Human Gene CBX4 (ENST00000269397.9_10) from GENCODE V47lift37
  Description: chromobox 4 (from RefSeq NM_003655.3)
Gencode Transcript: ENST00000269397.9_10
Gencode Gene: ENSG00000141582.15_12
Transcript (Including UTRs)
   Position: hg19 chr17:77,806,955-77,813,239 Size: 6,285 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:77,807,758-77,813,050 Size: 5,293 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 (chr17:77,806,955-77,813,239)mRNA (may differ from genome)Protein (560 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBX4_HUMAN
DESCRIPTION: RecName: Full=E3 SUMO-protein ligase CBX4; EC=6.3.2.-; AltName: Full=Chromobox protein homolog 4; AltName: Full=Polycomb 2 homolog; Short=Pc2; Short=hPc2;
FUNCTION: E3 SUMO-protein ligase which facilitates SUMO1 conjugation by UBE2I. Involved in the sumoylation of HNRNPK, a p53/TP53 transcriptional coactivator, hence indirectly regulates p53/TP53 transcriptional activation resulting in p21/CDKN1A expression.
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.
PATHWAY: Protein modification; protein sumoylation.
SUBUNIT: Interacts with histone H3-K9Me3 (By similarity). Component of a PRC1-like complex. Self-associates. Interacts with SUV39H1 and HIPK2. Interacts with CSNK2B.
INTERACTION: P35226:BMI1; NbExp=2; IntAct=EBI-4392727, EBI-2341576; P68400:CSNK2A1; NbExp=2; IntAct=EBI-4392727, EBI-347804; P67870:CSNK2B; NbExp=2; IntAct=EBI-4392727, EBI-348169; Q9BYE7:PCGF6; NbExp=2; IntAct=EBI-4392727, EBI-1048026; Q99496:RNF2; NbExp=2; IntAct=EBI-4392727, EBI-722416; P31946:YWHAB; NbExp=2; IntAct=EBI-722425, EBI-359815; P62258:YWHAE; NbExp=2; IntAct=EBI-4392727, EBI-356498; P63104:YWHAZ; NbExp=2; IntAct=EBI-4392727, EBI-347088;
SUBCELLULAR LOCATION: Nucleus. Nucleus speckle.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: The polyhistidine repeat may act as a targeting signal to nuclear speckles (PubMed:19266028).
PTM: Phosphorylated on Thr-497 by HIPK2 upon DNA damage. This phosphorylation stimulates E3 SUMO-protein ligase activity and promotes sumoylation on Lys-494, as well as sumoylation of other target proteins, such as HNRNPK.
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.
SEQUENCE CAUTION: Sequence=AAH14967.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  Primer design for this transcript
 

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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: 16.97 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 386.09 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 -126.00189-0.667 Picture PostScript Text
3' UTR -254.90803-0.317 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
2K28 - NMR MuPIT 3I8Z - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00257
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-  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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0003714 transcription corepressor activity
GO:0003727 single-stranded RNA binding
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0019789 SUMO transferase activity
GO:0019899 enzyme binding
GO:0032183 SUMO binding
GO:0035064 methylated histone binding
GO:0044212 transcription regulatory region DNA binding
GO:0051219 phosphoprotein 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
GO:0016925 protein sumoylation
GO:0043066 negative regulation of apoptotic process
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body
GO:0016607 nuclear speck
GO:0031519 PcG protein complex
GO:0035102 PRC1 complex


-  Descriptions from all associated GenBank mRNAs
  BC014967 - Homo sapiens chromobox homolog 4 (Pc class homolog, Drosophila), mRNA (cDNA clone MGC:23084 IMAGE:4856728), complete cds.
EU439707 - Homo sapiens CBX4 (CBX4) mRNA, complete cds.
AF013956 - Homo sapiens Polycomb 2 homolog (hPc2) mRNA, complete cds.
JD166646 - Sequence 147670 from Patent EP1572962.
AY390430 - Homo sapiens NS5ATP1-binding protein 16 mRNA, complete cds.
KJ904603 - Synthetic construct Homo sapiens clone ccsbBroadEn_13997 CBX4 gene, encodes complete protein.
U94344 - Human Polycomb 2 homolog (hPc2) mRNA, partial cds.
KU178422 - Homo sapiens chromobox-like protein 4 isoform 1 (CBX4) mRNA, partial cds, alternatively spliced.
KU178423 - Homo sapiens chromobox-like protein 4 isoform 2 (CBX4) mRNA, partial cds.
AB463501 - Synthetic construct DNA, clone: pF1KB7867, Homo sapiens CBX4 gene for chromobox homolog 4, without stop codon, in Flexi system.
CU677141 - Synthetic construct Homo sapiens gateway clone IMAGE:100018080 5' read CBX4 mRNA.
JD337269 - Sequence 318293 from Patent EP1572962.
JD458948 - Sequence 439972 from Patent EP1572962.

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

Protein O00257 (Reactome details) participates in the following event(s):

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-4551727 CBX4 SUMOylates CBX4 in PRC1 with SUMO1
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: B1PJR7, CBX4_HUMAN, ENST00000269397.1, ENST00000269397.2, ENST00000269397.3, ENST00000269397.4, ENST00000269397.5, ENST00000269397.6, ENST00000269397.7, ENST00000269397.8, NM_003655, O00257, Q6TPI8, Q96C04, uc317irm.1, uc317irm.2
UCSC ID: ENST00000269397.9_10
RefSeq Accession: NM_003655.3
Protein: O00257 (aka CBX4_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.