Human Gene CBX8 (ENST00000269385.9_7) from GENCODE V47lift37
  Description: chromobox 8 (from RefSeq NM_020649.3)
Gencode Transcript: ENST00000269385.9_7
Gencode Gene: ENSG00000141570.11_10
Transcript (Including UTRs)
   Position: hg19 chr17:77,765,931-77,770,876 Size: 4,946 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:77,768,434-77,770,797 Size: 2,364 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:77,765,931-77,770,876)mRNA (may differ from genome)Protein (389 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBX8_HUMAN
DESCRIPTION: RecName: Full=Chromobox protein homolog 8; AltName: Full=Polycomb 3 homolog; Short=Pc3; Short=hPc3; AltName: Full=Rectachrome 1;
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 RING1 RNF2, PCGF1, PCGF2, PCGF3, BMI1, PCGF5 AND PCGF6. Interacts with MLLT3 and histone H3. Interacts with PHC2 (By similarity).
INTERACTION: P35226:BMI1; NbExp=6; IntAct=EBI-712912, EBI-2341576; Q92993:KAT5; NbExp=2; IntAct=EBI-712912, EBI-399080; Q9BSM1:PCGF1; NbExp=2; IntAct=EBI-712912, EBI-749901; P35227:PCGF2; NbExp=6; IntAct=EBI-712912, EBI-2129767; Q3KNV8:PCGF3; NbExp=3; IntAct=EBI-712912, EBI-2339807; Q86SE9:PCGF5; NbExp=2; IntAct=EBI-712912, EBI-2827999; Q9BYE7:PCGF6; NbExp=2; IntAct=EBI-712912, EBI-1048026; Q06587:RING1; NbExp=3; IntAct=EBI-712912, EBI-752313; Q99496:RNF2; NbExp=4; IntAct=EBI-712912, EBI-722416;
SUBCELLULAR LOCATION: Nucleus.
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. The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different 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


-  MalaCards Disease Associations
  MalaCards Gene Search: CBX8
Diseases sorted by gene-association score: conversion disorder (7)

-  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: 5.48 RPKM in Testis
Total median expression: 54.73 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 -27.2079-0.344 Picture PostScript Text
3' UTR -999.302503-0.399 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
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
3I91 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HC52
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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 SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003727 single-stranded RNA binding
GO:0005515 protein binding
GO:0035064 methylated histone binding
GO:0097027 ubiquitin-protein transferase activator activity

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
GO:0008284 positive regulation of cell proliferation
GO:0016574 histone ubiquitination
GO:0032967 positive regulation of collagen biosynthetic process
GO:0045739 positive regulation of DNA repair
GO:0050790 regulation of catalytic activity
GO:0070301 cellular response to hydrogen peroxide

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0000790 nuclear chromatin
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031519 PcG protein complex
GO:0035102 PRC1 complex


-  Descriptions from all associated GenBank mRNAs
  JD054851 - Sequence 35875 from Patent EP1572962.
AF266479 - Homo sapiens rectachrome 1 (RC1) mRNA, complete cds.
AF174482 - Homo sapiens polycomb 3 mRNA, complete cds.
BC009376 - Homo sapiens chromobox homolog 8 (Pc class homolog, Drosophila), mRNA (cDNA clone MGC:15083 IMAGE:4121509), complete cds.
BC008937 - Homo sapiens chromobox homolog 8 (Pc class homolog, Drosophila), mRNA (cDNA clone MGC:2402 IMAGE:2821280), complete cds.
BC019289 - Homo sapiens chromobox homolog 8 (Pc class homolog, Drosophila), mRNA (cDNA clone MGC:4043 IMAGE:2821280), complete cds.
AK074560 - Homo sapiens cDNA FLJ90079 fis, clone HEMBA1004785, weakly similar to MODIFIER 3 PROTEIN.
JD364781 - Sequence 345805 from Patent EP1572962.
JD054315 - Sequence 35339 from Patent EP1572962.
JD126135 - Sequence 107159 from Patent EP1572962.
JD220558 - Sequence 201582 from Patent EP1572962.
JD560464 - Sequence 541488 from Patent EP1572962.
JD108914 - Sequence 89938 from Patent EP1572962.
JD068754 - Sequence 49778 from Patent EP1572962.
JD177205 - Sequence 158229 from Patent EP1572962.
JD466680 - Sequence 447704 from Patent EP1572962.
KJ904835 - Synthetic construct Homo sapiens clone ccsbBroadEn_14229 CBX8 gene, encodes complete protein.
EU446831 - Synthetic construct Homo sapiens clone IMAGE:100069841; IMAGE:100012040; FLH258545.01L chromobox homolog 8 (Pc class homolog, Drosophila) (CBX8) gene, encodes complete protein.
AB384672 - Synthetic construct DNA, clone: pF1KB0038, Homo sapiens CBX8 gene for chromobox protein homolog 8, complete cds, without stop codon, in Flexi system.
CU679333 - Synthetic construct Homo sapiens gateway clone IMAGE:100017155 5' read CBX8 mRNA.
LF212475 - JP 2014500723-A/19978: Polycomb-Associated Non-Coding RNAs.
LF213281 - JP 2014500723-A/20784: Polycomb-Associated Non-Coding RNAs.
JD466223 - Sequence 447247 from Patent EP1572962.
JD538070 - Sequence 519094 from Patent EP1572962.
JD230830 - Sequence 211854 from Patent EP1572962.
JD227936 - Sequence 208960 from Patent EP1572962.
MA448052 - JP 2018138019-A/19978: Polycomb-Associated Non-Coding RNAs.
MA448858 - JP 2018138019-A/20784: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9HC52 (Reactome details) participates in the following event(s):

R-HSA-4551727 CBX4 SUMOylates CBX4 in PRC1 with SUMO1
R-HSA-4551655 CBX4 SUMOylates BMI1 in PRC1 with SUMO1
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-4570463 CBX4 (Pc2) SUMOylates CETN2 with SUMO2,3
R-HSA-4570499 CBX4 (Pc2) SUMOylates HNRNPK with SUMO2
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2990846 SUMOylation
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-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-597592 Post-translational protein modification
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-6807070 PTEN Regulation
R-HSA-2262752 Cellular responses to stress
R-HSA-392499 Metabolism of proteins
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: CBX8_HUMAN, ENST00000269385.1, ENST00000269385.2, ENST00000269385.3, ENST00000269385.4, ENST00000269385.5, ENST00000269385.6, ENST00000269385.7, ENST00000269385.8, NM_020649, PC3, Q96H39, Q9HC52, Q9NR07, RC1, uc317irg.1, uc317irg.2
UCSC ID: ENST00000269385.9_7
RefSeq Accession: NM_020649.3
Protein: Q9HC52 (aka CBX8_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.