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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PHC3 Gene

protein-coding   GIFtS: 49
GCID: GC03M169804

polyhomeotic homolog 3 (Drosophila)

(Previous name: polyhomeotic like 3 (Drosophila) )
 Explore 6 diseases affiliated with
PHC3 via our new
 Human Malady Compendium 
Biological research products
for PHC3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Polyhomeotic Homolog 3 (Drosophila)1 2     Polyhomeotic Like 3 (Drosophila)1
EDR31 2 3     Early Development Regulator 32
HPH31 2     Polyhomeotic Like 32
Early Development Regulatory Protein 32 3     Polyhomeotic-Like Protein 32
Homolog Of Polyhomeotic 32 3     PH33
FLJ127291     HPH31 2
FLJ129671     

External Ids:    HGNC: 156821   Entrez Gene: 800122   Ensembl: ENSG000001738897   UniProtKB: Q8NDX53   

Export aliases for PHC3 gene to outside databases

Previous GC identifers: GC03M167082 GC03M170863 GC03M171216 GC03M171135 GC03M171297


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: PHC3_HUMAN, Q8NDX5
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 Wiki entry for PHC3


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PHC3 gene promoter:
         E4BP4   Meis-1b   C/EBPalpha   CHOP-10   AREB6   CREB   HEN1   deltaCREB   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPHC3 promoter sequence
   Search SABiosciences Chromatin IP Primers for PHC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PHC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.2   Ensembl cytogenetic band:  3q26.2   HGNC cytogenetic band: 3q26.32

PHC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHC3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M169804:  view genomic region     (about GC identifiers)

Start:
169,804,520 bp from pter      End:
169,899,537 bp from pter
Size:
95,018 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PHC3_HUMAN, Q8NDX5 (See protein sequence)
Recommended Name: Polyhomeotic-like protein 3  
Size: 983 amino acids; 106162 Da
Subunit: Component of a PRC1-like complex
Subcellular location: Nucleus
Miscellaneous: The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different
PRC1-like complexes
Secondary accessions: A2RRP9 Q5HYF0 Q6NSG2 Q8NFT7 Q8NFZ1 Q8TBM2 Q9H971 Q9H9I4
Alternative splicing: 7 isoforms:  Q8NDX5-1   Q8NDX5-2   Q8NDX5-3   Q8NDX5-4   Q8NDX5-5   Q8NDX5-6   Q8NDX5-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PHC3: NX_Q8NDX5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8NDX5

  • PHC3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_079223.3  
    ENSEMBL proteins: 
     ENSP00000418835   ENSP00000420271   ENSP00000420294   ENSP00000419089   ENSP00000417360  
     ENSP00000418039   ENSP00000417633   ENSP00000417860   ENSP00000419899   ENSP00000418266  
     ENSP00000420713   ENSP00000418377   ENSP00000420454   ENSP00000417540  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for PHC3

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0015629actin cytoskeleton IDA--
    GO:0031519PcG protein complex IDA--
    GO:0035102PRC1 complex IDA19636380


    PHC3 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for PHC3


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    PHC3 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR021129 SAM_type1
     IPR013761 SAM/pointed
     IPR001660 SAM
     IPR012313 Znf_FCS

    Graphical View of Domain Structure for InterPro Entry Q8NDX5

    ProtoNet protein and cluster: Q8NDX5

    1 Blocks protein family: IPB001660 Sterile alpha motif SAM

    UniProtKB/Swiss-Prot: PHC3_HUMAN, Q8NDX5
    Similarity: Contains 1 FCS-type zinc finger
    Similarity: Contains 1 SAM (sterile alpha motif) domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: PHC3_HUMAN, Q8NDX5
    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

    miRNA
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    8/175 QIAGEN miScript miRNA Assays for microRNAs that regulate PHC3 (see all 175):
    hsa-miR-124* hsa-miR-579 hsa-miR-640 hsa-miR-520f hsa-miR-106a hsa-miR-138-2* hsa-miR-519a hsa-miR-4275
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0008270zinc ion binding IEA--


    PHC3 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for PHC3:
     Decreased viability with pacli  Increased gamma-H2AX phosphory  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PHC3

    5/35 Interacting proteins for PHC3 (Q8NDX52, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 35)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RNF2Q994962, 3MINT-8010325 MINT-8010390 I2D: score=2 
    CBX2Q147812, 3MINT-8010325 MINT-8010390 I2D: score=1 
    BMI1P352262, 3MINT-8010325 I2D: score=2 
    PCGF2P352272, 3MINT-8010390 I2D: score=1 
    CBX4O002572MINT-8010325 MINT-8010390
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--


    PHC3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PHC3
    Search CenterWatch for drugs/clinical trials and news about PHC3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PHC3 gene: 
    NM_024947.3  

    Unigene Clusters for PHC3:

    Polyhomeotic homolog 3 (Drosophila)
    Hs.529592  [show with all ESTs], Hs.694467
    Unigene Representative Sequences: NM_024947, BC131773
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000484068 ENST00000494943(uc010hws.1 uc003fgl.2) ENST00000495893
    ENST00000467570(uc011bpq.1 uc011bpr.1) ENST00000486042 ENST00000484931
    ENST00000497171 ENST00000479467(uc003fgm.2) ENST00000466189 ENST00000475729
    ENST00000474275(uc003fgo.1) ENST00000472330 ENST00000465896 ENST00000497658(uc003fgp.3 uc003fgq.3)
    ENST00000481639 ENST00000491258 ENST00000490723

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    8/175 QIAGEN miScript miRNA Assays for microRNAs that regulate PHC3 (see all 175):
    hsa-miR-124* hsa-miR-579 hsa-miR-640 hsa-miR-520f hsa-miR-106a hsa-miR-138-2* hsa-miR-519a hsa-miR-4275
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    Additional cDNA sequence: BC131773.1 

    15 DOTS entries:

    DT.97837426  DT.97774911  DT.75180698  DT.422499  DT.40261189  DT.100747176  DT.120885288  DT.100736556 
    DT.91889250  DT.406575  DT.100746203  DT.120885286  DT.204393  DT.91660475  DT.91816052 

    24/129 AceView cDNA sequences (see all 129):

    BM722423 AV715725 CD678295 BE855466 AI042019 BC026001 AI275052 BE858742 
    AI560883 Z45269 AI680172 AI718462 BX279867 CB158879 AA278956 AI697425 
    AI418979 AW473428 BX955647 BC070164 BX647868 CA433106 BG779367 H95610 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PHC3    About this scheme

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


    ECgene alternative splicing isoforms for PHC3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PHC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGGGTCTGGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    PHC3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    TestisSeminiferous TubulesSecondary SpermatocyteGerm Cells, Male Gametocytes
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See PHC3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PHC3

    SOURCE GeneReport for Unigene clusters: Hs.529592 Hs.694467
        SABiosciences Expression via Pathway-Focused PCR Array including PHC3: 
              Polycomb & Trithorax Complexes in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHC3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for PHC3 gene from 3/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PHC31 polyhomeotic homolog 3 (Drosophila) 79.88(n)
    81.84(a)
      429159  XM_426714.3  XP_426714.3 
    lizard
    (Anolis carolinensis)
    Reptilia PHC36
    --
    73(a)
    1 ↔ 1
    3(7700925-7776389)
    zebrafish
    (Danio rerio)
    Actinopterygii phc31 polyhomeotic homolog 3 (Drosophila) 54.06(n)
    47.66(a)
      558094  XM_681265.3  XP_686357.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PHC3 gene
    PHC12  SAMD72  PHC22  SAMD112  
    16 SIMAP similar genes for PHC3 using alignment to 12 protein entries:     PHC3_HUMAN (see all proteins):
    HPH1    AURA2    SPATS2L    LOC100506792    SAMD13    TCF4
    CRCP    FKBP3    ZNF564    NF2    ZNF212    SAMD11
    CHID1    PHC1    ZNF74    PHC2

    PHC3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1506 NCBI SNPs in PHC3 are shown (see all 1506    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1414502951,2
    --169804890(+) CAGATC/TTGTTA 1 -- int10--------
    rs2017672221,2
    --169804975(+) GAGAA-/AATAATAA 1 -- int10--------
    rs1122543351,2
    C,--169805003(+) TCACATTCT/-  
            
    TTCTA
    1 -- int11Minor allele frequency- -:0.50CSA 2
    rs594706841,2
    C--169805007(+) ATTCT-/TTCT  
            
    ATAAA
    1 -- int10--------
    rs1453194141,2
    --169805086(+) ATCAGC/GGTGTG 1 -- int10--------
    rs1845483831,2
    --169805242(+) TTACAC/TTCTTT 1 -- int10--------
    rs790987321,2
    C,F,--169805447(+) AAACAA/GTATAA 1 -- ut311Minor allele frequency- G:0.03NA 120
    rs1881847131,2
    --169805460(+) AAATGA/CTCCTG 1 -- ut310--------
    rs1476409841,2
    --169805597(+) TTTAAC/TAGTTA 1 -- ut310--------
    rs774683551,2
    C,F,--169805832(+) CACCAA/CTCTAG 1 -- ut311Minor allele frequency- C:0.04EA 120

    HapMap Linkage Disequilibrium report for PHC3 (169804520 - 169899537 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for PHC3: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PHC3
    DNA2.0 Custom Variant and Variant Library Synthesis for PHC3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    PHC3 for disorders           About GeneDecksing

    6 diseases for PHC3:    About MalaCards
    acute chest syndrome    laryngeal squamous cell carcinoma    squamous cell carcinoma    laryngitis
    osteosarcoma    carcinoma

    1 disease from the University of Copenhagen DISEASES database for PHC3:
    Acute chest syndrome

    Export disorders for PHC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PHC3 gene, integrated from 9 sources (see all 24):
    (articles sorted by number of sources associating them with PHC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterisation of novel mammalian homologues of Drosophila polyhomeoticpermits new insights into relationships between members of the polyhomeotic family. (PubMed id 12384788)1, 2, 3, 9 Tonkin E....Strachan T. (2002)
    2. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. (PubMed id 12167701)1, 2, 3 Levine S.S....Kingston R.E. (2002)
    3. Several distinct polycomb complexes regulate and co-l ocalize on the INK4a tumor suppressor locus. (PubMed id 19636380)1, 2 Maertens G.N....Peters G. (2009)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Human polyhomeotic homolog 3 (PHC3) sterile alpha moti f (SAM) linker allows open-ended polymerization of PHC3 SAM. (PubMed id 22724443)1 Robinson A.K....Kim C.A. (2012)
    7. PCGF homologs, CBX proteins, and RYBP define functiona lly distinct PRC1 family complexes. (PubMed id 22325352)1 Gao Z....Reinberg D. (2012)
    8. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 Complexes in mammalian cells. (PubMed id 21282530)2 Vandamme J.... Angrand P.O. (2011)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    10. Polycomb group molecule PHC3 regulates polycomb compl ex composition and prognosis of osteosarcoma. (PubMed id 20491773)1 Iwata S....Kamijo T. (2010)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 80012 HGNC: 15682 AceView: PHC3 Ensembl:ENSG00000173889 euGenes: HUgn80012
    ECgene: PHC3 H-InvDB: PHC3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for PHC3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for PHC3 gene:
    Search GeneIP for patents involving PHC3

    GeneCards and IP:
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