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    PHC3 polyhomeotic homolog 3 [ Homo sapiens (human) ]

    Gene ID: 80012, updated on 19-May-2018
    Official Symbol
    PHC3provided by HGNC
    Official Full Name
    polyhomeotic homolog 3provided by HGNC
    Primary source
    HGNC:HGNC:15682
    See related
    Ensembl:ENSG00000173889 Vega:OTTHUMG00000158777
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EDR3; HPH3
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.6), thyroid (RPKM 6.5) and 25 other tissues See more
    Orthologs
    See PHC3 in Genome Data Viewer
    Location:
    3q26.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (170087580..170181752, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (169805368..169899537, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene lysine methyltransferase 5A pseudogene Neighboring gene G protein-coupled receptor 160 Neighboring gene RNA, U4 small nuclear 38, pseudogene Neighboring gene uncharacterized LOC105374209 Neighboring gene RNA, U6 small nuclear 315, pseudogene Neighboring gene RNA, U7 small nuclear 32 pseudogene Neighboring gene protein kinase C iota Neighboring gene SKI like proto-oncogene

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Cellular Senescence, organism-specific biosystem (from REACTOME)
      Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • Oxidative Stress Induced Senescence, organism-specific biosystem (from REACTOME)
      Oxidative Stress Induced Senescence, organism-specific biosystemOxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al...
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
    • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
      SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
    • SUMOylation, organism-specific biosystem (from REACTOME)
      SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
    • SUMOylation of DNA damage response and repair proteins, organism-specific biosystem (from REACTOME)
      SUMOylation of DNA damage response and repair proteins, organism-specific biosystemSeveral factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferr...
    • SUMOylation of RNA binding proteins, organism-specific biosystem (from REACTOME)
      SUMOylation of RNA binding proteins, organism-specific biosystemSUMOylation of RNA-binding proteins (Li et al. 2004, reviewed in Filosa et al. 2013) alters their interactions with nucleic acids and with proteins. Whereas SUMOylation of HNRNPC decreases its affini...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ12729, FLJ12967, MGC88144, DKFZp313K1221

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of G0 to G1 transition TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    PRC1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    PcG protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    polyhomeotic-like protein 3
    Names
    early development regulator 3
    early development regulatory protein 3
    homolog of polyhomeotic 3
    polyhomeotic like 3

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001308116.1NP_001295045.1  polyhomeotic-like protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001295045.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC008040, AI042019, AJ320486, AK304411
      Consensus CDS
      CCDS77858.1
      UniProtKB/Swiss-Prot
      Q8NDX5
      UniProtKB/TrEMBL
      B4E2T1
      Related
      ENSP00000420271.1, OTTHUMP00000213464, ENST00000494943.5, OTTHUMT00000352182
      Conserved Domains (2) summary
      cd09577
      Location:914982
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:916983
      SAM; Sterile alpha motif
    2. NM_024947.3NP_079223.3  polyhomeotic-like protein 3 isoform 1

      See identical proteins and their annotated locations for NP_079223.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC008040, AI042019, BC026001, BC131772, BP200133
      Consensus CDS
      CCDS46952.1
      UniProtKB/Swiss-Prot
      Q8NDX5
      Related
      ENSP00000420294.1, OTTHUMP00000213468, ENST00000495893.6, OTTHUMT00000352186
      Conserved Domains (2) summary
      cd09577
      Location:926994
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:928995
      SAM; Sterile alpha motif

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

      Range
      170087580..170181752 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007236.2XP_016862725.1  polyhomeotic-like protein 3 isoform X4

    2. XM_011513187.3XP_011511489.1  polyhomeotic-like protein 3 isoform X6

      Conserved Domains (2) summary
      cd09577
      Location:893961
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:895962
      SAM; Sterile alpha motif
    3. XM_011513186.3XP_011511488.1  polyhomeotic-like protein 3 isoform X5

      Conserved Domains (2) summary
      cd09577
      Location:909977
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:911978
      SAM; Sterile alpha motif
    4. XM_005247789.3XP_005247846.1  polyhomeotic-like protein 3 isoform X1

      Conserved Domains (2) summary
      cd09577
      Location:9421010
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:9441011
      SAM; Sterile alpha motif
    5. XM_017007235.2XP_016862724.1  polyhomeotic-like protein 3 isoform X2

    6. XM_017007238.2XP_016862727.1  polyhomeotic-like protein 3 isoform X10

    7. XM_006713756.3XP_006713819.1  polyhomeotic-like protein 3 isoform X9

      Conserved Domains (2) summary
      cd09577
      Location:856924
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:858925
      SAM; Sterile alpha motif
    8. XM_017007237.2XP_016862726.1  polyhomeotic-like protein 3 isoform X8

    9. XM_011513188.3XP_011511490.1  polyhomeotic-like protein 3 isoform X7

      Conserved Domains (2) summary
      cd09577
      Location:889957
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:891958
      SAM; Sterile alpha motif
    10. XM_006713753.2XP_006713816.1  polyhomeotic-like protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006713816.1

      Conserved Domains (2) summary
      cd09577
      Location:930998
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:932999
      SAM; Sterile alpha motif
    11. XM_006713754.4XP_006713817.1  polyhomeotic-like protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006713817.1

      Conserved Domains (2) summary
      cd09577
      Location:930998
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:932999
      SAM; Sterile alpha motif
    12. XM_017007239.2XP_016862728.1  polyhomeotic-like protein 3 isoform X12

    13. XM_005247791.4XP_005247848.1  polyhomeotic-like protein 3 isoform X11

      Conserved Domains (1) summary
      pfam09770
      Location:423518
      PAT1; Topoisomerase II-associated protein PAT1
    14. XM_011513189.3XP_011511491.1  polyhomeotic-like protein 3 isoform X13

      UniProtKB/TrEMBL
      E7EX82
      Related
      ENSP00000419089.1, OTTHUMP00000213462, ENST00000467570.5
      Conserved Domains (1) summary
      pfam09770
      Location:370465
      PAT1; Topoisomerase II-associated protein PAT1
    15. XM_005247793.3XP_005247850.1  polyhomeotic-like protein 3 isoform X14

      Conserved Domains (1) summary
      pfam09770
      Location:423518
      PAT1; Topoisomerase II-associated protein PAT1
    16. XM_006713757.4XP_006713820.1  polyhomeotic-like protein 3 isoform X15

      Conserved Domains (1) summary
      pfam09770
      Location:423518
      PAT1; Topoisomerase II-associated protein PAT1

    RNA

    1. XR_001740274.2 RNA Sequence

    2. XR_001740275.2 RNA Sequence

    3. XR_241509.4 RNA Sequence

    4. XR_924181.3 RNA Sequence

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