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Aliases for CBX6 Gene

Aliases for CBX6 Gene

  • Chromobox 6 2 3 5
  • Chromobox Homolog 6 2 3
  • Chromobox Protein Homolog 6 3

External Ids for CBX6 Gene

Previous GeneCards Identifiers for CBX6 Gene

  • GC22M035871
  • GC22M037500
  • GC22M037503
  • GC22M037584
  • GC22M039257
  • GC22M022225

Summaries for CBX6 Gene

GeneCards Summary for CBX6 Gene

CBX6 (Chromobox 6) is a Protein Coding gene. Among its related pathways are Cellular Senescence (REACTOME). Gene Ontology (GO) annotations related to this gene include single-stranded RNA binding. An important paralog of this gene is CBX8.

UniProtKB/Swiss-Prot for CBX6 Gene

  • Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development (PubMed:21282530). PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Possibly contributes to the target selectivity of the PRC1 complex by binding specific regions of chromatin (PubMed:18927235). Recruitment to chromatin might occur in an H3K27me3-independent fashion (By similarity). May have a PRC1-independent function in embryonic stem cells (By similarity).

Additional gene information for CBX6 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CBX6 Gene

Genomics for CBX6 Gene

GeneHancer (GH) Regulatory Elements for CBX6 Gene

Promoters and enhancers for CBX6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J038869 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 660.3 +0.2 186 4.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 CBX6 APOBEC3B-AS1 ENSG00000235209 SUN2 APOBEC3G GTPBP1 JOSD1 APOBEC3H NPTXR
GH22J039518 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 22.6 -652.0 -652049 12.3 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 ATF4 ENSG00000272834 RPL3 TAB1 ENSG00000230912 SNORD83B ENSG00000228274 CBY1 CBX6 TNRC6B
GH22J038174 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.7 +693.5 693525 8.7 MLX DMAP1 YBX1 IRF4 YY1 SLC30A9 E2F8 ZNF143 MCM3 SP3 PLA2G6 DDX17 MAFF ENSG00000228274 PRDX3P1 CSNK1E ANKRD54 CBY1 ENSG00000230912 TRIOBP
GH22J038691 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.8 +175.7 175714 10.9 MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 SSRP1 JOSD1 GC22M043056 CBY1 ENSG00000228274 FAM227A TAB1 ENSG00000230912 PLA2G6 CBX7 CBX6
GH22J039087 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 13.8 -218.2 -218158 5.6 HDGF ZSCAN4 IRF4 GLIS2 ETV6 RUNX3 EGR2 SMARCA5 GLIS1 ZNF341 LOC101927202 APOBEC3G APOBEC3H CBX6 NPTXR TAB1 ENSG00000228274 SYNGR1 CSNK1E CBX7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CBX6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CBX6 gene promoter:

Genomic Locations for CBX6 Gene

Genomic Locations for CBX6 Gene
chr22:38,861,216-38,872,334
(GRCh38/hg38)
Size:
11,119 bases
Orientation:
Minus strand
chr22:39,257,455-39,268,319
(GRCh37/hg19)

Genomic View for CBX6 Gene

Genes around CBX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CBX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CBX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CBX6 Gene

Proteins for CBX6 Gene

  • Protein details for CBX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95503-CBX6_HUMAN
    Recommended name:
    Chromobox protein homolog 6
    Protein Accession:
    O95503
    Secondary Accessions:
    • A8KAH0
    • Q96EM5

    Protein attributes for CBX6 Gene

    Size:
    412 amino acids
    Molecular mass:
    43898 Da
    Quaternary structure:
    • Component of a PRC1-like complex (PubMed:21282530). Distinct PRC1-like core complexes are composed of a RING1 subunit (RING1B or RING1A), one of the six PCGF proteins (PCGF1-6), one PHC protein (PHC1-3) and one of the CBX proteins (CBX2, CBX4, CBX6, CBX7 or CBX8) (PubMed:21282530). Interacts with PCGF1, PCGF2, PCGF3, BMI1, PCGF5, PCGF6, RING1 and RNF2 (PubMed:21282530, PubMed:18927235). May interact with HIST2H3A and HIST1H3A (PubMed:18927235). Interacts (via chromodomain) with single-stranded RNA (ssRNA) (By similarity).
    Miscellaneous:
    • The human orthologuous proteins of Drosphila Polycomb group protein Pc, CBX2, CBX4, CBX6, CBX7 and CBX8, show distinct nuclear localizations, contribute differently to transcriptional repression, and appear to be part of distinct PRC1-like protein complexes.

    Three dimensional structures from OCA and Proteopedia for CBX6 Gene

neXtProt entry for CBX6 Gene

Post-translational modifications for CBX6 Gene

  • Ubiquitination at posLast=100100
  • Modification sites at PhosphoSitePlus

Other Protein References for CBX6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CBX6 Gene

Domains & Families for CBX6 Gene

Gene Families for CBX6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CBX6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CBX6: view

No data available for UniProtKB/Swiss-Prot for CBX6 Gene

Function for CBX6 Gene

Molecular function for CBX6 Gene

UniProtKB/Swiss-Prot Function:
Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development (PubMed:21282530). PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A Lys-119, rendering chromatin heritably changed in its expressibility. Possibly contributes to the target selectivity of the PRC1 complex by binding specific regions of chromatin (PubMed:18927235). Recruitment to chromatin might occur in an H3K27me3-independent fashion (By similarity). May have a PRC1-independent function in embryonic stem cells (By similarity).
GENATLAS Biochemistry:
Drosophila polycomb-like (PcG) chromobox homolog 6,mouse ortholog,involved in the compaction of chromatin

Phenotypes From GWAS Catalog for CBX6 Gene

Gene Ontology (GO) - Molecular Function for CBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003727 single-stranded RNA binding IEA --
GO:0005515 protein binding IPI 18927235
genes like me logo Genes that share ontologies with CBX6: view
genes like me logo Genes that share phenotypes with CBX6: view

Animal Models for CBX6 Gene

MGI Knock Outs for CBX6:
  • Cbx6 Cbx6<tm1a(EUCOMM)Wtsi>

Animal Model Products

miRNA for CBX6 Gene

miRTarBase miRNAs that target CBX6

Clone Products

  • Addgene plasmids for CBX6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CBX6 Gene

Localization for CBX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CBX6 Gene

Nucleus. Chromosome. Note=Uniformely distributed in the nucleoplasm (PubMed:18927235). Localizes to the inactivated X chromosome in females (By similarity). {ECO:0000250 UniProtKB:Q9DBY5, ECO:0000269 PubMed:18927235}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CBX6 gene
Compartment Confidence
nucleus 5
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus IEA,IDA 21282530
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0031519 PcG protein complex IDA 21282530
genes like me logo Genes that share ontologies with CBX6: view

Pathways & Interactions for CBX6 Gene

genes like me logo Genes that share pathways with CBX6: view

Pathways by source for CBX6 Gene

Gene Ontology (GO) - Biological Process for CBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 21282530
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with CBX6: view

No data available for SIGNOR curated interactions for CBX6 Gene

Drugs & Compounds for CBX6 Gene

No Compound Related Data Available

Transcripts for CBX6 Gene

mRNA/cDNA for CBX6 Gene

Unigene Clusters for CBX6 Gene

Chromobox homolog 6:
Representative Sequences:

Clone Products

  • Addgene plasmids for CBX6

Alternative Splicing Database (ASD) splice patterns (SP) for CBX6 Gene

No ASD Table

Relevant External Links for CBX6 Gene

GeneLoc Exon Structure for
CBX6
ECgene alternative splicing isoforms for
CBX6

Expression for CBX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CBX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CBX6 Gene

This gene is overexpressed in Lung (21.1), Heart (10.8), Pancreas (8.4), Peripheral blood mononuclear cells (6.9), CD8 Tcells (6.3), and Fetal testis (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CBX6 Gene



Protein tissue co-expression partners for CBX6 Gene

NURSA nuclear receptor signaling pathways regulating expression of CBX6 Gene:

CBX6

SOURCE GeneReport for Unigene cluster for CBX6 Gene:

Hs.592201

Evidence on tissue expression from TISSUES for CBX6 Gene

  • Lung(4.2)
  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with CBX6: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CBX6 Gene

Orthologs for CBX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for CBX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CBX6 34 33
  • 99.82 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CBX6 34 33
  • 89.14 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CBX6 33
  • 89.14 (n)
mouse
(Mus musculus)
Mammalia Cbx6 16 34 33
  • 86.09 (n)
rat
(Rattus norvegicus)
Mammalia Cbx6 33
  • 85.42 (n)
oppossum
(Monodelphis domestica)
Mammalia CBX6 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CBX6 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx6 33
  • 67.61 (n)
Str.20464 33
zebrafish
(Danio rerio)
Actinopterygii LOC556231 33
  • 62.18 (n)
cbx6a 34
  • 38 (a)
OneToMany
cbx6b 34
  • 37 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Pc 34
  • 20 (a)
OneToMany
Species where no ortholog for CBX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CBX6 Gene

ENSEMBL:
Gene Tree for CBX6 (if available)
TreeFam:
Gene Tree for CBX6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CBX6: view image

Paralogs for CBX6 Gene

Paralogs for CBX6 Gene

(3) SIMAP similar genes for CBX6 Gene using alignment to 2 proteins:

  • CBX6_HUMAN
  • B0QXZ6_HUMAN
genes like me logo Genes that share paralogs with CBX6: view

Variants for CBX6 Gene

Sequence variations from dbSNP and Humsavar for CBX6 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000397628 -- 38,864,701(-) C/A 3_prime_UTR_variant
rs1000728666 -- 38,865,584(-) G/A 3_prime_UTR_variant
rs1000740137 -- 38,865,444(-) G/A 3_prime_UTR_variant
rs1001046923 -- 38,871,236(-) C/A intron_variant
rs1001059501 -- 38,870,908(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CBX6 Gene

Variant ID Type Subtype PubMed ID
dgv769n67 CNV gain 20364138
nsv1112815 CNV deletion 24896259
nsv471199 CNV loss 18288195
nsv520961 CNV loss 19592680
nsv525343 CNV loss 19592680
nsv589010 CNV loss 21841781
nsv829210 CNV loss 20364138

Variation tolerance for CBX6 Gene

Residual Variation Intolerance Score: 43.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.18; 23.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CBX6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CBX6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CBX6 Gene

Disorders for CBX6 Gene

Additional Disease Information for CBX6

No disorders were found for CBX6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CBX6 Gene

Publications for CBX6 Gene

  1. Recognition and specificity determinants of the human cbx chromodomains. (PMID: 21047797) Kaustov L … Arrowsmith CH (The Journal of biological chemistry 2011) 3 4 58
  2. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. (PMID: 21282530) Vandamme J … Angrand PO (Molecular & cellular proteomics : MCP 2011) 3 4 58
  3. A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci. (PMID: 20972438) Rothman N … Chanock SJ (Nature genetics 2010) 3 44 58
  4. Different polycomb group CBX family proteins associate with distinct regions of chromatin using nonhomologous protein sequences. (PMID: 18927235) Vincenz C … Kerppola TK (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for CBX6 Gene

  • Addgene plasmids for CBX6

Sources for CBX6 Gene

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