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

Gene ID: 313038, updated on 13-Apr-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
Ensembl: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 transcription, DNA-templated. 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, Apr 2022]
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
  
part_of 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
    Related
    ENSRNOP00000059238.1, ENSRNOT00000067912.2
    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
    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

  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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