U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Pcgf5 polycomb group ring finger 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 681178, updated on 11-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Pcgf5provided by RGD
    Official Full Name
    polycomb group ring finger 5provided by RGD
    Primary source
    RGD:1583513
    See related
    Ensembl:ENSRNOG00000018532 AllianceGenome:RGD:1583513
    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 metal ion binding activity. Predicted to be involved in histone H2A-K119 monoubiquitination; inactivation of X chromosome by genetic imprinting; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in Golgi apparatus; centrosome; and nucleoplasm. Predicted to be part of PRC1 complex. Predicted to colocalize with X chromosome. Orthologous to human PCGF5 (polycomb group ring finger 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 74.0), Heart (RPKM 64.0) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    1q53
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (243476450..243592603)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (234063854..234180022)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (254974688..255090925)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene glutamic acid-rich protein-like Neighboring gene uncharacterized LOC134485230 Neighboring gene ankyrin repeat domain 1 Neighboring gene uncharacterized LOC103691349 Neighboring gene HECT domain E3 ubiquitin protein ligase 2 Neighboring gene uncharacterized LOC134485231

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation. Almeida M, et al. Science, 2017 Jun 9. PMID 28596365, Free PMC Article
    2. PRC1 complex diversity: where is it taking us? Gil J, et al. Trends Cell Biol, 2014 Nov. PMID 25065329
    3. 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
    4. An AUTS2-Polycomb complex activates gene expression in the CNS. Gao Z, et al. Nature, 2014 Dec 18. PMID 25519132, Free PMC Article
    5. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Vandamme J, et al. Mol Cell Proteomics, 2011 Apr. PMID 21282530, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC189388

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables histone H2AK119 ubiquitin ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal 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 positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in random inactivation of X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of PRC1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PcG protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome 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
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    polycomb group RING finger protein 5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001129882.1 → NP_001123354.1  polycomb group RING finger protein 5

      See identical proteins and their annotated locations for NP_001123354.1

      Status: PROVISIONAL

      Source sequence(s)
      BC167067
      UniProtKB/TrEMBL
      A0A0G2K8R7, A0A8J8YBC5, B2RZ90, E9PTD5
      Related
      ENSRNOP00000074710.2, ENSRNOT00000092151.2
      Conserved Domains (3) summary
      TIGR00599
      Location:8 → 135
      rad18; DNA repair protein rad18
      cd16737
      Location:16 → 57
      RING-HC_PCGF5; RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins
      cd17084
      Location:136 → 236
      RAWUL_PCGF5; RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 5 (PCGF5) and similar proteins

    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_086019.1 Reference GRCr8

      Range
      243476450..243592603
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017589708.3 → XP_017445197.1  polycomb group RING finger protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ASY1, A0A8J8YBC5
      Conserved Domains (2) summary
      pfam00097
      Location:18 → 56
      zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
      pfam16207
      Location:154 → 216
      RAWUL; RAWUL domain RING finger- and WD40-associated ubiquitin-like

    2. XM_006231311.5 → XP_006231373.1  polycomb group RING finger protein 5 isoform X2

      See identical proteins and their annotated locations for XP_006231373.1

      UniProtKB/TrEMBL
      A0A0G2K8R7, A0A8J8YBC5, B2RZ90, E9PTD5
      Conserved Domains (3) summary
      TIGR00599
      Location:8 → 135
      rad18; DNA repair protein rad18
      cd16737
      Location:16 → 57
      RING-HC_PCGF5; RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins
      cd17084
      Location:136 → 236
      RAWUL_PCGF5; RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 5 (PCGF5) and similar proteins

    3. XM_017589707.3 → XP_017445196.1  polycomb group RING finger protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ASY1, A0A8J8YBC5
      Related
      ENSRNOP00000097432.1
      Conserved Domains (2) summary
      pfam00097
      Location:18 → 56
      zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
      pfam16207
      Location:154 → 216
      RAWUL; RAWUL domain RING finger- and WD40-associated ubiquitin-like

    4. XM_017589709.3 → XP_017445198.1  polycomb group RING finger protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ASY1, A0A8J8YBC5
      Conserved Domains (2) summary
      pfam00097
      Location:18 → 56
      zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
      pfam16207
      Location:154 → 216
      RAWUL; RAWUL domain RING finger- and WD40-associated ubiquitin-like

    5. XM_063273717.1 → XP_063129787.1  polycomb group RING finger protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K8R7, B2RZ90, E9PTD5
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous