At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association o... See more...

Aliases for CBX3 Gene

Aliases for CBX3 Gene

  • Chromobox 3 2 3 5
  • Heterochromatin Protein 1 Homolog Gamma 3 4
  • Chromobox Protein Homolog 3 3 4
  • Modifier 2 Protein 3 4
  • HP1Hs-Gamma 2 3
  • HECH 3 4
  • Chromobox Homolog 3 (HP1 Gamma Homolog, Drosophila) 3
  • Chromobox Homolog 3 (Drosophila HP1 Gamma) 2
  • Heterochromatin Protein HP1 Gamma 3
  • HP1 Gamma Homolog (Drosophila) 2
  • Heterochromatin-Like Protein 1 3
  • Chromobox Homolog 3 2
  • HP1 Gamma Homolog 3
  • HP1-GAMMA 3
  • HP1 Gamma 4
  • CBX3 5

External Ids for CBX3 Gene

Previous GeneCards Identifiers for CBX3 Gene

  • GC07P025883
  • GC07P025983
  • GC07P026014
  • GC07P026207
  • GC07P026240

Summaries for CBX3 Gene

Entrez Gene Summary for CBX3 Gene

  • At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.[provided by RefSeq, Mar 2011]

GeneCards Summary for CBX3 Gene

CBX3 (Chromobox 3) is a Protein Coding gene. Diseases associated with CBX3 include Hyperoxaluria, Primary, Type I and Carbohydrate Metabolic Disorder. Among its related pathways are Shigellosis and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein domain specific binding. An important paralog of this gene is CBX1.

UniProtKB/Swiss-Prot Summary for CBX3 Gene

  • Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1. Mediates the recruitment of NIPBL to sites of DNA damage at double-strand breaks (DSBs) (PubMed:28167679).

Gene Wiki entry for CBX3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CBX3 Gene

Genomics for CBX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CBX3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CBX3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CBX3

Top Transcription factor binding sites by QIAGEN in the CBX3 gene promoter:
  • p53
  • STAT1

Genomic Locations for CBX3 Gene

Genomic Locations for CBX3 Gene
chr7:26,201,162-26,213,607
(GRCh38/hg38)
Size:
12,446 bases
Orientation:
Plus strand
chr7:26,240,782-26,253,227
(GRCh37/hg19)
Size:
12,446 bases
Orientation:
Plus strand

Genomic View for CBX3 Gene

Genes around CBX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CBX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CBX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CBX3 Gene

Proteins for CBX3 Gene

  • Protein details for CBX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13185-CBX3_HUMAN
    Recommended name:
    Chromobox protein homolog 3
    Protein Accession:
    Q13185
    Secondary Accessions:
    • Q96CD7
    • Q99409
    • Q9BVS3
    • Q9P0Z6

    Protein attributes for CBX3 Gene

    Size:
    183 amino acids
    Molecular mass:
    20811 Da
    Quaternary structure:
    • Binds directly to CHAF1A. Interacts with histone H3 methylated at 'Lys-9' (PubMed:11242053). Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2. Interacts with INCENP, TRIM28/TIF1B, KMT5B, KMT5C and SP100 (PubMed:10330177, PubMed:12004135, PubMed:9636146). Interacts with TIF1A (By similarity). Interacts with MIS12 and DSN1 (PubMed:15502821). Can interact directly with CBX5 via the chromoshadow domain (PubMed:9169472). Interacts with POGZ (PubMed:20850016, PubMed:20562864). Interacts with CHAMP1 (PubMed:20850016). The large PER complex involved in the histone methylation is composed of at least PER2, CBX3, TRIM28, SUV39H1 and/or SUV39H2; CBX3 mediates the formation of the complex. Interacts with INCENP (PubMed:9864353, PubMed:21346195). Interacts with NIPBL (via PxVxL motif) (PubMed:28167679). Interacts with LRIF1 (via PxVxL motif) (PubMed:23542155). Interacts with TTLL12 (PubMed:23251473).

    Three dimensional structures from OCA and Proteopedia for CBX3 Gene

neXtProt entry for CBX3 Gene

Post-translational modifications for CBX3 Gene

  • Phosphorylated by PIM1. Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis.
  • Ubiquitination at Lys5, Lys34, Lys44, Lys50, Lys52, Lys92, Lys143, Lys154, and Lys159
  • Modification sites at PhosphoSitePlus

Other Protein References for CBX3 Gene

Antibody Products

No data available for DME Specific Peptides for CBX3 Gene

Domains & Families for CBX3 Gene

Gene Families for CBX3 Gene

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

Protein Domains for CBX3 Gene

Suggested Antigen Peptide Sequences for CBX3 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain containing 32, isoform CRA_c (A4D177_HUMAN)
  • Modifier 2 protein (CBX3_HUMAN)
genes like me logo Genes that share domains with CBX3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CBX3 Gene

Function for CBX3 Gene

Molecular function for CBX3 Gene

UniProtKB/Swiss-Prot Function:
Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1. Mediates the recruitment of NIPBL to sites of DNA damage at double-strand breaks (DSBs) (PubMed:28167679).

Phenotypes From GWAS Catalog for CBX3 Gene

Gene Ontology (GO) - Molecular Function for CBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 8663349
GO:0019899 enzyme binding IPI 19486527
GO:0019904 protein domain specific binding IPI 8663349
GO:0042802 identical protein binding IPI 19486527
GO:1990226 histone methyltransferase binding IPI 19486527
genes like me logo Genes that share ontologies with CBX3: view
genes like me logo Genes that share phenotypes with CBX3: view

Animal Models for CBX3 Gene

MGI Knock Outs for CBX3:

Animal Model Products

CRISPR Products

miRNA for CBX3 Gene

miRTarBase miRNAs that target CBX3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CBX3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CBX3 Gene

Localization for CBX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CBX3 Gene

Nucleus. Note=Associates with euchromatin and is largely excluded from constitutive heterochromatin. May be associated with microtubules and mitotic poles during mitosis (Potential). {ECO:0000305}.

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 CBX3 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for CBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IDA 10504293
GO:0000779 condensed chromosome, centromeric region ISS --
GO:0000784 nuclear chromosome, telomeric region HDA 19135898
GO:0000785 chromatin IDA 11101528
GO:0005634 nucleus IEA,IDA 17540172
genes like me logo Genes that share ontologies with CBX3: view

Pathways & Interactions for CBX3 Gene

genes like me logo Genes that share pathways with CBX3: view

SIGNOR curated interactions for CBX3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling NAS 8663349
GO:0006974 cellular response to DNA damage stimulus IMP 27248496
GO:0045892 negative regulation of transcription, DNA-templated IEA,IMP 9636147
GO:0048511 rhythmic process IEA --
genes like me logo Genes that share ontologies with CBX3: view

Drugs & Compounds for CBX3 Gene

No Compound Related Data Available

Transcripts for CBX3 Gene

mRNA/cDNA for CBX3 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CBX3

Alternative Splicing Database (ASD) splice patterns (SP) for CBX3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c · 8d
SP1: - - - - - -
SP2: - - -
SP3: - - -
SP4: - - - -
SP5: - - - - -
SP6: - - - - -
SP7:
SP8: -

Relevant External Links for CBX3 Gene

GeneLoc Exon Structure for
CBX3

Expression for CBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CBX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CBX3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (11.4), Fetal ovary (7.5), and Tlymphocyte (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CBX3 Gene



Protein tissue co-expression partners for CBX3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CBX3

SOURCE GeneReport for Unigene cluster for CBX3 Gene:

Hs.381189

Evidence on tissue expression from TISSUES for CBX3 Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Bone marrow(4.5)
  • Skin(3.6)
  • Lung(3.4)
  • Intestine(3.3)
  • Kidney(3.3)
  • Eye(3)
  • Blood(2.6)
  • Lymph node(2.6)
  • Muscle(2.6)
  • Heart(2.4)
  • Spleen(2.4)
  • Thyroid gland(2.3)
  • Adrenal gland(2.1)
  • Stomach(2.1)
genes like me logo Genes that share expression patterns with CBX3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CBX3 Gene

Orthologs for CBX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CBX3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CBX3 30 31
  • 100 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Gm10068 31
  • 100 (a)
OneToMany
Cbx3 30 17 31
  • 90.16 (n)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia CBX3 31
  • 99 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CBX3 31
  • 96 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia CBX3 30 31
  • 93.62 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CBX3 30
  • 91.06 (n)
-- 31
  • 91 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Cbx3 30
  • 90.53 (n)
Chicken
(Gallus gallus)
Aves CBX3 30 31
  • 85.55 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CBX3 31
  • 93 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cbx3 30
  • 83.82 (n)
Str.7994 30
Zebrafish
(Danio rerio)
Actinopterygii cbx3a 30 31
  • 72.09 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Su(var)205 31
  • 40 (a)
ManyToMany
HP1b 31 32
  • 38 (a)
ManyToMany
HP6 31
  • 38 (a)
ManyToMany
HP1e 31
  • 30 (a)
ManyToMany
HP1c 31
  • 29 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea hpl-1 31
  • 33 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3133 31
  • 43 (a)
OneToMany
Species where no ortholog for CBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for CBX3 Gene

ENSEMBL:
Gene Tree for CBX3 (if available)
TreeFam:
Gene Tree for CBX3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CBX3: view image

Paralogs for CBX3 Gene

Paralogs for CBX3 Gene

(7) SIMAP similar genes for CBX3 Gene using alignment to 5 proteins:

  • CBX3_HUMAN
  • A4D177_HUMAN
  • B8ZZ43_HUMAN
  • C9JMM0_HUMAN
  • S4R2Y4_HUMAN
genes like me logo Genes that share paralogs with CBX3: view

Variants for CBX3 Gene

Additional dbSNP identifiers (rs#s) for CBX3 Gene

Structural Variations from Database of Genomic Variants (DGV) for CBX3 Gene

Variant ID Type Subtype PubMed ID
dgv1093n67 CNV gain 20364138
dgv3757e59 CNV duplication 20981092
esv23140 CNV gain 19812545
esv2390496 CNV deletion 18987734
esv2734157 CNV deletion 23290073
esv2734158 CNV deletion 23290073
esv2734159 CNV deletion 23290073
esv3612632 CNV loss 21293372
nsv1076880 CNV deletion 25765185
nsv1130864 CNV deletion 24896259
nsv1140754 CNV deletion 24896259
nsv606459 CNV gain 21841781
nsv606460 CNV loss 21841781
nsv7393 OTHER inversion 18451855
nsv970454 CNV duplication 23825009

Variation tolerance for CBX3 Gene

Residual Variation Intolerance Score: 52.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.23; 5.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CBX3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CBX3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CBX3 Gene

Disorders for CBX3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CBX3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
hyperoxaluria, primary, type i
  • hp1
carbohydrate metabolic disorder
  • disorder of carbohydrate transport and metabolism
primary hyperoxaluria
  • glycolic aciduria
facioscapulohumeral muscular dystrophy 1
  • fmd
facioscapulohumeral muscular dystrophy 2
  • fshd2
- elite association - COSMIC cancer census association via MalaCards
Search CBX3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with CBX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CBX3 Gene

Publications for CBX3 Gene

  1. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. (PMID: 12004135) Ogawa H … Nakatani Y (Science (New York, N.Y.) 2002) 3 4 23
  2. Identification of heterochromatin protein 1 (HP1) as a phosphorylation target by Pim-1 kinase and the effect of phosphorylation on the transcriptional repression function of HP1(1). (PMID: 10664448) Koike N … Iguchi-Ariga SM (FEBS letters 2000) 3 4 23
  3. Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells. (PMID: 10460410) Minc E … Buendia B (Chromosoma 1999) 3 4 23
  4. KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Krüppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing. (PMID: 10330177) Ryan RF … Rauscher FJ (Molecular and cellular biology 1999) 3 4 23
  5. Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1. (PMID: 8663349) Ye Q … Worman HJ (The Journal of biological chemistry 1996) 2 3 4

Products for CBX3 Gene

  • Signalway ELISA kits for CBX3

Sources for CBX3 Gene