CBX6 chromobox 6 [Homo sapiens (human)] - Gene

Summary

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, Dec 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

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_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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 EBI GWAS CatalogPubMed
Genome-wide association study identifies multiple loci associated with bladder cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-144773 (e-PCR)
- UniSTS:183576

STS-R45141 (e-PCR)
- UniSTS:71076

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)

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
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