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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CBX6 Gene

protein-coding   GIFtS: 46
GCID: GC22M039257

chromobox homolog 6

  Search for CBX6
in our new
 Human Malady Compendium 
Biological research products
for CBX6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Chromobox Homolog 61 2
Chromobox Protein Homolog 62

External Ids:    HGNC: 15561   Entrez Gene: 234662   Ensembl: ENSG000001837417   UniProtKB: O955033   

Export aliases for CBX6 gene to outside databases

Previous GC identifers: GC22M035871 GC22M037500 GC22M037503 GC22M037584 GC22M022225


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: CBX6_HUMAN, O95503
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. 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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.1  NT_011520.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CBX6 gene promoter:
         AhR   Spz1   STAT1   ATF-2   RREB-1   STAT1beta   E47   STAT1alpha   CRE-BP1   Zic1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCBX6 promoter sequence
   Search SABiosciences Chromatin IP Primers for CBX6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CBX6


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q13.1   Ensembl cytogenetic band:  22q13.1   HGNC cytogenetic band: 22q13.1

CBX6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CBX6 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M039257:  view genomic region     (about GC identifiers)

Start:
39,257,455 bp from pter      End:
39,268,319 bp from pter
Size:
10,865 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CBX6_HUMAN, O95503 (See protein sequence)
Recommended Name: Chromobox protein homolog 6  
Size: 412 amino acids; 43898 Da
Subunit: Component of a PRC1-like complex. Interacts with PCGF1, PCGF2, PCGF3, BMI1, PCGF5, PCGF6, RING1 and RNF2
Subcellular location: Nucleus (By similarity)
Miscellaneous: The human orthologuous proteins of Drosphila Polycomb group protein Pc, CBX2, CBX4, CBX6, CBX7 and CBX8,
show distinct nulear localizations, contribute differently to transcriptional repression, and appear to be part of
distinct PRC1-like protein complexes
2 PDB 3D structures from and Proteopedia for CBX6:
3GV6 (3D)        3I90 (3D)    
Secondary accessions: A8KAH0 Q96EM5

Explore the universe of human proteins at neXtProt for CBX6: NX_O95503

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O95503

  • CBX6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055107.3  
    ENSEMBL proteins: 
     ENSP00000384490   ENSP00000216083  

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    Uscn Proteins for CBX6

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000792heterochromatin IEA--
    GO:0005634nucleus IDA--
    GO:0031519PcG protein complex IDA--


    CBX6 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CBX6 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR000953 Chromo_domain/shadow
     IPR023780 Chromo_domain
     IPR016197 Chromodomain-like
     IPR023779 Chromodomain_CS
     IPR017984 Chromo_dom_subgr

    Graphical View of Domain Structure for InterPro Entry O95503

    ProtoNet protein and cluster: O95503

    1 Blocks protein family: IPB000953 Chromo domain

    UniProtKB/Swiss-Prot: CBX6_HUMAN, O95503
    Similarity: Contains 1 chromo domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CBX6_HUMAN, O95503
    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. 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

         Genatlas biochemistry entry for CBX6:
    Drosophila polycomb-like (PcG) chromobox homolog 6,mouse ortholog,involved in the compaction of chromatin

    miRNA
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    hsa-miR-1321 hsa-miR-330-5p hsa-miR-938 hsa-miR-29a hsa-miR-507 hsa-miR-570 hsa-miR-890 hsa-miR-9
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003727single-stranded RNA binding IEA--
    GO:0005515protein binding IPI--


    CBX6 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for CBX6:
     Increased cell number in G2M,  

    Animal Models:
         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Cbx6):
     adipose tissue  cardiovascular system  growth/size  homeostasis/metabolism 

    CBX6 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CBX6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/105 Interacting proteins for CBX6 (O955031, 2, 3 ENSP000003844904) via UniProtKB, MINT, STRING, and/or I2D (see all 105)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628052, 3MINT-8010325 I2D: score=1 
    HIST1H4BP628052, 3MINT-8010325 I2D: score=1 
    HIST1H4CP628052, 3MINT-8010325 I2D: score=1 
    HIST1H4DP628052, 3MINT-8010325 I2D: score=1 
    HIST1H4EP628052, 3MINT-8010325 I2D: score=1 
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IMP--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0016568chromatin modification IEA--


    CBX6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CBX6
    Search CenterWatch for drugs/clinical trials and news about CBX6 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CBX6 gene: 
    NM_014292.3  

    Unigene Cluster for CBX6:

    Chromobox homolog 6
    Hs.592201  [show with all ESTs]
    Unigene Representative Sequence: NM_014292
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000407418(uc003awl.3) ENST00000216083 ENST00000469420(uc003awm.1)


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    8/42 QIAGEN miScript miRNA Assays for microRNAs that regulate CBX6 (see all 42):
    hsa-miR-1321 hsa-miR-330-5p hsa-miR-938 hsa-miR-29a hsa-miR-507 hsa-miR-570 hsa-miR-890 hsa-miR-9
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    Inhib. RNA
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    Additional cDNA sequence: 

    AK094829.1 AK293035.1 BC012111.1 BC064900.1 BC127848.1 

    11 DOTS entries:

    DT.411847  DT.100764798  DT.100030372  DT.100774140  DT.99933939  DT.75114816  DT.86842136  DT.100653721 
    DT.100775305  DT.100775304  DT.95203366 

    24/401 AceView cDNA sequences (see all 401):

    AA262944 AI458128 AW467549 AA988085 CR592957 AW299772 BQ673998 BU507736 
    AI360365 BX410088 BU501345 BE671383 BE219796 BU177591 AI951800 AW517688 
    BM273263 BE349092 CD625513 H55534 BF822168 AI457801 BU191576 CR621248 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CBX6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGCCCCTCCC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CBX6 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartAtrioventricular CanalAtrioventricular Canal CellsMyocardium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CBX6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CBX6

    SOURCE GeneReport for Unigene cluster: Hs.592201
        SABiosciences Expression via Pathway-Focused PCR Arrays including CBX6: 
              Polycomb & Trithorax Complexes in human mouse rat
              Epigenetic Chromatin Remodeling Factors in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CBX6

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for CBX6 gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CBX26
    Uncharacterized protein
    10(a)
    possible ortholog
    18(9617354-9618542)
    lizard
    (Anolis carolinensis)
    Reptilia NPTXR6
    --
    44(a)
    1 ↔ 1
    5(24307274-24385885)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.204642 Transcribed sequence with moderate similarity to protein refNP_055107.1 (H.sapiens) chromobox homolog 6 [Homo sapiens] less 77.09(n)    AL845721.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5562311 uncharacterized LOC556231 54.95(n)
    55.99(a)
      556231  XM_003198104.1  XP_003198152.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Pc6
    Polycomb
    19(a)
    1 → many
    3L(21299238-21311120)


    ENSEMBL Gene Tree for CBX6 (if available)
    TreeFam Gene Tree for CBX6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CBX6 gene
    NPTX22  APCS2  CRP2  PTX42  NPTX12  PTX32  NPTXR2  
    3 SIMAP similar genes for CBX6 using alignment to 2 protein entries:     CBX6_HUMAN (see all proteins):
    CBX5    CBX1    CBX7

    CBX6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for CBX6
         1 CNV: 50864
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CBX6
    DNA2.0 Custom Variant and Variant Library Synthesis for CBX6

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CBX6 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with CBX6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Recognition and specificity determinants of the human cbx chromodomains. (PubMed id 21047797)1, 2 Kaustov L.... Arrowsmith C.H. (2011)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I....O'Brien K.P. (1999)
    5. PCGF homologs, CBX proteins, and RYBP define functiona lly distinct PRC1 family complexes. (PubMed id 22325352)1 Gao Z....Reinberg D. (2012)
    6. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    7. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 Complexes in mammalian cells. (PubMed id 21282530)2 Vandamme J.... Angrand P.O. (2011)
    8. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. A multi-stage genome-wide association study of bladde r cancer identifies multiple susceptibility loci. (PubMed id 20972438)1 Rothman N....Chanock S.J. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23466 HGNC: 1556 AceView: CBX6 Ensembl:ENSG00000183741 euGenes: HUgn23466
    ECgene: CBX6 H-InvDB: CBX6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CBX6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CBX6 gene:
    Search GeneIP for patents involving CBX6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
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     CBX6 Proteins, Antibodies, CLIAs, and ELISAs
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     Search ThermoFisher Antibodies for CBX6
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CBX6
           
    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    VWF
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    von Willebrand factor
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