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    Phc2 polyhomeotic homolog 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313038, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Phc2provided by RGD
    Official Full Name
    polyhomeotic homolog 2provided by RGD
    Primary source
    RGD:1307912
    See related
    EnsemblRapid:ENSRNOG00000006004 AllianceGenome:RGD:1307912
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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; histone binding activity; and identical protein binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within spermatogenesis. Predicted to be located in heterochromatin and nucleoplasm. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. Orthologous to human PHC2 (polyhomeotic homolog 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 134.7), Spleen (RPKM 99.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phc2 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (146285000..146383664)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (141000604..141099268)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (146832552..146931444)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene zinc finger and SCAN domain containing 20 Neighboring gene toll-like receptor 12 Neighboring gene alpha 1,3-galactosyltransferase 2 Neighboring gene zinc finger protein 362

    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
    • 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. Mammalian Polycomb Scmh1 mediates exclusion of Polycomb complexes from the XY body in the pachytene spermatocytes. Takada Y, et al. Development, 2007 Feb. PMID 17215307
    2. The mouse Edr2 (Mph2) gene has two forms of mRNA encoding 90- and 36-kDa polypeptides. Yamaki M, et al. Gene, 2002 Apr 17. PMID 12034499
    3. PRC1 complex diversity: where is it taking us? Gil J, et al. Trends Cell Biol, 2014 Nov. PMID 25065329
    4. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Simon JA, et al. Mol Cell, 2013 Mar 7. PMID 23473600, Free PMC Article
    5. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Puschendorf M, et al. Nat Genet, 2008 Apr. PMID 18311137

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC105958

    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 histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    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
    		  
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    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 heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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 2
    Names
    polyhomeotic-like 2

    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_001013169.2 → NP_001013187.2  polyhomeotic-like protein 2

      See identical proteins and their annotated locations for NP_001013187.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A6ISF6, D4A0M3
      Conserved Domains (3) summary
      cd09577
      Location:781 → 849
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:783 → 850
      SAM; Sterile alpha motif
      pfam16616
      Location:662 → 780
      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_086023.1 Reference GRCr8

      Range
      146285000..146383664
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006238926.4 → XP_006238988.1  polyhomeotic-like protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006238988.1

      UniProtKB/TrEMBL
      A6ISF6, D4A0M3
      Related
      ENSRNOP00000059238.1, ENSRNOT00000067912.3
      Conserved Domains (3) summary
      cd09577
      Location:781 → 849
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:783 → 850
      SAM; Sterile alpha motif
      pfam16616
      Location:662 → 780
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    2. XM_039109792.2 → XP_038965720.1  polyhomeotic-like protein 2 isoform X4

      Conserved Domains (3) summary
      pfam05109
      Location:141 → 559
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam16616
      Location:662 → 781
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
      cl15755
      Location:781 → 800
      SAM_superfamily; SAM (Sterile alpha motif )

    3. XM_039109791.2 → XP_038965719.1  polyhomeotic-like protein 2 isoform X3

      Conserved Domains (3) summary
      PHA03247
      Location:197 → 530
      PHA03247; large tegument protein UL36; Provisional
      pfam16616
      Location:662 → 781
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
      cl15755
      Location:781 → 801
      SAM_superfamily; SAM (Sterile alpha motif )

    4. XM_017593333.3 → XP_017448822.1  polyhomeotic-like protein 2 isoform X2

      Related
      ENSRNOP00000107753.1, ENSRNOT00000132855.1

    5. XM_063287537.1 → XP_063143607.1  polyhomeotic-like protein 2 isoform X1

      UniProtKB/TrEMBL
      A6ISF6, D4A0M3

    6. XM_063287536.1 → XP_063143606.1  polyhomeotic-like protein 2 isoform X1

      UniProtKB/TrEMBL
      A6ISF6, D4A0M3

    7. XM_008764139.4 → XP_008762361.1  polyhomeotic-like protein 2 isoform X6

      Conserved Domains (3) summary
      cd09577
      Location:254 → 322
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      smart00454
      Location:256 → 323
      SAM; Sterile alpha motif
      pfam16616
      Location:135 → 253
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    8. XM_039109793.2 → XP_038965721.1  polyhomeotic-like protein 2 isoform X5

      UniProtKB/TrEMBL
      B5DFL1
      Conserved Domains (2) summary
      cd09577
      Location:296 → 364
      SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
      pfam16616
      Location:177 → 296
      PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

    RNA

    1. XR_005504429.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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