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CBX6 chromobox 6 [ Homo sapiens (human) ]

Gene ID: 23466, updated on 7-Oct-2018

Summary

Official Symbol
CBX6provided by HGNC
Official Full Name
chromobox 6provided by HGNC
Primary source
HGNC:HGNC:1556
See related
Ensembl:ENSG00000183741 MIM:617438; Vega:OTTHUMG00000150456
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
Expression
Ubiquitous expression in brain (RPKM 28.2), ovary (RPKM 14.0) and 24 other tissues See more
Orthologs

Genomic context

See CBX6 in Genome Data Viewer
Location:
22q13.1
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (38861427..38872334, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39257468..39268258, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene dynein axonemal light chain 4 Neighboring gene neuronal pentraxin receptor Neighboring gene uncharacterized LOC105373032 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3A

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Cellular Senescence, organism-specific biosystem (from REACTOME)
    Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Oxidative Stress Induced Senescence, organism-specific biosystem (from REACTOME)
    Oxidative Stress Induced Senescence, organism-specific biosystemOxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
PcG protein complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
filopodium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heterochromatin IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
chromobox protein homolog 6
Names
chromobox homolog 6

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_001303494.1NP_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, HY128779, HY151719
    Consensus CDS
    CCDS77675.1
    UniProtKB/Swiss-Prot
    O95503
    UniProtKB/TrEMBL
    B0QXZ6
    Related
    ENSP00000216083.6, OTTHUMP00000197413, ENST00000216083.6, OTTHUMT00000318192
    Conserved Domains (3) summary
    smart00298
    Location:1062
    CHROMO; Chromatin organization modifier domain
    pfam17218
    Location:339370
    CBX7_C; CBX family C-terminal motif
    cl26386
    Location:219313
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  2. NM_014292.4NP_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, HY128779
    Consensus CDS
    CCDS13980.1
    UniProtKB/Swiss-Prot
    O95503
    Related
    ENSP00000384490.3, OTTHUMP00000197412, ENST00000407418.7, OTTHUMT00000318190
    Conserved Domains (3) summary
    smart00298
    Location:1062
    CHROMO; Chromatin organization modifier domain
    pfam17218
    Location:357388
    CBX7_C; CBX family C-terminal motif
    cl26386
    Location:237331
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    38861427..38872334 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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