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    PHC3 polyhomeotic homolog 3 [ Homo sapiens (human) ]

    Gene ID: 80012, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PHC3provided by HGNC
    Official Full Name
    polyhomeotic homolog 3provided by HGNC
    Primary source
    HGNC:HGNC:15682
    See related
    Ensembl:ENSG00000173889 MIM:620031; AllianceGenome:HGNC:15682
    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
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of PRC1 complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.6), thyroid (RPKM 6.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHC3 in Genome Data Viewer
    Location:
    3q26.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (170087584..170181733, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172872255..172966417, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (169805372..169899521, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169779520-169780041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169780042-169780562 Neighboring gene G protein-coupled receptor 160 Neighboring gene MPRA-validated peak4913 silencer Neighboring gene uncharacterized LOC124909456 Neighboring gene KMT5A pseudogene 3 Neighboring gene MPRA-validated peak4915 silencer Neighboring gene uncharacterized LOC105374209 Neighboring gene RNA, U6 small nuclear 315, pseudogene Neighboring gene RNA, U7 small nuclear 32 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14883 Neighboring gene protein kinase C iota Neighboring gene Sharpr-MPRA regulatory region 5121 Neighboring gene MPRA-validated peak4916 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:170079595-170080095 Neighboring gene MPRA-validated peak4917 silencer Neighboring gene SKI like proto-oncogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Mutational analysis of Polycomb genes in solid tumours identifies PHC3 amplification as a possible cancer-driving genetic alteration. Crea F, et al. Br J Cancer, 2013 Sep 17. PMID 23942079, Free PMC Article
    2. Human polyhomeotic homolog 3 (PHC3) sterile alpha motif (SAM) linker allows open-ended polymerization of PHC3 SAM. Robinson AK, et al. Biochemistry, 2012 Jul 10. PMID 22724443, Free PMC Article
    3. Polycomb group molecule PHC3 regulates polycomb complex composition and prognosis of osteosarcoma. Iwata S, et al. Cancer Sci, 2010 Jul. PMID 20491773
    4. Identification and characterisation of novel mammalian homologues of Drosophila polyhomeoticpermits new insights into relationships between members of the polyhomeotic family. Tonkin E, et al. Hum Genet, 2002 Oct. PMID 12384788
    5. Polycomb genes are associated with response to imatinib in chronic myeloid leukemia. Crea F, et al. Epigenomics, 2015 Aug. PMID 26343356, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of circ-PHC3 enhances ovarian cancer progression via regulation of the miR-497-5p/SOX9 pathway.
      Title: Expression of circ-PHC3 enhances ovarian cancer progression via regulation of the miR-497-5p/SOX9 pathway.
    2. Data show that polycomb-group proteins BMI1, PHC3, CBX6 and CBX7 expression was significantly increased during imatinib treatment.
      Title: Polycomb genes are associated with response to imatinib in chronic myeloid leukemia.
    3. PHC3 amplification may emerge as a biomarker in cancer.
      Title: Mutational analysis of Polycomb genes in solid tumours identifies PHC3 amplification as a possible cancer-driving genetic alteration.
    4. SAM linker controls PHC3 SAM polymerization
      Title: Human polyhomeotic homolog 3 (PHC3) sterile alpha motif (SAM) linker allows open-ended polymerization of PHC3 SAM.
    5. PHC3 is a tumor suppressor in osteosarcoma cells abd its suppression may be caused by modification of polycomb repressive complex 1 in cancer cells.
      Title: Polycomb group molecule PHC3 regulates polycomb complex composition and prognosis of osteosarcoma.
    6. loss of PHC3 may favor tumorigenesis by potentially disrupting the ability of cells to remain in G(0)
      Title: PHC3, a component of the hPRC-H complex, associates with E2F6 during G0 and is lost in osteosarcoma tumors.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12729, FLJ12967, MGC88144, DKFZp313K1221

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of PRC1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PRC1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of PcG protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    polyhomeotic-like protein 3
    Names
    early development regulator 3
    early development regulatory protein 3
    homolog of polyhomeotic 3
    polyhomeotic like 3

    NCBI Reference Sequences (RefSeq)

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    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_001308116.2 → NP_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
      A2RRP9, Q5HYF0, Q6NSG2, Q8NDX5, Q8NFT7, Q8NFZ1, Q8TBM2, Q9H971, Q9H9I4
      UniProtKB/TrEMBL
      A5YM43
      Related
      ENSP00000420271.1, ENST00000494943.5
      Conserved Domains (2) summary
      cd09577
      Location:914 → 982
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:916 → 983
      SAM; Sterile alpha motif

    2. NM_024947.4 → NP_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, BC026001, BC131772, BP200133
      Consensus CDS
      CCDS46952.1
      UniProtKB/TrEMBL
      A5YM43
      Related
      ENSP00000420294.1, ENST00000495893.7
      Conserved Domains (2) summary
      cd09577
      Location:926 → 994
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:928 → 995
      SAM; Sterile alpha motif

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      170087584..170181733 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448988.1 → XP_047304944.1  polyhomeotic-like protein 3 isoform X12

    2. XM_047448987.1 → XP_047304943.1  polyhomeotic-like protein 3 isoform X10

    3. XM_047448986.1 → XP_047304942.1  polyhomeotic-like protein 3 isoform X8

    4. XM_047448984.1 → XP_047304940.1  polyhomeotic-like protein 3 isoform X6

    5. XM_047448983.1 → XP_047304939.1  polyhomeotic-like protein 3 isoform X4

    6. XM_017007235.3 → XP_016862724.1  polyhomeotic-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A5YM43

    7. XM_017007238.3 → XP_016862727.1  polyhomeotic-like protein 3 isoform X11

      UniProtKB/TrEMBL
      A5YM43

    8. XM_006713756.4 → XP_006713819.1  polyhomeotic-like protein 3 isoform X9

      UniProtKB/TrEMBL
      A5YM43
      Conserved Domains (2) summary
      cd09577
      Location:856 → 924
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:858 → 925
      SAM; Sterile alpha motif

    9. XM_017007237.3 → XP_016862726.1  polyhomeotic-like protein 3 isoform X7

      UniProtKB/TrEMBL
      A5YM43

    10. XM_011513188.4 → XP_011511490.1  polyhomeotic-like protein 3 isoform X5

      UniProtKB/TrEMBL
      A5YM43
      Conserved Domains (2) summary
      cd09577
      Location:889 → 957
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:891 → 958
      SAM; Sterile alpha motif

    11. XM_005247789.4 → XP_005247846.1  polyhomeotic-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A5YM43
      Conserved Domains (2) summary
      cd09577
      Location:942 → 1010
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:944 → 1011
      SAM; Sterile alpha motif

    12. XM_006713753.3 → XP_006713816.1  polyhomeotic-like protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006713816.1

      UniProtKB/TrEMBL
      A5YM43
      Conserved Domains (2) summary
      cd09577
      Location:930 → 998
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:932 → 999
      SAM; Sterile alpha motif

    13. XM_006713754.5 → XP_006713817.1  polyhomeotic-like protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006713817.1

      UniProtKB/TrEMBL
      A5YM43
      Conserved Domains (2) summary
      cd09577
      Location:930 → 998
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:932 → 999
      SAM; Sterile alpha motif

    14. XM_047448982.1 → XP_047304938.1  polyhomeotic-like protein 3 isoform X3

    15. XM_047448990.1 → XP_047304946.1  polyhomeotic-like protein 3 isoform X16

    16. XM_047448989.1 → XP_047304945.1  polyhomeotic-like protein 3 isoform X14

    17. XM_005247791.5 → XP_005247848.1  polyhomeotic-like protein 3 isoform X13

      UniProtKB/TrEMBL
      B4E2T1
      Conserved Domains (1) summary
      pfam09770
      Location:423 → 518
      PAT1; Topoisomerase II-associated protein PAT1

    18. XM_011513189.4 → XP_011511491.1  polyhomeotic-like protein 3 isoform X15

      UniProtKB/TrEMBL
      B4E2T1, E7EX82
      Related
      ENSP00000419089.1, ENST00000467570.5
      Conserved Domains (1) summary
      pfam09770
      Location:370 → 465
      PAT1; Topoisomerase II-associated protein PAT1

    19. XM_005247793.4 → XP_005247850.1  polyhomeotic-like protein 3 isoform X17

      Conserved Domains (1) summary
      pfam09770
      Location:423 → 518
      PAT1; Topoisomerase II-associated protein PAT1

    20. XM_047448991.1 → XP_047304947.1  polyhomeotic-like protein 3 isoform X19

    21. XM_006713757.5 → XP_006713820.1  polyhomeotic-like protein 3 isoform X18

      Conserved Domains (1) summary
      pfam09770
      Location:423 → 518
      PAT1; Topoisomerase II-associated protein PAT1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      172872255..172966417 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347955.1 → XP_054203930.1  polyhomeotic-like protein 3 isoform X12

    2. XM_054347953.1 → XP_054203928.1  polyhomeotic-like protein 3 isoform X10

    3. XM_054347951.1 → XP_054203926.1  polyhomeotic-like protein 3 isoform X8

    4. XM_054347949.1 → XP_054203924.1  polyhomeotic-like protein 3 isoform X6

    5. XM_054347947.1 → XP_054203922.1  polyhomeotic-like protein 3 isoform X4

    6. XM_054347943.1 → XP_054203918.1  polyhomeotic-like protein 3 isoform X2

    7. XM_054347954.1 → XP_054203929.1  polyhomeotic-like protein 3 isoform X11

    8. XM_054347952.1 → XP_054203927.1  polyhomeotic-like protein 3 isoform X9

    9. XM_054347950.1 → XP_054203925.1  polyhomeotic-like protein 3 isoform X7

    10. XM_054347948.1 → XP_054203923.1  polyhomeotic-like protein 3 isoform X5

    11. XM_054347942.1 → XP_054203917.1  polyhomeotic-like protein 3 isoform X1

    12. XM_054347944.1 → XP_054203919.1  polyhomeotic-like protein 3 isoform X3

    13. XM_054347945.1 → XP_054203920.1  polyhomeotic-like protein 3 isoform X3

    14. XM_054347946.1 → XP_054203921.1  polyhomeotic-like protein 3 isoform X3

    15. XM_054347958.1 → XP_054203933.1  polyhomeotic-like protein 3 isoform X20

    16. XM_054347960.1 → XP_054203935.1  polyhomeotic-like protein 3 isoform X16

    17. XM_054347957.1 → XP_054203932.1  polyhomeotic-like protein 3 isoform X14

    18. XM_054347956.1 → XP_054203931.1  polyhomeotic-like protein 3 isoform X13

    19. XM_054347959.1 → XP_054203934.1  polyhomeotic-like protein 3 isoform X15

      UniProtKB/TrEMBL
      E7EX82

    20. XM_054347961.1 → XP_054203936.1  polyhomeotic-like protein 3 isoform X17

    21. XM_054347963.1 → XP_054203938.1  polyhomeotic-like protein 3 isoform X19

    22. XM_054347962.1 → XP_054203937.1  polyhomeotic-like protein 3 isoform X18

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NDX5.1 GenPept UniProtKB/Swiss-Prot:Q8NDX5

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