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Aliases for CBX4 Gene

Aliases for CBX4 Gene

  • Chromobox 4 2 3 5
  • Chromobox Protein Homolog 4 3 4
  • NS5ATP1-Binding Protein 16 2 3
  • Polycomb 2 Homolog 3 4
  • PC2 3 4
  • Chromobox Homolog 4 (Pc Class Homolog, Drosophila) 3
  • Chromobox Homolog 4 (Drosophila Pc Class) 2
  • Pc Class 2 Homolog (Drosophila) 2
  • E3 SUMO-Protein Ligase CBX4 3
  • Chromobox-Like Protein 4 3
  • Chromobox Homolog 4 2
  • Pc Class 2 Homolog 3
  • EC 6.3.2.- 4
  • NBP16 3
  • HPc2 4

External Ids for CBX4 Gene

Previous GeneCards Identifiers for CBX4 Gene

  • GC17M077736
  • GC17M081095
  • GC17M078371
  • GC17M078507
  • GC17M075422
  • GC17M077806
  • GC17M073247

Summaries for CBX4 Gene

GeneCards Summary for CBX4 Gene

CBX4 (Chromobox 4) is a Protein Coding gene. Among its related pathways are Cellular Senescence (REACTOME) and SUMOylation. GO annotations related to this gene include chromatin binding and ligase activity. An important paralog of this gene is CBX6.

UniProtKB/Swiss-Prot for CBX4 Gene

  • 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. Monosumoylates ZNF131.

  • 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.

Additional gene information for CBX4 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 CBX4 Gene

Genomics for CBX4 Gene

Regulatory Elements for CBX4 Gene

Enhancers for CBX4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17H079808 2 FANTOM5 Ensembl ENCODE dbSUPER 12 +26.9 26860 8 HDGF PKNOX1 ZFP64 ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF766 ZNF416 CBX8 EIF4A3 ENSG00000262768 CBX2 CBX4 USP36 ENGASE CCDC40 PIR54271
GH17H079942 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.7 -103.4 -103377 1 SRF ESRRA ATF1 NFIB ELF1 ZBTB8A ATF2 NR2F2 CTBP1 CREB1 CBX4 SGSH GC17P079941 PIR49167
GH17H079745 1.4 Ensembl ENCODE dbSUPER 11.2 +92.1 92061 3 HDGF FOXA2 ZNF2 ZNF143 RUNX3 NCOA1 REST KAT8 SSRP1 MIER3 CBX2 CBX4 ENPP7
GH17H079792 1.3 Ensembl ENCODE dbSUPER 11.8 +45.7 45678 3 TBP KLF17 SIN3A RFX5 ZNF121 ZNF366 ZSCAN5C SMARCC1 ZNF680 ZNF362 CBX8 CBX4 GC17P079785 ENSG00000262768
GH17H079948 1.3 Ensembl ENCODE dbSUPER 11.3 -111.6 -111624 5 BCOR RING1 SOX13 PKNOX1 MXI1 ESRRA ZMYM3 ZIC2 TEAD3 ZFHX2 LOC100294362 ENDOV CBX4 CBX2 CCDC40 PIR49167 ENSG00000275516
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CBX4 on UCSC Golden Path with GeneCards custom track

Promoters for CBX4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000284666 529 2201 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF766 ZNF143

Genomic Location for CBX4 Gene

Chromosome:
17
Start:
79,833,156 bp from pter
End:
79,839,429 bp from pter
Size:
6,274 bases
Orientation:
Minus strand

Genomic View for CBX4 Gene

Genes around CBX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CBX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CBX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CBX4 Gene

Proteins for CBX4 Gene

  • Protein details for CBX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00257-CBX4_HUMAN
    Recommended name:
    E3 SUMO-protein ligase CBX4
    Protein Accession:
    O00257
    Secondary Accessions:
    • B1PJR7
    • Q6TPI8
    • Q96C04

    Protein attributes for CBX4 Gene

    Size:
    560 amino acids
    Molecular mass:
    61368 Da
    Quaternary structure:
    • Interacts with histone H3-K9Me3. Interacts with CHTOP (By similarity). Component of a PRC1-like complex. Self-associates. Interacts with SUV39H1 and HIPK2. Interacts with CSNK2B.
    Miscellaneous:
    • The human orthologs of the Drosophila Polycomb group protein Pc are CBX2, CBX4, CBX6, CBX7 and CBX8. These show distinct nuclear localizations, contribute differently to transcriptional repression, and appear to be part of distinct PRC1-like protein complexes. The hPRC-H complex purified in PubMed:12167701 probably presents a mixture of different complexes containing different Polycomb group proteins.
    SequenceCaution:
    • Sequence=AAH14967.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CBX4 Gene

    Alternative splice isoforms for CBX4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CBX4 Gene

Post-translational modifications for CBX4 Gene

  • 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.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CBX4 Gene

No data available for DME Specific Peptides for CBX4 Gene

Domains & Families for CBX4 Gene

Gene Families for CBX4 Gene

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

Suggested Antigen Peptide Sequences for CBX4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O00257

UniProtKB/Swiss-Prot:

CBX4_HUMAN :
  • The polyhistidine repeat may act as a targeting signal to nuclear speckles.
Domain:
  • The polyhistidine repeat may act as a targeting signal to nuclear speckles.
genes like me logo Genes that share domains with CBX4: view

Function for CBX4 Gene

Molecular function for CBX4 Gene

UniProtKB/Swiss-Prot 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. Monosumoylates ZNF131.
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. 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.

Enzyme Numbers (IUBMB) for CBX4 Gene

Phenotypes From GWAS Catalog for CBX4 Gene

Gene Ontology (GO) - Molecular Function for CBX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0003714 transcription corepressor activity TAS 9315667
GO:0003727 single-stranded RNA binding IEA --
GO:0005515 protein binding IPI 15710417
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with CBX4: view
genes like me logo Genes that share phenotypes with CBX4: view

Animal Models for CBX4 Gene

MGI Knock Outs for CBX4:

Animal Model Products

CRISPR Products

miRNA for CBX4 Gene

miRTarBase miRNAs that target CBX4

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX4
  • Applied Biological Materials Clones for CBX4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CBX4 Gene

Localization for CBX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CBX4 Gene

Nucleus. Nucleus speckle. Note=Localization to nuclear polycomb bodies is required for ZNF131 sumoylation (PubMed:22467880).

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 CBX4 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CBX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 9367786
GO:0005654 nucleoplasm TAS --
GO:0016604 nuclear body IEA,IDA --
GO:0016607 nuclear speck IEA --
GO:0031519 PcG protein complex IDA 21282530
genes like me logo Genes that share ontologies with CBX4: view

Pathways & Interactions for CBX4 Gene

genes like me logo Genes that share pathways with CBX4: view

Pathways by source for CBX4 Gene

UniProtKB/Swiss-Prot O00257-CBX4_HUMAN

  • Pathway: Protein modification; protein sumoylation.

Gene Ontology (GO) - Biological Process for CBX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 21282530
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0016925 protein sumoylation IEA --
genes like me logo Genes that share ontologies with CBX4: view

No data available for SIGNOR curated interactions for CBX4 Gene

Drugs & Compounds for CBX4 Gene

(2) Drugs for CBX4 Gene - From: ApexBio and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
UNC3866 Pharma a potent antagonist of CBX4 and CBX7 chromodomains 0

(1) ApexBio Compounds for CBX4 Gene

Compound Action Cas Number
UNC3866 a potent antagonist of CBX4 and CBX7 chromodomains
genes like me logo Genes that share compounds with CBX4: view

Drug Products

Transcripts for CBX4 Gene

Unigene Clusters for CBX4 Gene

Chromobox homolog 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX4
  • Applied Biological Materials Clones for CBX4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for CBX4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c · 5d
SP1: - -
SP2: - - -
SP3:
SP4: -

Relevant External Links for CBX4 Gene

GeneLoc Exon Structure for
CBX4
ECgene alternative splicing isoforms for
CBX4

Expression for CBX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CBX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CBX4 Gene

This gene is overexpressed in Platelet (65.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CBX4 Gene



Protein tissue co-expression partners for CBX4 Gene

NURSA nuclear receptor signaling pathways regulating expression of CBX4 Gene:

CBX4

SOURCE GeneReport for Unigene cluster for CBX4 Gene:

Hs.405046

mRNA Expression by UniProt/SwissProt for CBX4 Gene:

O00257-CBX4_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for CBX4 Gene

  • Intestine(4.2)
  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with CBX4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CBX4 Gene

Orthologs for CBX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for CBX4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CBX4 33 34
  • 99.76 (n)
cow
(Bos Taurus)
Mammalia CBX4 33 34
  • 91.15 (n)
dog
(Canis familiaris)
Mammalia CBX4 33 34
  • 89.77 (n)
rat
(Rattus norvegicus)
Mammalia Cbx4 33
  • 88.77 (n)
mouse
(Mus musculus)
Mammalia Cbx4 33 16 34
  • 85.85 (n)
oppossum
(Monodelphis domestica)
Mammalia CBX4 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves CBX4 33 34
  • 76.96 (n)
lizard
(Anolis carolinensis)
Reptilia CBX4 34
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx4 33
  • 58.75 (n)
Str.19494 33
African clawed frog
(Xenopus laevis)
Amphibia cbx4-A-prov 33
zebrafish
(Danio rerio)
Actinopterygii cbx4 33 34
  • 57 (n)
Dr.20970 33
fruit fly
(Drosophila melanogaster)
Insecta Pc 34
  • 21 (a)
OneToMany
Species where no ortholog for CBX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 CBX4 Gene

ENSEMBL:
Gene Tree for CBX4 (if available)
TreeFam:
Gene Tree for CBX4 (if available)

Paralogs for CBX4 Gene

Paralogs for CBX4 Gene

(6) SIMAP similar genes for CBX4 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CBX4: view

Variants for CBX4 Gene

Sequence variations from dbSNP and Humsavar for CBX4 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000012052 -- 79,840,693(+) GACAG(A/C)GCGGC upstream-variant-2KB
rs1000043234 -- 79,840,553(+) CCTCC(G/T)GCGGC upstream-variant-2KB
rs1000075979 -- 79,840,295(+) GGGAG(A/G)CCAGG upstream-variant-2KB
rs1000429929 -- 79,835,518(+) TGGGA(C/G)GTCTA intron-variant
rs1000922342 -- 79,835,781(+) CGGAA(A/T)CTTCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CBX4 Gene

Variant ID Type Subtype PubMed ID
dgv538n67 CNV gain 20364138
nsv469865 CNV loss 16826518
nsv828116 CNV loss 20364138
nsv828120 CNV gain 20364138

Variation tolerance for CBX4 Gene

Residual Variation Intolerance Score: 22.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.20; 76.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CBX4 Gene

Human Gene Mutation Database (HGMD)
CBX4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CBX4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CBX4 Gene

Disorders for CBX4 Gene

Relevant External Links for CBX4

Genetic Association Database (GAD)
CBX4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CBX4

No disorders were found for CBX4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CBX4 Gene

Publications for CBX4 Gene

  1. Pc2-mediated sumoylation of Smad-interacting protein 1 attenuates transcriptional repression of E-cadherin. (PMID: 16061479) Long J … Park M (The Journal of biological chemistry 2005) 3 4 22 60
  2. Multiple activities contribute to Pc2 E3 function. (PMID: 15592428) Kagey MH … Wotton D (The EMBO journal 2005) 3 4 22 60
  3. The polycomb protein Pc2 is a SUMO E3. (PMID: 12679040) Kagey MH … Wotton D (Cell 2003) 3 4 22 60
  4. Interference with the expression of a novel human polycomb protein, hPc2, results in cellular transformation and apoptosis. (PMID: 9315667) Satijn DP … Otte AP (Molecular and cellular biology 1997) 2 3 4 60
  5. DNA damage-induced heterogeneous nuclear ribonucleoprotein K sumoylation regulates p53 transcriptional activation. (PMID: 22825850) Pelisch F … Srebrow A (The Journal of biological chemistry 2012) 3 4 60

Products for CBX4 Gene

  • Addgene plasmids for CBX4

Sources for CBX4 Gene

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