cancer Antigen 3 2
  • HSALNG0072040 169
  • NONHSAG052609 94
  • Lnc-FOXB2-9 170
  • NCRNA00019 3
  • PRUNE2-AS1 3
  • PCAT3 3
  • DD3 3

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

Additional gene information for PCA3 Gene

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 for PCA3 Gene

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 1.6 Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 +0.3 307 1.7 USF2 PATZ1 ZBTB20 ZXDB ZBTB17 USF1 ZFP69B ZNF366 SIN3A L3MBTL2 PCA3 PRUNE2 piR-50437-667
GH09J076689 Enhancer 0.2 ENCODE 750.6 -1.9 -1922 0.9 PCA3 PRUNE2 piR-55361-570
GH09J076687 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 0.6 -3.8 -3826 2.2 NR2F1 NR2F6 MIXL1 HLF ZNF121 CEBPG PPARG KAT8 ZNF644 CEBPA PRUNE2 GCNT1 PCA3 piR-55361-570
GH09J076700 Enhancer 1 Ensembl ENCODE dbSUPER 0.4 +8.9 8921 8.6 ZNF24 CTCF SREBF1 RAD21 TEAD4 MAFK REST ZNF316 MAFG SMC3 PRUNE2 piR-50437-667 PCA3 DQ374659
GH09J076676 Enhancer 0.9 Ensembl ENCODE dbSUPER 0.4 -14.4 -14379 2 PRDM1 CEBPG IKZF1 CEBPA SP1 NR2F2 CEBPB JUN FOXA1 JUND PRUNE2 piR-55361-570 PCA3
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for PCA3 Gene
171,328 bases
Plus strand
23,134 bases
Plus strand

Genomic View for PCA3 Gene

Genes around PCA3 on UCSC Golden Path with GeneCards custom track

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

Animal Model Products

CRISPR Products

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 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 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 and SIGNOR curated interactions for PCA3 Gene

Drugs & Compounds for PCA3 Gene

No Compound Related Data Available

Transcripts for PCA3 Gene

mRNA/cDNA for PCA3 Gene

(3) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(18) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(21) RNACentral transcripts :
(1) ENA transcripts :
(3) NONCODE transcripts :
(10) LNCipedia transcripts :
(2) LncBook transcripts :

CRISPR Products

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

No ASD Table

Relevant External Links for PCA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCA3 Gene

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

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

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

NURSA nuclear receptor signaling pathways regulating expression of PCA3 Gene:


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)

No data available for Orthologs for PCA3 Gene

Paralogs for PCA3 Gene

No data available for Paralogs for PCA3 Gene

Variants for PCA3 Gene

Sequence variations from dbSNP and Humsavar for PCA3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000035301 -- 76,765,489(+) AGAGA/AGA intron_variant
rs1000085782 -- 76,765,181(+) C/A intron_variant
rs1000249965 -- 76,771,246(+) A/G intron_variant
rs1000279992 -- 76,768,083(+) C/G intron_variant
rs1000311059 -- 76,768,308(+) T/A intron_variant

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for PCA3 Gene

Disorders for PCA3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PCA3 Gene - From: LncRNADisease, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
prostate disease
  • prostate diseases
prostate cancer
  • prostate cancer, somatic
parkinson disease, late-onset
  • pd
male reproductive organ cancer
  • male genital cancer
male reproductive system disease
  • genital diseases, male
- 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 23 56
  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 56
  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 56
  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 23 56
  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 23 56

Products for PCA3 Gene

Sources for PCA3 Gene