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    CBX4 chromobox 4 [ Homo sapiens (human) ]

    Gene ID: 8535, updated on 21-Dec-2019

    Summary

    Official Symbol
    CBX4provided by HGNC
    Official Full Name
    chromobox 4provided by HGNC
    Primary source
    HGNC:HGNC:1554
    See related
    Ensembl:ENSG00000141582 MIM:603079
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PC2; NBP16
    Expression
    Broad expression in bone marrow (RPKM 17.4), spleen (RPKM 5.9) and 24 other tissues See more
    Orthologs

    Genomic context

    See CBX4 in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (79833156..79839440, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77806955..77813222, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723961 Neighboring gene long intergenic non-protein coding RNA 1977 Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene TBC1 domain family member 16

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.
    NHGRI GWA Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    SUMO binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    SUMO transferase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    methylated histone binding IEA
    Inferred from Electronic Annotation
    more info
     
    phosphoprotein binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    single-stranded RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcription corepressor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription regulatory region DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of apoptotic process TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein sumoylation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    PRC1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    PcG protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear body IDA
    Inferred from Direct Assay
    more info
     
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    E3 SUMO-protein ligase CBX4
    Names
    NS5ATP1-binding protein 16
    Pc class 2 homolog
    chromobox homolog 4 (Pc class homolog, Drosophila)
    chromobox protein homolog 4
    chromobox-like protein 4
    polycomb 2 homolog

    NCBI Reference Sequences (RefSeq)

    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_003655.3NP_003646.2  E3 SUMO-protein ligase CBX4

      See identical proteins and their annotated locations for NP_003646.2

      Status: VALIDATED

      Source sequence(s)
      AC100791, AF013956, AI796748, BC014967, BG029608, BQ225831
      Consensus CDS
      CCDS32758.1
      UniProtKB/Swiss-Prot
      O00257
      UniProtKB/TrEMBL
      A0A0S2Z5B2
      Related
      ENSP00000269397.4, ENST00000269397.9
      Conserved Domains (2) summary
      smart00298
      Location:1062
      CHROMO; Chromatin organization modifier domain
      pfam17218
      Location:538559
      CBX7_C; CBX family C-terminal motif

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      79833156..79839440 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525399.2XP_011523701.1  E3 SUMO-protein ligase CBX4 isoform X1

      Conserved Domains (1) summary
      pfam17218
      Location:472493
      CBX7_C; CBX family C-terminal motif
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