Human Gene CBX6 (ENST00000407418.8_10) from GENCODE V47lift37
  Description: chromobox 6, transcript variant 1 (from RefSeq NM_014292.5)
Gencode Transcript: ENST00000407418.8_10
Gencode Gene: ENSG00000183741.12_12
Transcript (Including UTRs)
   Position: hg19 chr22:39,257,427-39,268,221 Size: 10,795 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr22:39,262,214-39,268,195 Size: 5,982 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:39,257,427-39,268,221)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBX6_HUMAN
DESCRIPTION: RecName: Full=Chromobox protein homolog 6;
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.
SUBUNIT: Component of a PRC1-like complex. Interacts with PCGF1, PCGF2, PCGF3, BMI1, PCGF5, PCGF6, RING1 and RNF2.
INTERACTION: P35226:BMI1; NbExp=2; IntAct=EBI-3951758, EBI-2341576; Q3KNV8:PCGF3; NbExp=2; IntAct=EBI-3951758, EBI-2339807; Q06587:RING1; NbExp=3; IntAct=EBI-3951758, EBI-752313; Q99496:RNF2; NbExp=3; IntAct=EBI-3951758, EBI-722416;
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.
SIMILARITY: Contains 1 chromo domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 58.61 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 1114.16 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.4026-0.208 Picture PostScript Text
3' UTR -2115.004787-0.442 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017984 - Chromo_dom_subgr
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS

Pfam Domains:
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF17218 - CBX family C-terminal motif

SCOP Domains:
54160 - Chromo domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3GV6 - X-ray MuPIT 3I90 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95503
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003727 single-stranded RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0031519 PcG protein complex


-  Descriptions from all associated GenBank mRNAs
  JD192775 - Sequence 173799 from Patent EP1572962.
JD118636 - Sequence 99660 from Patent EP1572962.
JD401158 - Sequence 382182 from Patent EP1572962.
JD121236 - Sequence 102260 from Patent EP1572962.
JD498457 - Sequence 479481 from Patent EP1572962.
BC012111 - Homo sapiens chromobox homolog 6, mRNA (cDNA clone MGC:20115 IMAGE:4554483), complete cds.
BC064900 - Homo sapiens chromobox homolog 6, mRNA (cDNA clone MGC:74950 IMAGE:6009294), complete cds.
JD502588 - Sequence 483612 from Patent EP1572962.
JD150645 - Sequence 131669 from Patent EP1572962.
JD304379 - Sequence 285403 from Patent EP1572962.
JD453528 - Sequence 434552 from Patent EP1572962.
JD521485 - Sequence 502509 from Patent EP1572962.
JD402537 - Sequence 383561 from Patent EP1572962.
JD394443 - Sequence 375467 from Patent EP1572962.
JD425128 - Sequence 406152 from Patent EP1572962.
JD179387 - Sequence 160411 from Patent EP1572962.
JD165121 - Sequence 146145 from Patent EP1572962.
JD519192 - Sequence 500216 from Patent EP1572962.
JD125502 - Sequence 106526 from Patent EP1572962.
JD122867 - Sequence 103891 from Patent EP1572962.
JD066030 - Sequence 47054 from Patent EP1572962.
JD278693 - Sequence 259717 from Patent EP1572962.
JD085230 - Sequence 66254 from Patent EP1572962.
JD124422 - Sequence 105446 from Patent EP1572962.
JD046527 - Sequence 27551 from Patent EP1572962.
JD559546 - Sequence 540570 from Patent EP1572962.
JD108206 - Sequence 89230 from Patent EP1572962.
JD374935 - Sequence 355959 from Patent EP1572962.
JD400483 - Sequence 381507 from Patent EP1572962.
JD397642 - Sequence 378666 from Patent EP1572962.
JD399525 - Sequence 380549 from Patent EP1572962.
JD516293 - Sequence 497317 from Patent EP1572962.
JD311232 - Sequence 292256 from Patent EP1572962.
JD166949 - Sequence 147973 from Patent EP1572962.
JD559615 - Sequence 540639 from Patent EP1572962.
JD539040 - Sequence 520064 from Patent EP1572962.
JD483690 - Sequence 464714 from Patent EP1572962.
JD077059 - Sequence 58083 from Patent EP1572962.
JD116028 - Sequence 97052 from Patent EP1572962.
JD216283 - Sequence 197307 from Patent EP1572962.
JD116027 - Sequence 97051 from Patent EP1572962.
JD038546 - Sequence 19570 from Patent EP1572962.
JD493620 - Sequence 474644 from Patent EP1572962.
JD219357 - Sequence 200381 from Patent EP1572962.
AK293035 - Homo sapiens cDNA FLJ75278 complete cds, highly similar to Homo sapiens chromobox homolog 6, mRNA.
JD054331 - Sequence 35355 from Patent EP1572962.
JD404585 - Sequence 385609 from Patent EP1572962.
KJ898494 - Synthetic construct Homo sapiens clone ccsbBroadEn_07888 CBX6 gene, encodes complete protein.
DQ893667 - Synthetic construct clone IMAGE:100006297; FLH187655.01X; RZPDo839B09150D chromobox homolog 6 (CBX6) gene, encodes complete protein.
DQ895787 - Synthetic construct Homo sapiens clone IMAGE:100010247; FLH187651.01L; RZPDo839B09149D chromobox homolog 6 (CBX6) gene, encodes complete protein.
KJ906091 - Synthetic construct Homo sapiens clone ccsbBroadEn_15761 CBX6 gene, encodes complete protein.
CU687960 - Synthetic construct Homo sapiens gateway clone IMAGE:100021788 5' read CBX6 mRNA.
CU680218 - Synthetic construct Homo sapiens gateway clone IMAGE:100017644 5' read CBX6 mRNA.
AK094829 - Homo sapiens cDNA FLJ37510 fis, clone BRCAN1000149, moderately similar to Chromobox protein homolog 6.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95503 (Reactome details) participates in the following event(s):

R-HSA-3229089 PRC1.4 complex binds H3K27Me3 nucleosomes on CDKN2A promoter
R-HSA-3229102 p-MAPKAPK3 phosphorylates BMI1
R-HSA-8937989 RUNX1 binds PRC1 complexes
R-HSA-8943817 MECOM (EVI1) recruits polycomb repressor complexes (PRCs) to the PTEN gene promoter
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-2559583 Cellular Senescence
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-6807070 PTEN Regulation
R-HSA-2262752 Cellular responses to stress
R-HSA-212436 Generic Transcription Pathway
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-74160 Gene expression (Transcription)
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A8KAH0, CBX6_HUMAN, ENST00000407418.1, ENST00000407418.2, ENST00000407418.3, ENST00000407418.4, ENST00000407418.5, ENST00000407418.6, ENST00000407418.7, NM_014292, O95503, Q96EM5, uc319dwe.1, uc319dwe.2
UCSC ID: ENST00000407418.8_10
RefSeq Accession: NM_014292.5
Protein: O95503 (aka CBX6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.