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    Cbx4 chromobox 4 [ Mus musculus (house mouse) ]

    Gene ID: 12418, updated on 9-Dec-2024

    Summary

    Official Symbol
    Cbx4provided by MGI
    Official Full Name
    chromobox 4provided by MGI
    Primary source
    MGI:MGI:1195985
    See related
    Ensembl:ENSMUSG00000039989 AllianceGenome:MGI:1195985
    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
    PC2; MPc2
    Summary
    Enables several functions, including SUMO binding activity; SUMO transferase activity; and nucleic acid binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II and protein sumoylation. Located in nuclear body. Is expressed in several structures, including adrenal gland; brain; gut; lung; and thymus. Human ortholog(s) of this gene implicated in hepatocellular carcinoma. Orthologous to human CBX4 (chromobox 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in adrenal adult (RPKM 54.2), thymus adult (RPKM 19.2) and 22 other tissues See more
    Orthologs
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    Genomic context

    See Cbx4 in Genome Data Viewer
    Location:
    11 E2; 11 83.34 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (118968399..118977067, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (119077571..119086237, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E92 Neighboring gene chromobox 8 Neighboring gene predicted gene, 53657 Neighboring gene STARR-seq mESC enhancer starr_31312 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:118945094-118945295 Neighboring gene STARR-positive B cell enhancer ABC_E5312 Neighboring gene STARR-positive B cell enhancer ABC_E5313 Neighboring gene predicted gene, 39482 Neighboring gene STARR-positive B cell enhancer ABC_E7107 Neighboring gene predicted gene 11754 Neighboring gene predicted gene, 35878

    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 (1) 
    • Targeted (6)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC143697, MGC143698

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables SUMO binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables SUMO binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables SUMO binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables SUMO ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables SUMO ligase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables SUMO ligase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables SUMO transferase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables SUMO transferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables enzyme binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphoprotein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    part_of PcG protein complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    E3 SUMO-protein ligase CBX4
    Names
    E3 SUMO-protein transferase CBX4
    chromobox homolog 4
    chromobox protein homolog 4
    polycomb 2 homolog

    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_007625.3NP_031651.2  E3 SUMO-protein ligase CBX4

      See identical proteins and their annotated locations for NP_031651.2

      Status: VALIDATED

      Source sequence(s)
      AL662835
      Consensus CDS
      CCDS25710.1
      UniProtKB/Swiss-Prot
      O55187, Q149G5, Q149G6
      Related
      ENSMUSP00000026665.8, ENSMUST00000026665.8
      Conserved Domains (1) summary
      smart00298
      Location:1062
      CHROMO; Chromatin organization modifier domain

    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_000077.7 Reference GRCm39 C57BL/6J

      Range
      118968399..118977067 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)