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Phc1 polyhomeotic 1 [ Mus musculus (house mouse) ]

Gene ID: 13619, updated on 21-Apr-2024

Summary

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Official Symbol
Phc1provided by MGI
Official Full Name
polyhomeotic 1provided by MGI
Primary source
MGI:MGI:103248
See related
Ensembl:ENSMUSG00000040669 AllianceGenome:MGI:103248
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
Edr; Edr1; Mph1; rae28; Rae-28
Summary
Enables chromatin binding activity. Acts upstream of or within cellular response to leukemia inhibitory factor and cellular response to retinoic acid. Located in nuclear body and sex chromatin. Is expressed in several structures, including alimentary system; genitourinary system; hemolymphoid system; nervous system; and sensory organ. Used to study dilated cardiomyopathy and tetralogy of Fallot. Human ortholog(s) of this gene implicated in primary autosomal recessive microcephaly 11. Orthologous to human PHC1 (polyhomeotic homolog 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 55.8), CNS E14 (RPKM 22.1) and 20 other tissues See more
Orthologs
human all
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Genomic context

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Location:
6 F1; 6 57.52 cM
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (122294690..122317551, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (122317731..122340227, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6637 Neighboring gene STARR-positive B cell enhancer ABC_E345 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene STARR-seq mESC enhancer starr_17220 Neighboring gene STARR-seq mESC enhancer starr_17223 Neighboring gene STARR-positive B cell enhancer mm9_chr6:122337361-122337661 Neighboring gene RIKEN cDNA 1700063H04 gene Neighboring gene VISTA enhancer mm94 Neighboring gene mitochondrial ribosomal protein S36 pseudogene

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. Defective long-term repopulating ability in hematopoietic stem cells lacking the Polycomb-group gene rae28. Kim JY, et al. Eur J Haematol, 2004 Aug. PMID 15245505
  2. Polycomb group gene rae28 is required for sustaining activity of hematopoietic stem cells. Ohta H, et al. J Exp Med, 2002 Mar 18. PMID 11901201, Free PMC Article
  3. Lack of the Polycomb-group gene rae28 causes maturation arrest at the early B-cell developmental stage. Tokimasa S, et al. Exp Hematol, 2001 Jan. PMID 11164110
  4. Sequence-specific DNA binding activity in the RAE28 protein, a mouse homologue of the Drosophila polyhomeotic protein. Nomura M, et al. Biochem Mol Biol Int, 1998 Dec. PMID 9861444
  5. Structural organization of the rae28 gene, a putative murine homologue of the Drosophila polyhomeotic gene. Abdul Motaleb M, et al. J Biochem, 1996 Oct. PMID 8947844

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PcG complex 1, involving Rae28 and Cdt1, supports the activity of hematopoietic stem cells by enhancing cycling capability and hematopoietic activity through direct regulation of Geminin
    Title: Polycomb-group complex 1 acts as an E3 ubiquitin ligase for Geminin to sustain hematopoietic stem cell activity.
  2. rae28 has a crucial role in sustaining the activity of hematopoietic stem cells to maintain hematopoiesis
    Title: Polycomb group gene rae28 is required for sustaining activity of hematopoietic stem cells.
  3. in vivo results clearly indicate that Polycomb-group gene rae28 is indispensable for the long-term repopulating ability of HSCs
    Title: Defective long-term repopulating ability in hematopoietic stem cells lacking the Polycomb-group gene rae28.
  4. Gene rae28 is involved in cardiac morphogenesis through a non cardiomyocyte pathway. However, cardiomyocyte-specific overexpression of rae28 caused dilated cardiomyopathy.
    Title: Overexpression of Polycomb-group gene rae28 in cardiomyocytes does not complement abnormal cardiac morphogenesis in mice lacking rae28 but causes dilated cardiomyopathy.
  5. The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis.
    Title: The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis.
  6. polymeric Scm complexes could extend beyond the local domains of polymeric Ph complexes on chromatin, possibly playing a role in long range repression
    Title: Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer.
  7. functional overlap between Phc2 and Phc1 along with a strict dose-dependent requirement during anterior-posterior (A-P) patterning
    Title: Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate polycomb repression of Hox genes.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (3) 

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 chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
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
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within cellular response to retinoic acid IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of sex chromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
polyhomeotic-like protein 1
Names
early development regulator1 (homolog of polyhomeotic 1)
early development regulatory protein 1
polyhomeotic-like 1

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_001042623.3 → NP_001036088.1  polyhomeotic-like protein 1 isoform b

    See identical proteins and their annotated locations for NP_001036088.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform b which is shorter than isoform a. Variants 2, 6, and 7 all encode the same isoform (b).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS39620.1
    UniProtKB/TrEMBL
    Q3TJ47, Q3V116
    Related
    ENSMUSP00000123911.2, ENSMUST00000161054.8
    Conserved Domains (3) summary
    cd09577
    Location:889 → 957
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:427 → 557
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:782 → 889
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  2. NM_001271579.2 → NP_001258508.1  polyhomeotic-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_001258508.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same isoform (a).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS20494.1
    UniProtKB/Swiss-Prot
    P70359, Q64028, Q64307, Q7TT35, Q8BZ80
    UniProtKB/TrEMBL
    Q3TJ47
    Related
    ENSMUSP00000078514.4, ENSMUST00000079560.10
    Conserved Domains (4) summary
    cd09577
    Location:941 → 1009
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:943 → 1010
    SAM; Sterile alpha motif
    pfam06467
    Location:798 → 833
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:834 → 940
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  3. NM_001355215.2 → NP_001342144.1  polyhomeotic-like protein 1 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate in-frame exon in the coding region which results in the use of a novel translation start site compared to variant 1. It encodes isoform c which has a longer N-terminus than isoform a. Variants 5 and 8 both encode the same isoform (c).
    Source sequence(s)
    AC153579
    UniProtKB/TrEMBL
    Q3TJ47
    Conserved Domains (3) summary
    cd09577
    Location:957 → 1025
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam16616
    Location:850 → 956
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    cl26464
    Location:495 → 625
    Atrophin-1; Atrophin-1 family

  4. NM_001408247.1 → NP_001395176.1  polyhomeotic-like protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC153579
    UniProtKB/TrEMBL
    Q3V116
    Related
    ENSMUSP00000080532.4, ENSMUST00000081849.10

  5. NM_001408248.1 → NP_001395177.1  polyhomeotic-like protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC153579
    UniProtKB/TrEMBL
    Q3V116
    Related
    ENSMUSP00000108219.3, ENSMUST00000112600.9

  6. NM_001408249.1 → NP_001395178.1  polyhomeotic-like protein 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC153579

  7. NM_001408250.1 → NP_001395179.1  polyhomeotic-like protein 1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AC153579

  8. NM_007905.4 → NP_031931.2  polyhomeotic-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_031931.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (a). Both variants 1 and 3 encode the same isoform (a).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS20494.1
    UniProtKB/Swiss-Prot
    P70359, Q64028, Q64307, Q7TT35, Q8BZ80
    UniProtKB/TrEMBL
    Q3TJ47
    Related
    ENSMUSP00000125568.2, ENSMUST00000161739.8
    Conserved Domains (4) summary
    cd09577
    Location:941 → 1009
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:943 → 1010
    SAM; Sterile alpha motif
    pfam06467
    Location:798 → 833
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:834 → 940
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RNA

  1. NR_073364.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate donor splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC153579
    Related
    ENSMUST00000160163.8

  2. NR_176619.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC153579

  3. NR_176620.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC153579

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_000072.7 Reference GRCm39 C57BL/6J

    Range
    122294690..122317551 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030255141.2 → XP_030111001.1  polyhomeotic-like protein 1 isoform X4

    UniProtKB/TrEMBL
    Q3TJ47
    Conserved Domains (3) summary
    cd09577
    Location:916 → 984
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:454 → 584
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:809 → 915
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  2. XM_006505498.2 → XP_006505561.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    Q3TJ47
    Conserved Domains (3) summary
    cd09577
    Location:971 → 1039
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:509 → 639
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:864 → 970
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  3. XM_006505500.2 → XP_006505563.1  polyhomeotic-like protein 1 isoform X3

    UniProtKB/TrEMBL
    Q3TJ47
    Conserved Domains (3) summary
    cd09577
    Location:919 → 987
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:457 → 587
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:812 → 918
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  4. XM_017321382.3 → XP_017176871.1  polyhomeotic-like protein 1 isoform X6

    UniProtKB/TrEMBL
    E0CXV8
    Conserved Domains (3) summary
    cd09577
    Location:839 → 907
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:377 → 507
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:732 → 838
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  5. XM_030255142.2 → XP_030111002.1  polyhomeotic-like protein 1 isoform X7

    UniProtKB/TrEMBL
    E0CXV8
    Conserved Domains (3) summary
    cd09577
    Location:764 → 832
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:302 → 432
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:657 → 763
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q64028.3 GenPept UniProtKB/Swiss-Prot:Q64028

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