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Phc3 polyhomeotic 3 [ Mus musculus (house mouse) ]

Gene ID: 241915, updated on 5-Mar-2024

Summary

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Official Symbol
Phc3provided by MGI
Official Full Name
polyhomeotic 3provided by MGI
Primary source
MGI:MGI:2181434
See related
Ensembl:ENSMUSG00000037652 AllianceGenome:MGI:2181434
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Edr3; Hph3; E030046K01Rik
Summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Part of PcG protein complex. Is expressed in several structures, including adipose tissue; alimentary system; brain; genitourinary system; and hemolymphoid system gland. Orthologous to human PHC3 (polyhomeotic homolog 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 7.9), genital fat pad adult (RPKM 7.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
3 A3; 3 14.36 cM
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (30953444..31023628, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (30899295..30969479, complement)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 42198 Neighboring gene predicted gene, 42199 Neighboring gene G protein-coupled receptor 160 Neighboring gene STARR-seq mESC enhancer starr_07303 Neighboring gene STARR-positive B cell enhancer ABC_E4537 Neighboring gene predicted gene 2979 Neighboring gene STARR-positive B cell enhancer ABC_E4538 Neighboring gene STARR-seq mESC enhancer starr_07307 Neighboring gene STARR-seq mESC enhancer starr_07308 Neighboring gene protein kinase C, iota Neighboring gene microRNA 7008

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. 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
  2. Differential expression of polycomb repression complex 1 (PRC1) members in the developing mouse brain reveals multiple complexes. Vogel T, et al. Dev Dyn, 2006 Sep. PMID 16786585
  3. PHC3, a component of the hPRC-H complex, associates with E2F6 during G0 and is lost in osteosarcoma tumors. Deshpande AM, et al. Oncogene, 2007 Mar 15. PMID 17001316, Free PMC Article
  4. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Puschendorf M, et al. Nat Genet, 2008 Apr. PMID 18311137
  5. Proteomics analysis of Ring1B/Rnf2 interactors identifies a novel complex with the Fbxl10/Jhdm1B histone demethylase and the Bcl6 interacting corepressor. Sánchez C, et al. Mol Cell Proteomics, 2007 May. PMID 17296600

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4) 

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

Gene Ontology Provided by MGI

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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
part_of PcG protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of PcG protein complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
polyhomeotic-like protein 3
Names
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_001165954.1 → NP_001159426.1  polyhomeotic-like protein 3 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC111093, BC132533
    UniProtKB/Swiss-Prot
    Q8CHP6
    Conserved Domains (2) summary
    cd09577
    Location:924 → 992
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:926 → 993
    SAM; Sterile alpha motif

  2. NM_001165955.1 → NP_001159427.1  polyhomeotic-like protein 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, uses a downstream translational start codon, and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC111093, AK087339
    Consensus CDS
    CCDS50884.1
    UniProtKB/TrEMBL
    D3YY34
    Related
    ENSMUSP00000103890.2, ENSMUST00000108255.8
    Conserved Domains (2) summary
    cd09577
    Location:879 → 947
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:881 → 948
    SAM; Sterile alpha motif

  3. NM_001165956.1 → NP_001159428.1  polyhomeotic-like protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001159428.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame segment in the central coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    AC111093, BC145123
    Consensus CDS
    CCDS50885.1
    UniProtKB/TrEMBL
    B7ZNA5
    Related
    ENSMUSP00000065617.6, ENSMUST00000064718.12
    Conserved Domains (2) summary
    cd09577
    Location:882 → 950
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:884 → 951
    SAM; Sterile alpha motif

  4. NM_153421.2 → NP_700470.2  polyhomeotic-like protein 3 isoform 2

    See identical proteins and their annotated locations for NP_700470.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream translational start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AC111093, AJ414610, BC132533
    Consensus CDS
    CCDS17288.1
    UniProtKB/Swiss-Prot
    A2RTJ9, Q3TLV5, Q8CHP6
    Related
    ENSMUSP00000130142.2, ENSMUST00000168645.8
    Conserved Domains (2) summary
    cd09577
    Location:912 → 980
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:914 → 981
    SAM; Sterile alpha motif

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    30953444..31023628 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030252612.2 → XP_030108472.1  polyhomeotic-like protein 3 isoform X5

    Conserved Domains (2) summary
    cd09577
    Location:881 → 949
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam03154
    Location:145 → 536
    Atrophin-1; Atrophin-1 family

  2. XM_006535468.4 → XP_006535531.1  polyhomeotic-like protein 3 isoform X2

    Conserved Domains (3) summary
    cd09577
    Location:914 → 982
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam03154
    Location:198 → 569
    Atrophin-1; Atrophin-1 family
    pfam09770
    Location:326 → 490
    PAT1; Topoisomerase II-associated protein PAT1

  3. XM_006535470.2 → XP_006535533.1  polyhomeotic-like protein 3 isoform X4

    Conserved Domains (3) summary
    cd09577
    Location:891 → 959
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam03154
    Location:171 → 544
    Atrophin-1; Atrophin-1 family
    pfam09770
    Location:319 → 483
    PAT1; Topoisomerase II-associated protein PAT1

  4. XM_006535469.4 → XP_006535532.1  polyhomeotic-like protein 3 isoform X3

    Conserved Domains (3) summary
    cd09577
    Location:907 → 975
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam03154
    Location:171 → 562
    Atrophin-1; Atrophin-1 family
    pfam09770
    Location:319 → 483
    PAT1; Topoisomerase II-associated protein PAT1

  5. XM_006535467.3 → XP_006535530.1  polyhomeotic-like protein 3 isoform X1

    Conserved Domains (3) summary
    cd09577
    Location:940 → 1008
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam03154
    Location:224 → 595
    Atrophin-1; Atrophin-1 family
    pfam09770
    Location:352 → 516
    PAT1; Topoisomerase II-associated protein PAT1

  6. XM_036163096.1 → XP_036018989.1  polyhomeotic-like protein 3 isoform X6

    Conserved Domains (1) summary
    pfam09770
    Location:352 → 516
    PAT1; Topoisomerase II-associated protein PAT1

RNA

  1. XR_389590.2 RNA Sequence

  2. XR_004941320.1 RNA Sequence

  3. XR_004941321.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8CHP6.2 GenPept UniProtKB/Swiss-Prot:Q8CHP6

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