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    PHC2 polyhomeotic homolog 2 [ Homo sapiens (human) ]

    Gene ID: 1912, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PHC2provided by HGNC
    Official Full Name
    polyhomeotic homolog 2provided by HGNC
    Primary source
    HGNC:HGNC:3183
    See related
    Ensembl:ENSG00000134686 MIM:602979; AllianceGenome:HGNC:3183
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PH2; EDR2; HPH2
    Summary
    In Drosophila melanogaster, the 'Polycomb' group (PcG) of genes are part of a cellular memory system that is responsible for the stable inheritance of gene activity. PcG proteins form a large multimeric, chromatin-associated protein complex. The protein encoded by this gene has homology to the Drosophila PcG protein 'polyhomeotic' (Ph) and is known to heterodimerize with EDR1 and colocalize with BMI1 in interphase nuclei of human cells. The specific function in human cells has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 13.8), endometrium (RPKM 13.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHC2 in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33323626..33431095, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33185234..33292697, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33789227..33896696, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene antizyme inhibitor 2 Neighboring gene zinc finger protein 362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33628780-33629512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33629513-33630245 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7027 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7034 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 617 Neighboring gene tripartite motif containing 62 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 619 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685009-33685609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685744-33686528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33709758-33710342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 622 Neighboring gene Sharpr-MPRA regulatory region 4113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33729134-33729634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33734235-33734736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33760897-33761407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33764984-33765933 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:33764372-33764552 Neighboring gene MPRA-validated peak168 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33795184-33795684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33795685-33796185 Neighboring gene alpha 1,3-galactosyltransferase 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33807831-33808439 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33814757-33815686 Neighboring gene NANOG hESC enhancer GRCh37_chr1:33821846-33822366 Neighboring gene RN7SK pseudogene 16 Neighboring gene microRNA 3605 Neighboring gene VISTA enhancer hs1388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33832336-33833239 Neighboring gene PHC2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33920469-33920968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33933768-33934294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33934295-33934819 Neighboring gene Sharpr-MPRA regulatory region 11456 Neighboring gene toll like receptor 12, pseudogene Neighboring gene zinc finger and SCAN domain containing 20

    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. BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization. Gray F, et al. Nat Commun, 2016 Nov 9. PMID 27827373, Free PMC Article
    2. SIAH-1 interacts with mammalian polyhomeotic homologues HPH2 and affects its stability via the ubiquitin-proteasome pathway. Wu H, et al. Biochem Biophys Res Commun, 2010 Jul 2. PMID 20471960
    3. Identification and characterization of interactions between the vertebrate polycomb-group protein BMI1 and human homologs of polyhomeotic. Gunster MJ, et al. Mol Cell Biol, 1997 Apr. PMID 9121482, Free PMC Article
    4. Role of Bmi1 in H2A ubiquitylation and Hox gene silencing. Wei J, et al. J Biol Chem, 2006 Aug 11. PMID 16751658
    5. 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

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interaction of BMI1 with polyhomeotic protein PHC2 and homo-oligomerization via ubiquitin-like domain are necessary for H2A ubiquitination activity of PRC1 and for clonogenic potential of U2OS cells.
      Title: BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization.
    2. these results propose a novel role of SIAH-1 in regulating the expression level of HPH2 through the ubiquitin-proteasome pathway.
      Title: SIAH-1 interacts with mammalian polyhomeotic homologues HPH2 and affects its stability via the ubiquitin-proteasome pathway.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    • MGC163502

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    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 
    part_of heterochromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 2
    Names
    early development regulator 2 (homolog of polyhomeotic 2)
    early development regulatory protein 2
    polyhomeotic 2
    polyhomeotic-like 2

    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_001330488.2 → NP_001317417.1  polyhomeotic-like protein 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS81298.1
      UniProtKB/TrEMBL
      A0A0A0MSI2, B7ZLY0
      Related
      ENSP00000389436.2, ENST00000431992.6
      Conserved Domains (4) summary
      cd09577
      Location:761 → 829
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:193 → 520
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:642 → 761
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
      cl41773
      Location:39 → 224
      SP1-4_N; N-terminal domain of transcription factor Specificity Proteins (SP) 1-4

    2. NM_001385109.1 → NP_001372038.1  polyhomeotic-like protein 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS90911.1
      UniProtKB/TrEMBL
      B7ZLY0
      Related
      ENSP00000507877.1, ENST00000683057.1
      Conserved Domains (3) summary
      cd09577
      Location:790 → 858
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:131 → 549
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:671 → 790
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    3. NM_001385112.1 → NP_001372041.1  polyhomeotic-like protein 2 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS90912.1
      UniProtKB/TrEMBL
      A0A994J5J9, B7ZLY0
      Related
      ENSP00000516348.1, ENST00000706360.1
      Conserved Domains (3) summary
      cd09577
      Location:812 → 880
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:116 → 571
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:693 → 812
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    4. NM_001385119.1 → NP_001372048.1  polyhomeotic-like protein 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS90911.1
      UniProtKB/TrEMBL
      B7ZLY0
      Conserved Domains (3) summary
      cd09577
      Location:790 → 858
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:131 → 549
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:671 → 790
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    5. NM_001385120.1 → NP_001372049.1  polyhomeotic-like protein 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS90911.1
      UniProtKB/TrEMBL
      B7ZLY0
      Conserved Domains (3) summary
      cd09577
      Location:790 → 858
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:131 → 549
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:671 → 790
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    6. NM_001385121.1 → NP_001372050.1  polyhomeotic-like protein 2 isoform f

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      UniProtKB/TrEMBL
      B7ZLY0
      Conserved Domains (3) summary
      cd09577
      Location:788 → 856
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:131 → 547
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:669 → 788
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    7. NM_001385122.1 → NP_001372051.1  polyhomeotic-like protein 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS81298.1
      UniProtKB/TrEMBL
      A0A0A0MSI2, B7ZLY0
      Related
      ENSP00000362521.4, ENST00000373422.8
      Conserved Domains (4) summary
      cd09577
      Location:761 → 829
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:193 → 520
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:642 → 761
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
      cl41773
      Location:39 → 224
      SP1-4_N; N-terminal domain of transcription factor Specificity Proteins (SP) 1-4

    8. NM_001385123.1 → NP_001372052.1  polyhomeotic-like protein 2 isoform g

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      UniProtKB/TrEMBL
      B4DG61
      Conserved Domains (3) summary
      cd09577
      Location:548 → 616
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:107 → 307
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:429 → 548
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    9. NM_004427.4 → NP_004418.2  polyhomeotic-like protein 2 isoform b

      See identical proteins and their annotated locations for NP_004418.2

      Status: REVIEWED

      Source sequence(s)
      AL513327, BC018602, CD109667
      Consensus CDS
      CCDS379.1
      UniProtKB/Swiss-Prot
      Q8IXK0
      Related
      ENSP00000362517.3, ENST00000373418.7
      Conserved Domains (2) summary
      cd09577
      Location:254 → 322
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      pfam16616
      Location:135 → 254
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    10. NM_198040.3 → NP_932157.1  polyhomeotic-like protein 2 isoform a

      See identical proteins and their annotated locations for NP_932157.1

      Status: REVIEWED

      Source sequence(s)
      AL138837, AL513327
      Consensus CDS
      CCDS378.1
      UniProtKB/Swiss-Prot
      A1L4Q1, A8KA40, D3DPR2, Q2TAL3, Q5T0C1, Q6NUJ6, Q6ZQR1, Q8IXK0, Q8N306, Q8TAG8, Q96BL4, Q9Y4Y7
      UniProtKB/TrEMBL
      B7ZLY0
      Related
      ENSP00000257118.5, ENST00000257118.5
      Conserved Domains (4) summary
      cd09577
      Location:789 → 857
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:791 → 858
      SAM; Sterile alpha motif
      COG3416
      Location:53 → 176
      COG3416; Uncharacterized protein [Function unknown]
      pfam16616
      Location:670 → 788
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      33323626..33431095 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      33185234..33292697 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IXK0.1 GenPept UniProtKB/Swiss-Prot:Q8IXK0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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