Aliases for PHC3 Gene

Aliases for PHC3 Gene

  • Polyhomeotic Homolog 3 2 3 5
  • EDR3 2 3 4
  • HPH3 2 3 4
  • Early Development Regulatory Protein 3 3 4
  • Early Development Regulator 3 2 3
  • Polyhomeotic-Like Protein 3 3 4
  • Homolog Of Polyhomeotic 3 3 4
  • Polyhomeotic Like 3 2 3
  • Polyhomeotic Homolog 3 (Drosophila) 2
  • Polyhomeotic Like 3 (Drosophila) 2
  • FLJ12967 2
  • FLJ12729 2
  • PHC3 5
  • 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. Diseases associated with PHC3 include Myasthenic Syndrome, Congenital, 7, Presynaptic and Hyperoxaluria, Primary, Type Iii. Among its related pathways are SUMOylation and Cellular Senescence (REACTOME). Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is PHC2.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHC3 Gene

Genomics for PHC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PHC3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHC3

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

Genomic Locations for PHC3 Gene

Latest Assembly
chr3:170,086,732-170,181,752
(GRCh38/hg38)
Size:
95,021 bases
Orientation:
Minus strand

Previous Assembly
chr3:169,805,372-169,899,521
(GRCh37/hg19 by Entrez Gene)
Size:
94,150 bases
Orientation:
Minus strand

chr3:169,804,520-169,899,537
(GRCh37/hg19 by Ensembl)
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

  • Glycosylation at Thr283
  • Ubiquitination at Lys222
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

No data available for DME Specific Peptides for PHC3 Gene

Domains & Families for PHC3 Gene

Gene Families for PHC3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHC3 Gene

InterPro:
Blocks:
  • Sterile alpha motif SAM

Suggested Antigen Peptide Sequences for PHC3 Gene

GenScript: Design optimal peptide antigens:
  • PHC3 protein (A5YM43_HUMAN)
  • cDNA FLJ57195, highly similar to Polyhomeotic-like protein 3 (B4DTC4_HUMAN)
  • Homolog of polyhomeotic 3 (PHC3_HUMAN)
genes like me logo Genes that share domains with PHC3: view

No data available for Graphical View of Domain Structure and 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:0003682 chromatin binding IBA 21873635
GO:0005515 protein binding IPI 25416956
GO:0008270 zinc ion binding IEA --
GO:0042393 histone binding IBA 21873635
genes like me logo Genes that share ontologies with PHC3: view
genes like me logo Genes that share phenotypes with PHC3: view

Animal Models for PHC3 Gene

MGI Knock Outs for PHC3:
  • Phc3 Phc3<tm2b(KOMP)Wtsi>

Inhibitory RNAs for research

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

Clone products for research

  • Addgene plasmids for PHC3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
cytoskeleton 3
cytosol 3
plasma membrane 2
extracellular 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 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 IBA,IDA 17001316
GO:0005654 nucleoplasm TAS --
GO:0031519 PcG protein complex IDA 21282530
GO:0035102 PRC1 complex IBA,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:0045892 negative regulation of transcription, DNA-templated IBA 21873635
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

mRNA/cDNA for PHC3 Gene

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

Inhibitory RNAs for research

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

Clone products for research

  • 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

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, MaxQB, and MOPED for PHC3 Gene



Protein tissue co-expression partners for PHC3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHC3

SOURCE GeneReport for Unigene cluster for PHC3 Gene:

Hs.529592

Evidence on tissue expression from TISSUES for PHC3 Gene

  • Nervous system(4.7)
  • Liver(4.6)
  • Intestine(3)
  • Heart(2.8)
  • Muscle(2.8)
  • Kidney(2.8)
  • Skin(2.6)
  • Lung(2.5)
  • Eye(2.4)
  • Stomach(2.4)
  • Blood(2.3)
  • Spleen(2.2)
  • Bone marrow(2.2)
  • Thyroid gland(2.1)
genes like me logo Genes that share expression patterns with PHC3: view

Primer products for research

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 29 30
  • 99.87 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PHC3 29 30
  • 95.37 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PHC3 29 30
  • 94.07 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Phc3 29
  • 89.13 (n)
Mouse
(Mus musculus)
Mammalia Phc3 29 16 30
  • 88.94 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PHC3 30
  • 87 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PHC3 30
  • 58 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PHC3 29 30
  • 79.04 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PHC3 30
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia phc3 29
  • 65.8 (n)
Zebrafish
(Danio rerio)
Actinopterygii phc3 30
  • 42 (a)
OneToMany
PHC3 (2 of 2) 30
  • 27 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta ph-d 30
  • 14 (a)
ManyToMany
ph-p 30
  • 14 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 28 (a)
OneToMany
Species where no ortholog for PHC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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
Alliance of Genome Resources:
Additional Orthologs for PHC3

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

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PHC3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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
Leiden Open Variation Database (LOVD)
PHC3

SNP Genotyping and Copy Number Assays for research

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 PHC3 Gene

Disorders for PHC3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PHC3 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search PHC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PHC3

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

No data available for 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
  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
  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
  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
  5. 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

Products for PHC3 Gene

Sources for PHC3 Gene