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    Phc1 polyhomeotic 1 [ Mus musculus (house mouse) ]

    Gene ID: 13619, updated on 9-Dec-2024

    Summary

    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; brain; genitourinary system; hemolymphoid 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, Dec 2024]
    Expression
    Broad expression in testis adult (RPKM 55.8), CNS E14 (RPKM 22.1) and 20 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Phc1 in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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
     
    involved_in chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    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 PRC1 complex ISS
    Inferred from Sequence or Structural Similarity
    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
     
    located_in sex chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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)

    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_001042623.3NP_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:889957
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:427557
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:782889
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    2. NM_001271579.2NP_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:9411009
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:9431010
      SAM; Sterile alpha motif
      pfam06467
      Location:798833
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:834940
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    3. NM_001355215.2NP_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:9571025
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      pfam16616
      Location:850956
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
      cl26464
      Location:495625
      Atrophin-1; Atrophin-1 family
    4. NM_001408247.1NP_001395176.1  polyhomeotic-like protein 1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153579
      UniProtKB/TrEMBL
      Q3TJ47, Q3V116
      Related
      ENSMUSP00000080532.4, ENSMUST00000081849.10
    5. NM_001408248.1NP_001395177.1  polyhomeotic-like protein 1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC153579
      UniProtKB/TrEMBL
      Q3TJ47, Q3V116
      Related
      ENSMUSP00000108219.3, ENSMUST00000112600.9
    6. NM_001408249.1NP_001395178.1  polyhomeotic-like protein 1 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC153579
      UniProtKB/TrEMBL
      Q3TJ47
    7. NM_001408250.1NP_001395179.1  polyhomeotic-like protein 1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC153579
      UniProtKB/TrEMBL
      Q3TJ47
    8. NM_007905.4NP_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:9411009
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:9431010
      SAM; Sterile alpha motif
      pfam06467
      Location:798833
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:834940
      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_030255141.2XP_030111001.1  polyhomeotic-like protein 1 isoform X4

      UniProtKB/TrEMBL
      Q3TJ47
      Conserved Domains (3) summary
      cd09577
      Location:916984
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:454584
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:809915
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    2. XM_006505498.2XP_006505561.1  polyhomeotic-like protein 1 isoform X1

      UniProtKB/TrEMBL
      Q3TJ47
      Conserved Domains (3) summary
      cd09577
      Location:9711039
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:509639
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:864970
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    3. XM_006505500.2XP_006505563.1  polyhomeotic-like protein 1 isoform X3

      UniProtKB/TrEMBL
      Q3TJ47
      Conserved Domains (3) summary
      cd09577
      Location:919987
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:457587
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:812918
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    4. XM_017321382.3XP_017176871.1  polyhomeotic-like protein 1 isoform X6

      UniProtKB/TrEMBL
      E0CXV8
      Conserved Domains (3) summary
      cd09577
      Location:839907
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:377507
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:732838
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    5. XM_030255142.2XP_030111002.1  polyhomeotic-like protein 1 isoform X7

      UniProtKB/TrEMBL
      E0CXV8
      Conserved Domains (3) summary
      cd09577
      Location:764832
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      PHA03247
      Location:302432
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:657763
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2