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Aliases for PCGF3 Gene

Aliases for PCGF3 Gene

  • Polycomb Group Ring Finger 3 2 3 5
  • RING Finger Protein 3A 3 4
  • Ring Finger Protein 3 2 3
  • RNF3A 3 4
  • RNF3 3 4
  • Polycomb Group RING Finger Protein 3 3
  • DONG1 3

External Ids for PCGF3 Gene

Previous HGNC Symbols for PCGF3 Gene

  • RNF3

Summaries for PCGF3 Gene

Entrez Gene Summary for PCGF3 Gene

  • The protein encoded by this gene contains a C3HC4 type RING finger, which is a motif known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCGF3 Gene

PCGF3 (Polycomb Group Ring Finger 3) is a Protein Coding gene. Among its related pathways are Signaling pathways regulating pluripotency of stem cells. An important paralog of this gene is PCGF5.

UniProtKB/Swiss-Prot for PCGF3 Gene

  • Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Plays a redundant role with PCGF5 as part of a PRC1-like complex that mediates monoubiquitination of histone H2A Lys-119 on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females (By similarity).

Additional gene information for PCGF3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCGF3 Gene

Genomics for PCGF3 Gene

GeneHancer (GH) Regulatory Elements for PCGF3 Gene

Promoters and enhancers for PCGF3 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
GH04J000704 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 673.6 +0.5 507 2.6 HDGF PKNOX1 CLOCK SMAD1 ARNT SIN3A YBX1 ZNF2 POLR2B ZNF207 PCGF3 CRIPAK PIGG ENSG00000281016 LOC100129917 ZNF718 ENSG00000207009 ZNF141 ENSG00000272588 PDE6B
GH04J000711 Promoter 0.6 EPDnew 650.4 +5.4 5365 0.1 GABPA PCGF3 CPLX1 ENSG00000248416
GH04J000929 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 32.3 +225.9 225881 3.5 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 ZNF207 ZNF143 GAK TMEM175 PCGF3 DGKQ CRIPAK PIGG MAEA ZNF141 ZNF718 ENSG00000281016
GH04J000050 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 27.6 -652.1 -652089 6.1 PKNOX1 CBX3 ZSCAN4 SIN3A IRF4 YY1 ETS1 ZNF335 ZNF350 ZNF143 ZNF595 PIGG PCGF3 ZNF718 ZNF141 GAK ENSG00000272588 LOC100129917 IDUA GC04P000106
GH04J000780 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 25 +76.4 76386 3.6 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A DMAP1 YY1 POLR2B FOS LOC100129917 SLC49A3 PCGF3 CRIPAK CPLX1 LOC105374339
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCGF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCGF3 gene promoter:
  • HEN1
  • ARP-1
  • NF-1/L
  • NF-1
  • STAT1
  • TGIF
  • Evi-1
  • Max1
  • c-Myc
  • deltaCREB

Genomic Locations for PCGF3 Gene

Genomic Locations for PCGF3 Gene
chr4:705,748-770,640
(GRCh38/hg38)
Size:
64,893 bases
Orientation:
Plus strand
chr4:699,537-764,428
(GRCh37/hg19)
Size:
64,892 bases
Orientation:
Plus strand

Genomic View for PCGF3 Gene

Genes around PCGF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCGF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCGF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCGF3 Gene

Proteins for PCGF3 Gene

  • Protein details for PCGF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3KNV8-PCGF3_HUMAN
    Recommended name:
    Polycomb group RING finger protein 3
    Protein Accession:
    Q3KNV8
    Secondary Accessions:
    • D3DVN1
    • O15262

    Protein attributes for PCGF3 Gene

    Size:
    242 amino acids
    Molecular mass:
    28115 Da
    Quaternary structure:
    • Component of a PRC1-like complex that contains PCGF3, RNF2 and RYBP (PubMed:21282530, PubMed:26151332). Interacts with CBX6, CBX7 and CBX8 (PubMed:21282530).

    Alternative splice isoforms for PCGF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCGF3 Gene

Post-translational modifications for PCGF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PCGF3 Gene

Domains & Families for PCGF3 Gene

Gene Families for PCGF3 Gene

Protein Domains for PCGF3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCGF3: view

No data available for UniProtKB/Swiss-Prot for PCGF3 Gene

Function for PCGF3 Gene

Molecular function for PCGF3 Gene

UniProtKB/Swiss-Prot Function:
Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Plays a redundant role with PCGF5 as part of a PRC1-like complex that mediates monoubiquitination of histone H2A Lys-119 on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females (By similarity).

Phenotypes From GWAS Catalog for PCGF3 Gene

Gene Ontology (GO) - Molecular Function for PCGF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21282530
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PCGF3: view
genes like me logo Genes that share phenotypes with PCGF3: view

Animal Model Products

CRISPR Products

miRNA for PCGF3 Gene

miRTarBase miRNAs that target PCGF3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCGF3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCGF3 Gene

Localization for PCGF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCGF3 Gene

Nucleus. Nucleus, nucleoplasm. Note=Recruited by the non-coding RNA Xist to specific nuclear foci that probably correspond to the inactivated X chromosome. {ECO:0000250 UniProtKB:Q8BTQ0}.

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 PCGF3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCGF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000805 colocalizes_with X chromosome ISS --
GO:0005634 nucleus IEA,IDA 21282530
GO:0005654 nucleoplasm IEA,IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCGF3: view

Pathways & Interactions for PCGF3 Gene

genes like me logo Genes that share pathways with PCGF3: view

Pathways by source for PCGF3 Gene

Gene Ontology (GO) - Biological Process for PCGF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0036353 histone H2A-K119 monoubiquitination ISS --
GO:0060819 inactivation of X chromosome by genetic imprinting ISS --
genes like me logo Genes that share ontologies with PCGF3: view

No data available for SIGNOR curated interactions for PCGF3 Gene

Drugs & Compounds for PCGF3 Gene

No Compound Related Data Available

Transcripts for PCGF3 Gene

mRNA/cDNA for PCGF3 Gene

Unigene Clusters for PCGF3 Gene

Polycomb group ring finger 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCGF3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCGF3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b
SP1: - - -
SP2: - - - - -
SP3:
SP4: - - -
SP5: - -
SP6: - -
SP7:

Relevant External Links for PCGF3 Gene

GeneLoc Exon Structure for
PCGF3
ECgene alternative splicing isoforms for
PCGF3

Expression for PCGF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCGF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCGF3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCGF3 Gene



Protein tissue co-expression partners for PCGF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCGF3 Gene:

PCGF3

SOURCE GeneReport for Unigene cluster for PCGF3 Gene:

Hs.144309

Evidence on tissue expression from TISSUES for PCGF3 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with PCGF3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCGF3 Gene

Orthologs for PCGF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCGF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCGF3 34 33
  • 99.04 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCGF3 34
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PCGF3 34 33
  • 90.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PCGF3 34 33
  • 90.5 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pcgf3 33
  • 88.93 (n)
mouse
(Mus musculus)
Mammalia Pcgf3 16 34 33
  • 88.52 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PCGF3 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves PCGF3 34 33
  • 82.64 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PCGF3 34
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcgf3 33
  • 76.86 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(3)73Ah 34 33
  • 64.24 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002533 33
  • 63.79 (n)
worm
(Caenorhabditis elegans)
Secernentea mig-32 34 33
  • 43.32 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
OneToOne
Cin.7639 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7639 33
Species where no ortholog for PCGF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for PCGF3 Gene

ENSEMBL:
Gene Tree for PCGF3 (if available)
TreeFam:
Gene Tree for PCGF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCGF3: view image

Paralogs for PCGF3 Gene

Paralogs for PCGF3 Gene

(20) SIMAP similar genes for PCGF3 Gene using alignment to 8 proteins:

  • PCGF3_HUMAN
  • B3KWT8_HUMAN
  • B5MEC4_HUMAN
  • C9J3G7_HUMAN
  • C9JGV3_HUMAN
  • C9JYD0_HUMAN
  • F2Z3P3_HUMAN
  • Q8NDP9_HUMAN

Pseudogenes.org Pseudogenes for PCGF3 Gene

genes like me logo Genes that share paralogs with PCGF3: view

Variants for PCGF3 Gene

Sequence variations from dbSNP and Humsavar for PCGF3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000006109 -- 769,010(+) G/A 3_prime_UTR_variant
rs1000045520 -- 717,673(+) C/T intron_variant
rs1000049992 -- 737,412(+) A/G intron_variant
rs1000074377 -- 769,577(+) G/A 3_prime_UTR_variant
rs1000213127 -- 748,701(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCGF3 Gene

Variant ID Type Subtype PubMed ID
dgv132n6 CNV deletion 16902084
dgv8876n54 CNV loss 21841781
dgv8877n54 CNV loss 21841781
dgv8878n54 CNV loss 21841781
esv1002264 CNV loss 20482838
esv1002699 CNV deletion 20482838
esv1335990 CNV deletion 17803354
esv1347923 CNV deletion 17803354
esv1431312 CNV deletion 17803354
esv22794 CNV gain+loss 19812545
esv2315321 CNV deletion 18987734
esv23784 CNV loss 19812545
esv2441628 CNV deletion 19546169
esv2660636 CNV deletion 23128226
esv2665221 CNV deletion 23128226
esv2666806 CNV deletion 23128226
esv2670226 CNV deletion 23128226
esv2678759 CNV deletion 23128226
esv2726685 CNV deletion 23290073
esv2726686 CNV deletion 23290073
esv2726687 CNV deletion 23290073
esv2726688 CNV deletion 23290073
esv2726689 CNV deletion 23290073
esv2726690 CNV deletion 23290073
esv2726691 CNV deletion 23290073
esv2726692 CNV deletion 23290073
esv2726693 CNV deletion 23290073
esv2726694 CNV deletion 23290073
esv2726697 CNV deletion 23290073
esv2726698 CNV deletion 23290073
esv2726699 CNV deletion 23290073
esv2726700 CNV deletion 23290073
esv2726701 CNV deletion 23290073
esv2726702 CNV deletion 23290073
esv2726703 CNV deletion 23290073
esv2726704 CNV deletion 23290073
esv2726705 CNV deletion 23290073
esv2726706 CNV deletion 23290073
esv2726708 CNV deletion 23290073
esv2741953 CNV deletion 23290073
esv2759217 CNV loss 17122850
esv27696 CNV gain+loss 19812545
esv29088 CNV loss 19812545
esv3418074 CNV duplication 20981092
esv3563223 CNV deletion 23714750
esv3599379 CNV loss 21293372
esv3599380 CNV loss 21293372
esv3599381 CNV gain 21293372
nsv10414 CNV gain 18304495
nsv10415 CNV loss 18304495
nsv10416 CNV gain 18304495
nsv10418 CNV loss 18304495
nsv1073279 CNV deletion 25765185
nsv1074659 CNV deletion 25765185
nsv1074660 CNV deletion 25765185
nsv1109573 CNV deletion 24896259
nsv1112393 CNV deletion 24896259
nsv1117958 CNV deletion 24896259
nsv1145012 CNV deletion 24896259
nsv1150996 CNV deletion 26484159
nsv1153394 CNV deletion 26484159
nsv290420 CNV deletion 16902084
nsv293714 CNV deletion 16902084
nsv4195 CNV deletion 18451855
nsv508986 CNV insertion 20534489
nsv513112 CNV loss 21212237
nsv513113 CNV loss 21212237
nsv520136 CNV gain 19592680
nsv593206 CNV loss 21841781
nsv593209 CNV loss 21841781
nsv593210 CNV loss 21841781
nsv593214 CNV gain 21841781
nsv593219 CNV loss 21841781
nsv593222 CNV loss 21841781
nsv818207 CNV gain 17921354
nsv822425 CNV loss 20364138
nsv822426 CNV gain 20364138
nsv829834 CNV loss 17160897
nsv950325 CNV deletion 24416366

Variation tolerance for PCGF3 Gene

Residual Variation Intolerance Score: 48.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.53; 11.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCGF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCGF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCGF3 Gene

Disorders for PCGF3 Gene

Additional Disease Information for PCGF3

No disorders were found for PCGF3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCGF3 Gene

Publications for PCGF3 Gene

  1. BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase. (PMID: 26151332) Taherbhoy AM … Cochran AG (Nature communications 2015) 3 4 58
  2. Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project. (PMID: 22443383) Oudot-Mellakh T … Morange PE (British journal of haematology 2012) 3 44 58
  3. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. (PMID: 21282530) Vandamme J … Angrand PO (Molecular & cellular proteomics : MCP 2011) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PCGF3 Gene

Sources for PCGF3 Gene

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