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    Phc1 polyhomeotic homolog 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 312690, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Phc1provided by RGD
    Official Full Name
    polyhomeotic homolog 1provided by RGD
    Primary source
    RGD:1309203
    See related
    EnsemblRapid:ENSRNOG00000015191 AllianceGenome:RGD:1309203
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in chromatin remodeling and negative regulation of DNA-templated transcription. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and cellular response to retinoic acid. Predicted to be located in nuclear body and sex chromatin. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. 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, Nov 2024]
    Expression
    Biased expression in Testes (RPKM 142.7), Adrenal (RPKM 77.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phc1 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (157182348..157205504, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (155510274..155532636, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (155093947..155118838, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene killer cell lectin like receptor G1 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene alpha-ketoglutarate dehydrogenase component 4-like Neighboring gene transfer RNA alanine (anticodon AGC) 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. Awad S, et al. Hum Mol Genet, 2013 Jun 1. PMID 23418308
    2. The mouse YAF2 gene generates two distinct transcripts and is expressed in pre-and postimplantation embryos. Kaneko T, et al. Gene, 2003 Oct 2. PMID 14557078
    3. Isolation and characterization of retinoic acid-inducible cDNA clones in F9 cells: one of the early inducible clones encodes a novel protein sharing several highly homologous regions with a Drosophila polyhomeotic protein. Nomura M, et al. Differentiation, 1994 Jun. PMID 8070621
    4. PRC1 complex diversity: where is it taking us? Gil J, et al. Trends Cell Biol, 2014 Nov. PMID 25065329
    5. Distinct roles of Polycomb group gene products in transcriptionally repressed and active domains of Hoxb8. Fujimura Y, et al. Development, 2006 Jun. PMID 16687444

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to retinoic acid ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    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 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
    		  
    located_in sex chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    polyhomeotic-like protein 1
    Names
    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_001107886.1 → NP_001101356.1  polyhomeotic-like protein 1

      See identical proteins and their annotated locations for NP_001101356.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473964
      UniProtKB/TrEMBL
      A0A8I6AHM8, A6ILE3, D3ZVD1
      Related
      ENSRNOP00000020529.5, ENSRNOT00000020529.7
      Conserved Domains (4) summary
      cd09577
      Location:973 → 1041
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:975 → 1042
      SAM; Sterile alpha motif
      pfam06467
      Location:830 → 865
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam16616
      Location:866 → 972
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      157182348..157205504 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286125.1 → XP_063142195.1  polyhomeotic-like protein 1 isoform X3

    2. XM_063286129.1 → XP_063142199.1  polyhomeotic-like protein 1 isoform X7

    3. XM_063286126.1 → XP_063142196.1  polyhomeotic-like protein 1 isoform X4

    4. XM_039107670.2 → XP_038963598.1  polyhomeotic-like protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AHM8
      Conserved Domains (2) summary
      cd09577
      Location:946 → 1014
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      pfam16616
      Location:839 → 946
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    5. XM_063286128.1 → XP_063142198.1  polyhomeotic-like protein 1 isoform X6

    6. XM_063286127.1 → XP_063142197.1  polyhomeotic-like protein 1 isoform X5

      Related
      ENSRNOP00000087501.2, ENSRNOT00000104598.2

    7. XM_063286123.1 → XP_063142193.1  polyhomeotic-like protein 1 isoform X1

    8. XM_063286124.1 → XP_063142194.1  polyhomeotic-like protein 1 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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