Free for academic non-profit institutions. Other users need a Commercial license

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 Cellular Senescence (REACTOME) and SUMOylation. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is PHC2.

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

Additional gene information for PHC3 Gene

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

Genomics for PHC3 Gene

GeneHancer (GH) Regulatory Elements for PHC3 Gene

Promoters and enhancers for PHC3 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
GH03J170178 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 661.5 +1.2 1200 3.9 HDGF PKNOX1 CLOCK SMAD1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZBTB7B PHC3 GPR160 MYNN SEC62-AS1 RPL22L1 GC03P170161
GH03J169657 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 51.9 +518.1 518081 12.4 PKNOX1 FOXA2 ARNT ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B MECOM MYNN PHC3 SEC62-AS1 ENSG00000270096 PRKCI ENSG00000239628 RPL22P1 SLC7A14 ACTRT3
GH03J169771 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 37 +408.7 408669 3.4 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MYNN PIR36992 TRV-AAC1-1 PHC3 SEC62-AS1 PRKCI CLDN11 LRRC34 ENSG00000270096 ENSG00000269889
GH03J170907 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 29.2 -727.1 -727067 2.9 CLOCK MLX ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B CBX5 ZNF548 EIF5A2 PHC3 SEC62-AS1 RPL22L1 PRKCI GC03M170953
GH03J169762 Promoter/Enhancer 1.8 Ensembl ENCODE 31.4 +417.3 417330 3.1 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B ENSG00000277925 GC03M169767 GC03M169768 GC03M169769 TERC MYNN SEC62-AS1 PHC3 ENSG00000239628 PRKCI
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHC3 gene promoter:
  • CHOP-10
  • C/EBPalpha
  • AREB6
  • deltaCREB
  • CREB
  • HEN1
  • Meis-1
  • Meis-1a
  • Meis-1b
  • E4BP4

Genomic Locations for PHC3 Gene

Genomic Locations for PHC3 Gene
chr3:170,086,731-170,181,749
(GRCh38/hg38)
Size:
95,019 bases
Orientation:
Minus strand
chr3:169,804,520-169,899,537
(GRCh37/hg19)
Size:
95,018 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 Lys222
  • 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

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

No data available for UniProtKB/Swiss-Prot for PHC3 Gene

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.

Phenotypes From GWAS Catalog for PHC3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHC3

Clone Products

  • Addgene plasmids for PHC3

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

Subcellular locations from the

Human Protein Atlas (HPA)

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: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:0070317 negative regulation of G0 to G1 transition TAS --
genes like me logo Genes that share ontologies with PHC3: view

No data available for SIGNOR curated interactions for PHC3 Gene

Drugs & Compounds for PHC3 Gene

No Compound Related Data Available

Transcripts for PHC3 Gene

Unigene Clusters for PHC3 Gene

Polyhomeotic homolog 3 (Drosophila):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHC3

Clone Products

  • Addgene plasmids for PHC3

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 CGAP 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, 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

Evidence on tissue expression from TISSUES for PHC3 Gene

  • Liver(4.5)
  • Nervous system(4.5)
  • Intestine(2.4)
  • Kidney(2.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with PHC3: 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 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 33
  • 99.87 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PHC3 34 33
  • 95.37 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PHC3 34 33
  • 94.07 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phc3 33
  • 89.13 (n)
mouse
(Mus musculus)
Mammalia Phc3 16 34 33
  • 88.94 (n)
oppossum
(Monodelphis domestica)
Mammalia PHC3 34
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHC3 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHC3 34 33
  • 79.04 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHC3 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phc3 33
  • 65.8 (n)
zebrafish
(Danio rerio)
Actinopterygii phc3 34
  • 42 (a)
OneToMany
PHC3 (2 of 2) 34
  • 27 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta ph-d 34
  • 14 (a)
ManyToMany
ph-p 34
  • 14 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for PHC3: view image

Paralogs for PHC3 Gene

Paralogs for PHC3 Gene

(22) SIMAP similar genes for PHC3 Gene using alignment to 12 proteins:

  • PHC3_HUMAN
  • A5YM43_HUMAN
  • B4DTC4_HUMAN
  • C9J6H0_HUMAN
  • C9J6P8_HUMAN
  • C9JAU4_HUMAN
  • C9JYH7_HUMAN
  • E7EX82_HUMAN
  • F8WDA4_HUMAN
  • G5E9U7_HUMAN
  • H7C4H9_HUMAN
  • H7C528_HUMAN
genes like me logo Genes that share paralogs with PHC3: view

Variants for PHC3 Gene

Sequence variations from dbSNP and Humsavar for PHC3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000002200 -- 170,168,541(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000003413 -- 170,124,467(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000071008 -- 170,136,302(-) A/T intron_variant
rs1000147933 -- 170,131,602(-) G/C intron_variant
rs1000148931 -- 170,161,124(-) A/G 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)

Additional Variant Information for PHC3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PHC3 Gene

Additional Disease Information for 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 polyhomeoticpermits new insights into relationships between members of the polyhomeotic family. (PMID: 12384788) Tonkin E … Strachan T (Human genetics 2002) 2 3 4 22 58
  2. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. (PMID: 12167701) Levine SS … Kingston RE (Molecular and cellular biology 2002) 2 3 4 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. Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus. (PMID: 19636380) Maertens GN … Peters G (PloS one 2009) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for PHC3 Gene

  • Addgene plasmids for PHC3

Sources for PHC3 Gene

Content
Loading form....