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CBX6 chromobox 6 [ Homo sapiens (human) ]

Gene ID: 23466, updated on 19-Sep-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 single-stranded RNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. Part of PcG protein complex. Biomarker of glioblastoma. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 28.2), ovary (RPKM 14.0) and 24 other tissues See more
Orthologs
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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. 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
  2. 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
  3. 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
  4. Polycomb genes are associated with response to imatinib in chronic myeloid leukemia. Crea F, et al. Epigenomics, 2015 Aug. PMID 26343356, Free PMC Article
  5. Recognition and specificity determinants of the human cbx chromodomains. Kaustov L, et al. J Biol Chem, 2011 Jan 7. PMID 21047797, Free PMC Article

See all (36) 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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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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