U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PHC3 polyhomeotic homolog 3 [ Homo sapiens (human) ]

Gene ID: 80012, updated on 2-Nov-2024

Summary

Go to the top of the page Help
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 DNA-templated transcription. Located in nucleoplasm. Part of PRC1 complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 7.6), thyroid (RPKM 6.5) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See PHC3 in Genome Data Viewer
Location:
3q26.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (170087584..170181733, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172872255..172966417, complement)
RS_2024_09 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues 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

Go to the top of the pageHelp

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, Free PMC Article
  4. Expression of circ-PHC3 enhances ovarian cancer progression via regulation of the miR-497-5p/SOX9 pathway. Wang H, et al. J Ovarian Res, 2023 Jul 20. PMID 37468993, Free PMC Article
  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 (57) 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

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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_2024_08

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

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous