PCGF1 is a mammalian homolog of the Drosophila polycomb group genes, which act as transcriptional repressors to regulate anterior-posterior patterning in early embryonic development (Nunes et al., 2001 [PubMed 11287196]). See also PCGF2 (MIM 600346).[supplied by OMIM, Aug 2008] See more...

Aliases for PCGF1 Gene

Aliases for PCGF1 Gene

  • Polycomb Group Ring Finger 1 2 3 5
  • Polycomb Group RING Finger Protein 1 3 4
  • Nervous System Polycomb-1 3 4
  • RING Finger Protein 68 3 4
  • NSPC1 3 4
  • RNF68 3 4
  • 2010002K04Rik 3
  • RNF3A-2 3
  • NSPc1 4

External Ids for PCGF1 Gene

Previous GeneCards Identifiers for PCGF1 Gene

  • GC02M074644
  • GC02M074646
  • GC02M074585
  • GC02M074732
  • GC02M074468

Summaries for PCGF1 Gene

Entrez Gene Summary for PCGF1 Gene

  • PCGF1 is a mammalian homolog of the Drosophila polycomb group genes, which act as transcriptional repressors to regulate anterior-posterior patterning in early embryonic development (Nunes et al., 2001 [PubMed 11287196]). See also PCGF2 (MIM 600346).[supplied by OMIM, Aug 2008]

GeneCards Summary for PCGF1 Gene

PCGF1 (Polycomb Group Ring Finger 1) is a Protein Coding gene. Diseases associated with PCGF1 include Bardet-Biedl Syndrome 2 and Kidney Clear Cell Sarcoma. Among its related pathways are Signaling pathways regulating pluripotency of stem cells. Gene Ontology (GO) annotations related to this gene include protein C-terminus binding. An important paralog of this gene is COMMD3-BMI1.

UniProtKB/Swiss-Prot Summary for PCGF1 Gene

  • Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down-regulating CDKN1A. 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 (PubMed:26151332). Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Regulates the expression of DPPA4 and NANOG in the NT2 embryonic carcinoma cells (PubMed:26687479).

Gene Wiki entry for PCGF1 Gene

Additional gene information for PCGF1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCGF1 Gene

Genomics for PCGF1 Gene

GeneHancer (GH) Regulatory Elements for PCGF1 Gene

Promoters and enhancers for PCGF1 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
GH02J074496 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 528 +4.9 4858 12.7 EP300 HNRNPK FOXK2 ZBTB40 ZNF217 CTCF ZSCAN5C NRF1 POLR2G USF1 PCGF1 LBX2 ENSG00000272183 lnc-PCGF1-2 DUSP11 TTC31 ENSG00000273245 CCDC142 HTRA2 MOB1A
GH02J074515 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 500.4 -5.7 -5706 0.4 POLR2G TGIF2 ZBTB7A SKI ZKSCAN8 EZH2 MXI1 SRSF1 PTBP1 GABPB1 NONHSAG028227.2 TLX2 PCGF1
GH02J074196 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 37.8 +308.1 308087 5.6 HNRNPK ZNF217 CTCF TCF12 SIN3A NRF1 MYC USF1 POLR2G SP1 MTHFD2 ENSG00000279070 DUSP11 WBP1 ENSG00000273245 PCGF1 TTC31 CCDC142 INO80B ENSG00000270571
GH02J074471 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 34.6 +35.2 35200 2.6 RXRA ZBTB40 ZNF217 EP300 SIN3A TCF12 NRF1 POLR2G NCOR1 GTF2E2 MRPL53 CCDC142 TTC31 PCGF1 AUP1 MOGS WBP1 DUSP11 INO80B LBX2
GH02J074528 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 32.8 -22.6 -22630 4.4 EP300 RXRA ZBTB40 ZNF217 CTCF TCF12 SIN3A NRF1 POLR2G SP1 AUP1 HTRA2 HSALNG0016075 lnc-DQX1-1 TTC31 PCGF1 CCDC142 LBX2 DUSP11 MOB1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCGF1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCGF1

Top Transcription factor binding sites by QIAGEN in the PCGF1 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT1
  • STAT1alpha

Genomic Locations for PCGF1 Gene

Genomic Locations for PCGF1 Gene
chr2:74,505,043-74,507,695
(GRCh38/hg38)
Size:
2,653 bases
Orientation:
Minus strand
chr2:74,732,170-74,735,707
(GRCh37/hg19)
Size:
3,538 bases
Orientation:
Minus strand

Genomic View for PCGF1 Gene

Genes around PCGF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCGF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCGF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCGF1 Gene

Proteins for PCGF1 Gene

  • Protein details for PCGF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BSM1-PCGF1_HUMAN
    Recommended name:
    Polycomb group RING finger protein 1
    Protein Accession:
    Q9BSM1
    Secondary Accessions:
    • Q7Z506

    Protein attributes for PCGF1 Gene

    Size:
    259 amino acids
    Molecular mass:
    30346 Da
    Quaternary structure:
    • Interacts with BCORL1, forming heterodimers (PubMed:23523425, PubMed:27568929). The PCGF1-BCORL1 heterodimeric complex interacts with the KDM2B-SKP1 heterodimeric complex to form a homotetrameric polycomb repression complex 1 (PRC1.1) (PubMed:27568929). Component of the repressive BCOR complex containing a Polycomb group subcomplex at least composed of RYBP, RING1 and RNF2/RING2 (PubMed:16943429). Specifically interacts with BCOR, RING1 and RNF2/RING2 (PubMed:16943429, PubMed:26687479, PubMed:23523425). Component of a PRC1-like complex (PubMed:21282530, PubMed:26151332). Interacts with CBX6, CBX7 and CBX8 (PubMed:21282530). Interacts with DPPA4, NANOG, POU5F1 and RYBP (PubMed:26687479).
    SequenceCaution:
    • Sequence=AAH04952.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAP97183.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCGF1 Gene

    Alternative splice isoforms for PCGF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCGF1 Gene

Post-translational modifications for PCGF1 Gene

  • Ubiquitination at Lys74, Lys159, and Lys190
  • Modification sites at PhosphoSitePlus

Other Protein References for PCGF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCGF1 Gene

Domains & Families for PCGF1 Gene

Gene Families for PCGF1 Gene

Protein Domains for PCGF1 Gene

Blocks:
  • Zn-finger, RING
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PCGF1 Gene

GenScript: Design optimal peptide antigens:
  • RING finger protein 68 (PCGF1_HUMAN)
genes like me logo Genes that share domains with PCGF1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCGF1 Gene

Function for PCGF1 Gene

Molecular function for PCGF1 Gene

UniProtKB/Swiss-Prot Function:
Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down-regulating CDKN1A. 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 (PubMed:26151332). Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Regulates the expression of DPPA4 and NANOG in the NT2 embryonic carcinoma cells (PubMed:26687479).

Phenotypes From GWAS Catalog for PCGF1 Gene

Gene Ontology (GO) - Molecular Function for PCGF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16943429
GO:0008022 protein C-terminus binding IPI 16943429
GO:0046872 metal ion binding IEA --
GO:1990841 promoter-specific chromatin binding IBA 21873635
genes like me logo Genes that share ontologies with PCGF1: view
genes like me logo Genes that share phenotypes with PCGF1: view

Animal Models for PCGF1 Gene

MGI Knock Outs for PCGF1:
  • Pcgf1 Pcgf1<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for PCGF1 Gene

miRTarBase miRNAs that target PCGF1

Clone Products

  • Addgene plasmids for PCGF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCGF1 Gene

Localization for PCGF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCGF1 Gene

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 PCGF1 gene
Compartment Confidence
nucleus 5
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCGF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 21282530
GO:0005654 nucleoplasm IDA --
GO:0031519 PcG protein complex IDA 16943429
GO:0035102 PRC1 complex IBA 21873635
genes like me logo Genes that share ontologies with PCGF1: view

Pathways & Interactions for PCGF1 Gene

genes like me logo Genes that share pathways with PCGF1: view

Pathways by source for PCGF1 Gene

Gene Ontology (GO) - Biological Process for PCGF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0006342 chromatin silencing IBA 21873635
GO:0006355 regulation of transcription, DNA-templated TAS 26687479
GO:0035518 histone H2A monoubiquitination IDA 16943429
GO:0036353 histone H2A-K119 monoubiquitination IBA,IMP 26151332
genes like me logo Genes that share ontologies with PCGF1: view

No data available for SIGNOR curated interactions for PCGF1 Gene

Drugs & Compounds for PCGF1 Gene

No Compound Related Data Available

Transcripts for PCGF1 Gene

mRNA/cDNA for PCGF1 Gene

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

CRISPR Products

Clone Products

  • Addgene plasmids for PCGF1

Alternative Splicing Database (ASD) splice patterns (SP) for PCGF1 Gene

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

Relevant External Links for PCGF1 Gene

GeneLoc Exon Structure for
PCGF1

Expression for PCGF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCGF1 Gene

Protein differential expression in normal tissues from HIPED for PCGF1 Gene

This gene is overexpressed in Plasma (61.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCGF1 Gene



Protein tissue co-expression partners for PCGF1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCGF1

SOURCE GeneReport for Unigene cluster for PCGF1 Gene:

Hs.316750

mRNA Expression by UniProt/SwissProt for PCGF1 Gene:

Q9BSM1-PCGF1_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with PCGF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCGF1 Gene

Orthologs for PCGF1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCGF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCGF1 31 30
  • 99.87 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PCGF1 31 30
  • 94.72 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCGF1 31
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PCGF1 31 30
  • 93.44 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pcgf1 17 31 30
  • 91.5 (n)
rat
(Rattus norvegicus)
Mammalia Pcgf1 30
  • 90.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PCGF1 31
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves PCGF1 31 30
  • 76.27 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PCGF1 31
  • 71 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.19589 30
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20413 30
zebrafish
(Danio rerio)
Actinopterygii pcgf1 31 30
  • 71.26 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6470 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 42 (a)
OneToOne
Cin.692 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.692 30
Species where no ortholog for PCGF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PCGF1 Gene

ENSEMBL:
Gene Tree for PCGF1 (if available)
TreeFam:
Gene Tree for PCGF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCGF1: view image

Paralogs for PCGF1 Gene

Paralogs for PCGF1 Gene

(7) SIMAP similar genes for PCGF1 Gene using alignment to 1 proteins:

  • PCGF1_HUMAN

Pseudogenes.org Pseudogenes for PCGF1 Gene

genes like me logo Genes that share paralogs with PCGF1: view

Variants for PCGF1 Gene

Additional dbSNP identifiers (rs#s) for PCGF1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCGF1 Gene

Variant ID Type Subtype PubMed ID
esv2759061 CNV loss 17122850
esv3445786 CNV insertion 20981092
nsv458185 CNV loss 19166990
nsv515851 CNV loss 19592680
nsv582214 CNV loss 21841781
nsv582215 CNV loss 21841781

Variation tolerance for PCGF1 Gene

Residual Variation Intolerance Score: 53.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.71; 15.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCGF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCGF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCGF1 Gene

Disorders for PCGF1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCGF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
bardet-biedl syndrome 2
  • bbs2
kidney clear cell sarcoma
  • childhood kidney clear cell sarcoma
- elite association - COSMIC cancer census association via MalaCards
Search PCGF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCGF1

genes like me logo Genes that share disorders with PCGF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCGF1 Gene

Publications for PCGF1 Gene

  1. NSPc1, a novel mammalian Polycomb gene, is expressed in neural crest-derived structures of the peripheral nervous system. (PMID: 11287196) Nunes M … McElreavey K (Mechanisms of development 2001) 2 3 4 54
  2. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. (PMID: 26687479) Oliviero G … Cagney G (Scientific reports 2015) 3 4 54
  3. BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase. (PMID: 26151332) Taherbhoy AM … Cochran AG (Nature communications 2015) 3 4 54
  4. Structure of the polycomb group protein PCGF1 in complex with BCOR reveals basis for binding selectivity of PCGF homologs. (PMID: 23523425) Junco SE … Kim CA (Structure (London, England : 1993) 2013) 3 4 54
  5. 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 54

Products for PCGF1 Gene

Sources for PCGF1 Gene