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Aliases for CBX1 Gene

Aliases for CBX1 Gene

  • Chromobox 1 2 3 5
  • Heterochromatin Protein 1 Homolog Beta 3 4
  • Modifier 1 Protein 3 4
  • HP1Hsbeta 3 4
  • P25beta 3 4
  • CBX 3 4
  • M31 3 4
  • Chromobox Homolog 1 (HP1 Beta Homolog Drosophila ) 3
  • Chromobox Homolog 1 (Drosophila HP1 Beta) 2
  • Heterochromatin Protein P25 Beta 3
  • HP1 Beta Homolog (Drosophila ) 2
  • Heterochromatin Protein 1-Beta 3
  • Chromobox Protein Homolog 1 3
  • Heterochromatin Protein P25 4
  • Chromobox Homolog 1 2
  • HP1 Beta Homolog 3
  • HP1Hs-Beta 3
  • HP1-BETA 3
  • HP1 Beta 4
  • MOD1 3

External Ids for CBX1 Gene

Previous GeneCards Identifiers for CBX1 Gene

  • GC17M045852
  • GC17M048627
  • GC17M046489
  • GC17M046622
  • GC17M043502
  • GC17M046147
  • GC17M041515

Summaries for CBX1 Gene

Entrez Gene Summary for CBX1 Gene

  • This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family . The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The protein may play an important role in the epigenetic control of chromatin structure and gene expression. Several related pseudogenes are located on chromosomes 1, 3, and X. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for CBX1 Gene

CBX1 (Chromobox 1) is a Protein Coding gene. Diseases associated with CBX1 include Warsaw Breakage Syndrome. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and chromatin binding. An important paralog of this gene is CBX3.

UniProtKB/Swiss-Prot for CBX1 Gene

  • Component of heterochromatin. Recognizes and binds histone H3 tails methylated at Lys-9, leading to epigenetic repression. Interaction with lamin B receptor (LBR) can contribute to the association of the heterochromatin with the inner nuclear membrane.

Gene Wiki entry for CBX1 Gene

Additional gene information for CBX1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CBX1 Gene

Genomics for CBX1 Gene

GeneHancer (GH) Regulatory Elements for CBX1 Gene

Promoters and enhancers for CBX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I048099 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 550.8 0.0 -2 4.2 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B SLC30A9 SNX11 CBX1 CDK5RAP3 ENSG00000253347 ENSG00000230532
GH17I048044 Promoter/Enhancer 2.5 VISTA EPDnew Ensembl ENCODE dbSUPER 23.5 +50.4 50414 13 CLOCK DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC NFE2L1 SP2 SNX11 ENSG00000266601 KPNB1 MRPL45P2 CBX1 UBE2Z ENSG00000253347 EFCAB13
GH17I047941 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 21.2 +159.7 159664 2 CLOCK MLX DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 SP3 SP2-AS1 PNPO MRPL45P2 UBE2Z EFCAB13 SP2 ENSG00000264701 ENSG00000266601 CDK5RAP3 RPS2P47
GH17I048023 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 23.4 +76.2 76198 4.6 HDGF PKNOX1 CLOCK FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SP2 ENSG00000253347 CBX1 MRPL45P2 EFCAB13 ENSG00000266601 SNX11 CDK5RAP3 COPZ2 SKAP1
GH17I048728 Promoter/Enhancer 1.7 EPDnew ENCODE dbSUPER 21.1 -627.3 -627345 0.8 PKNOX1 SIN3A FEZF1 GLI4 ZNF2 GLIS2 ZNF213 ZNF302 KLF7 SP3 HOXB13 UBE2Z SP2 ENSG00000264701 CDK5RAP3 SCRN2 ENSG00000266601 CBX1 ENSG00000263412 SUMO2P17
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CBX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CBX1 gene promoter:

Genomic Locations for CBX1 Gene

Genomic Locations for CBX1 Gene
31,470 bases
Minus strand

Genomic View for CBX1 Gene

Genes around CBX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CBX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CBX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CBX1 Gene

Proteins for CBX1 Gene

  • Protein details for CBX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chromobox protein homolog 1
    Protein Accession:
    Secondary Accessions:
    • P23197

    Protein attributes for CBX1 Gene

    185 amino acids
    Molecular mass:
    21418 Da
    Quaternary structure:
    • Homodimer. Interacts directly with CHAF1A, EMSY, LBR, TIF1/TIF1A and TRIM28/TIF1B PXVXL motif via the chromoshadow domain. Interacts directly with histone H3 methylated at Lys-9 via the chromo domain. Interacts with SUV39H1 and SETDB1, KMT5B and KMT5C. Interacts with PRDM6. Interacts with POGZ. Interacts with CHAMP1. Interacts with ASXL1. Interacts with INCENP. Interacts with SGO1; the CBX1 homodimer binds to one molecule of SGO1.

    Three dimensional structures from OCA and Proteopedia for CBX1 Gene

neXtProt entry for CBX1 Gene

Post-translational modifications for CBX1 Gene

Other Protein References for CBX1 Gene

No data available for DME Specific Peptides for CBX1 Gene

Domains & Families for CBX1 Gene

Gene Families for CBX1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CBX1: view

No data available for UniProtKB/Swiss-Prot for CBX1 Gene

Function for CBX1 Gene

Molecular function for CBX1 Gene

UniProtKB/Swiss-Prot Function:
Component of heterochromatin. Recognizes and binds histone H3 tails methylated at Lys-9, leading to epigenetic repression. Interaction with lamin B receptor (LBR) can contribute to the association of the heterochromatin with the inner nuclear membrane.

Phenotypes From GWAS Catalog for CBX1 Gene

Gene Ontology (GO) - Molecular Function for CBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding TAS 9169582
GO:0005515 protein binding IPI 9636146
GO:0019899 enzyme binding IPI 19486527
GO:0042802 identical protein binding IEA --
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with CBX1: view
genes like me logo Genes that share phenotypes with CBX1: view

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CBX1 Gene

Localization for CBX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CBX1 Gene

Nucleus. Note=Unassociated with chromosomes during mitosis.

Subcellular locations from

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 CBX1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for CBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IDA 8287692
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0000785 chromatin IDA 11101528
GO:0001939 female pronucleus IEA --
GO:0001940 male pronucleus IEA --
genes like me logo Genes that share ontologies with CBX1: view

Pathways & Interactions for CBX1 Gene

genes like me logo Genes that share pathways with CBX1: view

Pathways by source for CBX1 Gene

1 Cell Signaling Technology pathway for CBX1 Gene

SIGNOR curated interactions for CBX1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for CBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045892 negative regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with CBX1: view

Drugs & Compounds for CBX1 Gene

(1) Drugs for CBX1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with CBX1: view

Transcripts for CBX1 Gene

Unigene Clusters for CBX1 Gene

Chromobox homolog 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX1

Alternative Splicing Database (ASD) splice patterns (SP) for CBX1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6
SP2: -
SP3: -

Relevant External Links for CBX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CBX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CBX1 Gene

Protein differential expression in normal tissues from HIPED for CBX1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.3), Liver (12.0), and Fetal ovary (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CBX1 Gene

Protein tissue co-expression partners for CBX1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CBX1 Gene:


SOURCE GeneReport for Unigene cluster for CBX1 Gene:


mRNA Expression by UniProt/SwissProt for CBX1 Gene:

Tissue specificity: Expressed in all adult and embryonic tissues.

Evidence on tissue expression from TISSUES for CBX1 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Lung(2.8)
  • Eye(2.3)
  • Muscle(2.2)
genes like me logo Genes that share expression patterns with CBX1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CBX1 Gene

Orthologs for CBX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CBX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CBX1 33 34
  • 100 (n)
(Bos Taurus)
Mammalia CBX1 34
  • 100 (a)
LOC101904753 33
  • 95.14 (n)
(Monodelphis domestica)
Mammalia CBX1 34
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia CBX1 34
  • 98 (a)
(Canis familiaris)
Mammalia CBX1 33 34
  • 96.04 (n)
(Mus musculus)
Mammalia Cbx1 33 16 34
  • 94.59 (n)
(Rattus norvegicus)
Mammalia Cbx1 33
  • 93.33 (n)
(Gallus gallus)
Aves CBX1 33 34
  • 84.47 (n)
(Anolis carolinensis)
Reptilia CBX1 34
  • 93 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx1 33
  • 79.43 (n)
Str.16928 33
(Danio rerio)
Actinopterygii cbx1b 33 34
  • 78.31 (n)
cbx1a 34
  • 70 (a)
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10237 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004723 33
  • 61.07 (n)
fruit fly
(Drosophila melanogaster)
Insecta HP1b 35 33 34
  • 56.74 (n)
HP6 34
  • 41 (a)
Su(var)205 34
  • 41 (a)
HP1e 34
  • 34 (a)
HP1c 34
  • 28 (a)
(Caenorhabditis elegans)
Secernentea hpl-1 34
  • 32 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3133 34
  • 45 (a)
Species where no ortholog for CBX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 CBX1 Gene

Gene Tree for CBX1 (if available)
Gene Tree for CBX1 (if available)

Paralogs for CBX1 Gene

Paralogs for CBX1 Gene

(10) SIMAP similar genes for CBX1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with CBX1: view

Variants for CBX1 Gene

Sequence variations from dbSNP and Humsavar for CBX1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000041252 -- 48,102,266(-) G/A upstream_transcript_variant
rs1000050851 -- 48,084,594(-) G/A intron_variant
rs1000113924 -- 48,085,009(-) T/C intron_variant
rs1000249796 -- 48,101,230(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000351057 -- 48,071,729(-) C/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CBX1 Gene

Variant ID Type Subtype PubMed ID
esv1003767 CNV insertion 20482838
esv2582446 CNV deletion 19546169
esv2663382 CNV deletion 23128226
esv2716011 CNV deletion 23290073
esv3310437 CNV novel sequence insertion 20981092
esv3410940 CNV duplication 20981092
esv3582798 CNV loss 25503493
esv3640709 CNV loss 21293372
esv3640710 CNV gain 21293372
esv3640711 CNV loss 21293372
esv3640712 CNV loss 21293372
nsv469808 CNV loss 16826518
nsv513477 CNV insertion 21212237
nsv962336 CNV duplication 23825009

Variation tolerance for CBX1 Gene

Residual Variation Intolerance Score: 44.4% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CBX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CBX1 Gene

Disorders for CBX1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CBX1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
warsaw breakage syndrome
  • wabs
- elite association - COSMIC cancer census association via MalaCards
Search CBX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CBX1

genes like me logo Genes that share disorders with CBX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CBX1 Gene

Publications for CBX1 Gene

  1. Heterochromatin protein HP1Hsbeta (p25beta) and its localization with centromeres in mitosis. (PMID: 9169582) Furuta K … Tan EM (Chromosoma 1997) 2 3 4 22 58
  2. In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. (PMID: 15899859) Verschure PJ … van Driel R (Molecular and cellular biology 2005) 3 4 22 58
  3. Binding of EMSY to HP1beta: implications for recruitment of HP1beta and BS69. (PMID: 15947784) Ekblad CM … Itzhaki LS (EMBO reports 2005) 3 4 22 58
  4. Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells. (PMID: 10460410) Minc E … Buendia B (Chromosoma 1999) 3 4 22 58
  5. Mitotic centromeric targeting of HP1 and its binding to Sgo1 are dispensable for sister-chromatid cohesion in human cells. (PMID: 21346195) Kang J … Yu H (Molecular biology of the cell 2011) 3 4 58

Products for CBX1 Gene

  • Addgene plasmids for CBX1

Sources for CBX1 Gene

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