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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
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Genomic context

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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

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