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Aliases for PHC3 Gene

Aliases for PHC3 Gene

  • Polyhomeotic Homolog 3 2 3 5
  • Early Development Regulatory Protein 3 3 4
  • Early Development Regulator 3 2 3
  • Homolog Of Polyhomeotic 3 3 4
  • Polyhomeotic Like 3 2 3
  • HPH3 3 4
  • EDR3 3 4
  • Polyhomeotic Homolog 3 (Drosophila) 2
  • Polyhomeotic Like 3 (Drosophila) 2
  • Polyhomeotic-Like Protein 3 3
  • PH3 4

External Ids for PHC3 Gene

Previous GeneCards Identifiers for PHC3 Gene

  • GC03M167082
  • GC03M170863
  • GC03M171216
  • GC03M171135
  • GC03M171297
  • GC03M169804

Summaries for PHC3 Gene

GeneCards Summary for PHC3 Gene

PHC3 (Polyhomeotic Homolog 3) is a Protein Coding gene. Among its related pathways are SUMOylation and Cellular Senescence. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is MIR3605.

UniProtKB/Swiss-Prot for PHC3 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.

Gene Wiki entry for PHC3 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHC3 Gene

Genomics for PHC3 Gene

Regulatory Elements for PHC3 Gene

Enhancers for PHC3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F170221 1.5 FANTOM5 ENCODE 3.2 -41.3 -41275 2.8 HDGF PKNOX1 ARNT CREB3L1 SIN3A ZNF2 YY1 SLC30A9 CBX5 ZNF143 ENSG00000239628 ENSG00000270096 PRKCI SEC62-AS1 RPL22P1 GPR160 ENSG00000270135 MYNN PHC3 LRRIQ4
GH03F170178 1.1 ENCODE 0.8 +1.2 1201 3.9 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 YY1 SP3 SP5 ZHX2 GPR160 PRKCI SEC62-AS1 ENSG00000270096 PHC3 GC03P170161
GH03F170189 1.1 Ensembl ENCODE 0.4 -7.8 -7752 1.0 CTCF ESRRA MAX ZNF384 ZNF2 RAD21 RFX5 HIC1 GTF3C2 ZNF664 GPR160 SEC62-AS1 PHC3 PRKCI
GH03F170206 0.7 ENCODE 0.3 -24.8 -24849 0.1 SOX13 GATAD2A ELF3 DRAP1 SAP130 FOXA3 CEBPG HMG20A THRB ZNF644 RNU7-32P GPR160 PRKCI PHC3
GH03F170203 0.7 ENCODE 0.3 -22.5 -22504 1.0 ELF3 ZNF680 ZNF384 ZIC2 ZFHX2 ZNF316 CEBPA ETV4 ZBTB33 EMSY GPR160 RNU7-32P PRKCI PHC3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHC3 on UCSC Golden Path with GeneCards custom track

Promoters for PHC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001379034 1049 3001 HDGF ATF1 PKNOX1 ARID4B SIN3A FEZF1 GLI4 DMAP1 ZNF48 YY1

Genomic Location for PHC3 Gene

Chromosome:
3
Start:
170,086,731 bp from pter
End:
170,181,749 bp from pter
Size:
95,019 bases
Orientation:
Minus strand

Genomic View for PHC3 Gene

Genes around PHC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHC3 Gene

Proteins for PHC3 Gene

  • Protein details for PHC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NDX5-PHC3_HUMAN
    Recommended name:
    Polyhomeotic-like protein 3
    Protein Accession:
    Q8NDX5
    Secondary Accessions:
    • A2RRP9
    • Q5HYF0
    • Q6NSG2
    • Q8NFT7
    • Q8NFZ1
    • Q8TBM2
    • Q9H971
    • Q9H9I4

    Protein attributes for PHC3 Gene

    Size:
    983 amino acids
    Molecular mass:
    106162 Da
    Quaternary structure:
    • Component of a PRC1-like complex.
    Miscellaneous:
    • The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different PRC1-like complexes.

    Three dimensional structures from OCA and Proteopedia for PHC3 Gene

    Alternative splice isoforms for PHC3 Gene

neXtProt entry for PHC3 Gene

Post-translational modifications for PHC3 Gene

  • Ubiquitination at Lys 222
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHC3 Gene

Domains & Families for PHC3 Gene

Gene Families for PHC3 Gene

Protein Domains for PHC3 Gene

Suggested Antigen Peptide Sequences for PHC3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8NDX5

UniProtKB/Swiss-Prot:

PHC3_HUMAN :
  • Contains 1 SAM (sterile alpha motif) domain.
  • Contains 1 FCS-type zinc finger.
Domain:
  • Contains 1 SAM (sterile alpha motif) domain.
Similarity:
  • Contains 1 FCS-type zinc finger.
genes like me logo Genes that share domains with PHC3: view

Function for PHC3 Gene

Molecular function for PHC3 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.

Gene Ontology (GO) - Molecular Function for PHC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHC3: view
genes like me logo Genes that share phenotypes with PHC3: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHC3 Gene

Localization for PHC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHC3 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 PHC3 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 2
lysosome 1

Gene Ontology (GO) - Cellular Components for PHC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 17001316
GO:0005654 nucleoplasm TAS --
GO:0015629 actin cytoskeleton IDA --
GO:0031519 PcG protein complex IDA 21282530
GO:0035102 PRC1 complex IDA 12167701
genes like me logo Genes that share ontologies with PHC3: view

Pathways & Interactions for PHC3 Gene

genes like me logo Genes that share pathways with PHC3: view

Gene Ontology (GO) - Biological Process for PHC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0016925 protein sumoylation TAS --
genes like me logo Genes that share ontologies with PHC3: view

No data available for SIGNOR curated interactions for PHC3 Gene

Transcripts for PHC3 Gene

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHC3 Gene

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

Relevant External Links for PHC3 Gene

GeneLoc Exon Structure for
PHC3
ECgene alternative splicing isoforms for
PHC3

Expression for PHC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHC3 Gene

This gene is overexpressed in CD8 Tcells (32.1), CD4 Tcells (10.3), and Blymphocyte (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHC3 Gene



Protein tissue co-expression partners for PHC3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHC3 Gene:

PHC3

SOURCE GeneReport for Unigene cluster for PHC3 Gene:

Hs.529592
genes like me logo Genes that share expression patterns with PHC3: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHC3 Gene

Orthologs for PHC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHC3 34 35
  • 99.87 (n)
dog
(Canis familiaris)
Mammalia PHC3 34 35
  • 95.37 (n)
cow
(Bos Taurus)
Mammalia PHC3 34 35
  • 94.07 (n)
rat
(Rattus norvegicus)
Mammalia Phc3 34
  • 89.13 (n)
mouse
(Mus musculus)
Mammalia Phc3 34 16 35
  • 88.94 (n)
oppossum
(Monodelphis domestica)
Mammalia PHC3 35
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHC3 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHC3 34 35
  • 79.04 (n)
lizard
(Anolis carolinensis)
Reptilia PHC3 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phc3 34
  • 65.8 (n)
zebrafish
(Danio rerio)
Actinopterygii phc3 35
  • 42 (a)
OneToMany
PHC3 (2 of 2) 35
  • 27 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta ph-d 35
  • 14 (a)
ManyToMany
ph-p 35
  • 14 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
OneToMany
Species where no ortholog for PHC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PHC3 Gene

ENSEMBL:
Gene Tree for PHC3 (if available)
TreeFam:
Gene Tree for PHC3 (if available)

Paralogs for PHC3 Gene

Variants for PHC3 Gene

Sequence variations from dbSNP and Humsavar for PHC3 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1052228 -- 170,095,566(-) AAAAA(C/G)ATTGT nc-transcript-variant, utr-variant-3-prime
rs1052229 -- 170,095,308(-) TCATG(A/T)TCCAG nc-transcript-variant, utr-variant-3-prime
rs10646670 -- 170,107,688(+) AAAAT(-/CA)CAGTT intron-variant
rs10714410 -- 170,116,910(+) TGTCT(-/A)AAAAA intron-variant
rs10804838 -- 170,139,219(+) CTTAA(C/T)AGATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PHC3 Gene

Variant ID Type Subtype PubMed ID
nsv7356 OTHER inversion 18451855
nsv1009884 CNV gain 25217958
esv3598619 CNV loss 21293372
esv2668922 CNV deletion 23128226
dgv8728n54 CNV loss 21841781

Variation tolerance for PHC3 Gene

Residual Variation Intolerance Score: 9.63% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.93; 49.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHC3 Gene

Disorders for PHC3 Gene

Relevant External Links for PHC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHC3

No disorders were found for PHC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHC3 Gene

Publications for PHC3 Gene

  1. Identification and characterisation of novel mammalian homologues of Drosophila polyhomeotic permits new insights into relationships between members of the polyhomeotic family. (PMID: 12384788) Tonkin E. … Strachan T. (Hum. Genet. 2002) 2 3 4 22 64
  2. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. (PMID: 12167701) Levine S.S. … Kingston R.E. (Mol. Cell. Biol. 2002) 2 3 4 64
  3. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 Complexes in mammalian cells. (PMID: 21282530) Vandamme J. … Angrand P.O. (Mol. Cell. Proteomics 2011) 3 4 64
  4. Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus. (PMID: 19636380) Maertens G.N. … Peters G. (PLoS ONE 2009) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for PHC3 Gene

Sources for PHC3 Gene

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