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    CBX6 chromobox 6 [ Homo sapiens (human) ]

    Gene ID: 23466, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CBX6provided by HGNC
    Official Full Name
    chromobox 6provided by HGNC
    Primary source
    HGNC:HGNC:1556
    See related
    Ensembl:ENSG00000183741 MIM:617438; AllianceGenome:HGNC:1556
    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
    Summary
    Predicted to enable chromatin binding activity and methylated histone binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of PcG protein complex. Biomarker of glioblastoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 28.2), ovary (RPKM 14.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CBX6 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (38861422..38872216, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39331798..39342593, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39257427..39268221, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39175672-39176172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13732 Neighboring gene dynein axonemal light chain 4 Neighboring gene neuronal pentraxin receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39255577-39256456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39260057-39260936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39260937-39261814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39261933-39262744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39268427-39268977 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:39269364-39270563 Neighboring gene uncharacterized LOC105373032 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63270 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63315 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63367 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_63385 and experimental_63387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39332328-39333149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39345610-39346460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39350327-39351206 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. CBX6 overexpression contributes to tumor progression and is predictive of a poor prognosis in hepatocellular carcinoma. Zheng H, et al. Oncotarget, 2017 Mar 21. PMID 28122351, Free PMC Article
    2. Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion. Sakai K, et al. Sci Rep, 2020 Oct 7. PMID 33028834, Free PMC Article
    3. Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. Tajul-Arifin K, et al. Genome Res, 2003 Jun. PMID 12819141, Free PMC Article
    4. CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer. Deng H, et al. Sci Rep, 2019 Jan 17. PMID 30655550, Free PMC Article
    5. Polycomb genes are associated with response to imatinib in chronic myeloid leukemia. Crea F, et al. Epigenomics, 2015 Aug. PMID 26343356, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion.
      Title: Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion.
    2. CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer.
      Title: CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer.
    3. Data show that USP26 interacts with PRC1 components chromobox (CBX)-containing proteins CBX4 and CBX6.
      Title: USP26 functions as a negative regulator of cellular reprogramming by stabilising PRC1 complex components.
    4. our results represent the first evidence that CBX6 contributes to tumor progression and indicate that the protein may serve as a novel prognostic biomarker for hepatocellular carcinoma and as a therapeutic target in the treatment of the disease.
      Title: CBX6 overexpression contributes to tumor progression and is predictive of a poor prognosis in hepatocellular carcinoma.
    5. Data show that polycomb-group proteins BMI1, PHC3, CBX6 and CBX7 expression was significantly increased during imatinib treatment.
      Title: Polycomb genes are associated with response to imatinib in chronic myeloid leukemia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with bladder cancer risk.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of PRC1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PcG protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in heterochromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    chromobox protein homolog 6
    Names
    chromobox homolog 6

    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_001303494.2 → NP_001290423.1  chromobox protein homolog 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL008583, BC064900, HY151719
      Consensus CDS
      CCDS77675.1
      UniProtKB/TrEMBL
      B0QXZ6
      Related
      ENSP00000216083.6, ENST00000216083.6
      Conserved Domains (3) summary
      PRK14951
      Location:219 → 313
      PRK14951; DNA polymerase III subunits gamma and tau; Provisional
      cd18648
      Location:8 → 65
      CD_Cbx6; chromodomain of chromobox homolog 6
      pfam17218
      Location:339 → 368
      CBX7_C; CBX family C-terminal motif

    2. NM_014292.5 → NP_055107.3  chromobox protein homolog 6 isoform 1

      See identical proteins and their annotated locations for NP_055107.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL008583, BC064900, CD625491
      Consensus CDS
      CCDS13980.1
      UniProtKB/Swiss-Prot
      A8KAH0, O95503, Q96EM5
      Related
      ENSP00000384490.3, ENST00000407418.8
      Conserved Domains (3) summary
      smart00298
      Location:10 → 62
      CHROMO; Chromatin organization modifier domain
      pfam17218
      Location:357 → 388
      CBX7_C; CBX family C-terminal motif
      cl26386
      Location:237 → 331
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      38861422..38872216 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      39331798..39342593 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95503.1 GenPept UniProtKB/Swiss-Prot:O95503

    Gene LinkOut

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

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