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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 Mandibuloacral Dysplasia. Among its related pathways are Chromatin Regulation / Acetylation. 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

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

Genomics for CBX1 Gene

Regulatory Elements for CBX1 Gene

Enhancers for CBX1 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
GH17F048011 1.7 FANTOM5 Ensembl ENCODE 12 +88.1 88134 4.4 HDGF PKNOX1 ARNT SIN3A ZNF2 ZNF121 GLIS2 ZNF143 ZNF207 KLF7 PRR15L SCRN2 COPZ2 CDK5RAP3 SKAP1 MRPL45P2 CBX1 MIR152 RPS2P47 NFE2L1
GH17F048127 0.6 Ensembl ENCODE 11.6 -26.1 -26080 0.4 PKNOX1 JUN SIN3A CTBP1 POLR2A RCOR1 FOSL2 FOS ZNF687 SMARCC1 SNX11 RNU6-1201P CBX1 ENSG00000253347 MIR1203 COPZ2 MIR152 NFE2L1 HOXB9 HOXB-AS4
GH17F048128 0.4 FANTOM5 11.6 -27.2 -27223 0.2 KDM1A SNX11 RNU6-1201P CBX1 MIR1203 COPZ2 MIR152 NFE2L1 HOXB-AS4 HOXB9 TBX21
GH17F048131 0.7 ENCODE 11.6 -29.9 -29893 0.2 CTCF ESRRA ARID4B THRB RAD21 RFX5 ZFHX2 ZNF143 SMC3 EGR2 RNU6-1201P SNX11 CBX1 MIR1203 COPZ2 MIR152 NFE2L1 HOXB-AS4 HOXB9 PNPO
GH17F048044 1.2 VISTA ENCODE 11.4 +50.4 50415 13.0 CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TBX21 MRPL45P2 SNX11 ENSG00000266601 COPZ2 ENSG00000253347 SCRN2 CDK5RAP3 ENSG00000264701 KPNB1 CBX1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CBX1 on UCSC Golden Path with GeneCards custom track

Promoters for CBX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001348080 421 2201 HDGF PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 CBX5

Genomic Location for CBX1 Gene

Chromosome:
17
Start:
48,070,052 bp from pter
End:
48,101,521 bp from pter
Size:
31,470 bases
Orientation:
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:
    P83916-CBX1_HUMAN
    Recommended name:
    Chromobox protein homolog 1
    Protein Accession:
    P83916
    Secondary Accessions:
    • P23197

    Protein attributes for CBX1 Gene

    Size:
    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

Graphical View of Domain Structure for InterPro Entry

P83916

UniProtKB/Swiss-Prot:

CBX1_HUMAN :
  • Contains 2 chromo domains.
Domain:
  • Contains 2 chromo domains.
genes like me logo Genes that share domains with CBX1: view

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.

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

Flow Cytometry Products

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

COMPARTMENTS
Jensen Localization Image for CBX1 Gene COMPARTMENTS Subcellular localization image for CBX1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 2
golgi apparatus 2

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

Flow Cytometry Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6
SP1:
SP2: -
SP3: -
SP4:

Relevant External Links for CBX1 Gene

GeneLoc Exon Structure for
CBX1
ECgene alternative splicing isoforms for
CBX1

Expression for CBX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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:

CBX1

SOURCE GeneReport for Unigene cluster for CBX1 Gene:

Hs.77254

mRNA Expression by UniProt/SwissProt for CBX1 Gene:

P83916-CBX1_HUMAN
Tissue specificity: Expressed in all adult and embryonic tissues.
genes like me logo Genes that share expression patterns with CBX1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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
chimpanzee
(Pan troglodytes)
Mammalia CBX1 34 35
  • 100 (n)
cow
(Bos Taurus)
Mammalia CBX1 35
  • 100 (a)
OneToOne
LOC101904753 34
  • 95.14 (n)
oppossum
(Monodelphis domestica)
Mammalia CBX1 35
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CBX1 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CBX1 34 35
  • 96.04 (n)
mouse
(Mus musculus)
Mammalia Cbx1 34 16 35
  • 94.59 (n)
rat
(Rattus norvegicus)
Mammalia Cbx1 34
  • 93.33 (n)
chicken
(Gallus gallus)
Aves CBX1 34 35
  • 84.47 (n)
lizard
(Anolis carolinensis)
Reptilia CBX1 35
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx1 34
  • 79.43 (n)
Str.16928 34
zebrafish
(Danio rerio)
Actinopterygii cbx1b 34 35
  • 78.31 (n)
cbx1a 35
  • 70 (a)
OneToMany
-- 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10237 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004723 34
  • 61.07 (n)
fruit fly
(Drosophila melanogaster)
Insecta HP1b 36 34 35
  • 56.74 (n)
HP6 35
  • 41 (a)
ManyToMany
Su(var)205 35
  • 41 (a)
ManyToMany
HP1e 35
  • 34 (a)
ManyToMany
HP1c 35
  • 28 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea hpl-1 35
  • 32 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3133 35
  • 45 (a)
OneToMany
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

ENSEMBL:
Gene Tree for CBX1 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs1050025 -- 48,070,793(-) AGTCT(A/G)AAACC utr-variant-3-prime
rs1063470 -- 48,076,975(-) AAAGT(A/G)GAGGA reference, synonymous-codon
rs1063487 -- 48,070,129(-) CTGTG(A/T)AAACT utr-variant-3-prime
rs1063488 -- 48,070,114(-) TTAAA(C/T)GTAAA utr-variant-3-prime
rs1063489 -- 48,070,107(-) TAAAC(C/T)TCATA utr-variant-3-prime

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)

Relevant External Links for CBX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CBX1

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: GeneCards

Disorder Aliases PubMed IDs
mandibuloacral dysplasia
  • mandibuloacral dysplasia with type a lipodystrophy
- elite association - COSMIC cancer census association via MalaCards
Search CBX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CBX1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 E.M. (Chromosoma 1997) 2 3 4 22 64
  2. In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. (PMID: 15899859) Verschure P.J. … van Driel R. (Mol. Cell. Biol. 2005) 3 4 22 64
  3. Binding of EMSY to HP1beta: implications for recruitment of HP1beta and BS69. (PMID: 15947784) Ekblad C.M.S. … Itzhaki L.S. (EMBO Rep. 2005) 3 4 22 64
  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 64
  5. The core binding factor CBF negatively regulates skeletal muscle terminal differentiation. (PMID: 20195544) Philipot O. … Ait-Si-Ali S. (PLoS ONE 2010) 3 22 64

Products for CBX1 Gene

Sources for CBX1 Gene

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