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Aliases for CBX5 Gene

Aliases for CBX5 Gene

  • Chromobox 5 2 3 5
  • Chromobox Homolog 5 (HP1 Alpha Homolog, Drosophila) 2 3
  • Heterochromatin Protein 1 Homolog Alpha 3 4
  • Antigen P25 3 4
  • HP1A 3 4
  • Chromobox Homolog 5 (Drosophila HP1 Alpha) 2
  • Heterochromatin Protein 1-Alpha 3
  • HP1 Alpha Homolog (Drosophila) 2
  • Epididymis Luminal Protein 25 3
  • Chromobox Protein Homolog 5 3
  • Chromobox Homolog 5 2
  • HP1 Alpha Homolog 3
  • HP1Hs Alpha 3
  • HP1-ALPHA 3
  • HP1 Alpha 4
  • HEL25 3
  • HP1 3

External Ids for CBX5 Gene

Previous GeneCards Identifiers for CBX5 Gene

  • GC12M054761
  • GC12M054351
  • GC12M052921
  • GC12M054624

Summaries for CBX5 Gene

Entrez Gene Summary for CBX5 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 encoded product is involved in the formation of functional kinetochore through interaction with essential kinetochore proteins. The gene has a pseudogene located on chromosome 3. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for CBX5 Gene

CBX5 (Chromobox 5) is a Protein Coding gene. Diseases associated with CBX5 include Reynolds Syndrome and Immunodeficiency, Centromere Instability And Facial Anomalies Syndrome. Among its related pathways are E2F mediated regulation of DNA replication and Factors involved in megakaryocyte development and platelet production. GO annotations related to this gene include protein homodimerization activity and histone deacetylase binding. An important paralog of this gene is CBX3.

UniProtKB/Swiss-Prot for CBX5 Gene

  • Component of heterochromatin that recognizes and binds histone H3 tails methylated at Lys-9 (H3K9me), leading to epigenetic repression. In contrast, it is excluded from chromatin when Tyr-41 of histone H3 is phosphorylated (H3Y41ph). Can interact with lamin-B receptor (LBR). This interaction can contribute to the association of the heterochromatin with the inner nuclear membrane. Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins.

Gene Wiki entry for CBX5 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CBX5 Gene

Genomics for CBX5 Gene

Regulatory Elements for CBX5 Gene

Enhancers for CBX5 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
GH12F054354 1.9 FANTOM5 Ensembl ENCODE 11.2 -77.9 -77924 6.7 FEZF1 YBX1 YY1 ZNF143 ZNF263 MCM3 SP3 NFYC TBX21 MEF2D SP1 ENSG00000258344 GPR84 ZNF385A LOC100652999 OR10A7 OR6C74 LOC105378250 MAP3K12 ENSG00000258086
GH12F054350 1.3 FANTOM5 ENCODE 10.7 -72.2 -72183 4.0 PKNOX1 FEZF1 ZNF121 GLIS2 ZNF263 SP3 YY2 SMARCA4 GLIS1 MYNN RNU6-950P COPZ1 ZNF385A CBX5 MIR3198-2 GPR84 PDE1B LOC102724050 RN7SL744P
GH12F054227 1.2 Ensembl ENCODE 11 +50.9 50937 3.6 PKNOX1 INSM2 ZNF76 SIN3A KLF17 FEZF1 ZNF2 ZEB1 ZNF366 SCRT2 GPR84 PFDN5 AAAS CBX5 MIR3198-2 MIR148B COPZ1 RNU6-950P HOXC8 HOXC-AS1
GH12F054219 1.1 Ensembl ENCODE 11.1 +59.9 59893 1.2 CBX3 ARNT KLF17 ZNF2 RAD21 ZEB1 RFX5 ZNF143 CREM ZNF654 GPR84 COPZ1 RNU6-950P CBX5 MIR3198-2 MIR148B HOXC8 HOXC-AS1 HOXC-AS2 HOXC6
GH12F054336 1.2 Ensembl ENCODE 9.9 -58.0 -58030 2.7 ARNT SIN3A FOS NCOA1 REST SMARCB1 MEF2D SMARCA4 NBN HMBOX1 GPR84 RNU6-950P COPZ1 CBX5 MIR3198-2 GC12P054339 RN7SL744P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CBX5 on UCSC Golden Path with GeneCards custom track

Promoters for CBX5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000653664 -467 4801 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1

Genomic Location for CBX5 Gene

Chromosome:
12
Start:
54,230,940 bp from pter
End:
54,280,133 bp from pter
Size:
49,194 bases
Orientation:
Minus strand

Genomic View for CBX5 Gene

Genes around CBX5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CBX5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CBX5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CBX5 Gene

Proteins for CBX5 Gene

  • Protein details for CBX5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P45973-CBX5_HUMAN
    Recommended name:
    Chromobox protein homolog 5
    Protein Accession:
    P45973
    Secondary Accessions:
    • B2R8T9

    Protein attributes for CBX5 Gene

    Size:
    191 amino acids
    Molecular mass:
    22225 Da
    Quaternary structure:
    • Interacts with KMT5B and KMT5C (By similarity). Interacts with HP1BP3. Interacts directly with ATRX, CHAF1A, LBR, NIPBL, SP100, STAM2 and TRIM28 via the chromoshadow domain. Can interact directly with CBX3 via the chromoshadow domain. Interacts with histone H3 methylated at Lys-9. Interacts with BAHD1, MIS12 and DSN1. Interacts with POGZ; POGZ and PXVXL motif-containing proteins such as INCENP and TRIM28 compete for interaction with CBX5. Interacts with INCENP and TRIM24. Interacts with JC virus agnoprotein; this interaction induces the dissociation of CBX5 from LBR, resulting in destabilization of the nuclear envelope. Interacts with CHAMP1. Interacts with ASXL1.
    • Interacts with KMT5B and KMT5C (By similarity). Interacts with HP1BP3. Interacts directly with ATRX, CHAF1A, LBR, NIPBL, SP100, STAM2 and TRIM28 via the chromoshadow domain. Can interact directly with CBX3 via the chromoshadow domain. Interacts with histone H3 methylated at Lys-9. Interacts with BAHD1, MIS12 and DSN1. Interacts with POGZ; POGZ and PXVXL motif-containing proteins such as INCENP and TRIM28 compete for interaction with CBX5. Interacts with INCENP and TRIM24. Interacts with JC virus agnoprotein; this interaction induces the dissociation of CBX5 from LBR, resulting in destabilization of the nuclear envelope. Interacts with CHAMP1. Interacts with ASXL1.

    Three dimensional structures from OCA and Proteopedia for CBX5 Gene

neXtProt entry for CBX5 Gene

Post-translational modifications for CBX5 Gene

  • Phosphorylation of HP1 and LBR may be responsible for some of the alterations in chromatin organization and nuclear structure which occur at various times during the cell cycle (By similarity). Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis.
  • Ubiquitinated.
  • Ubiquitination at Lys 32, Lys 42, Lys 91, Lys 102, Lys 125, Lys 143, Lys 154, and Lys 159
  • Modification sites at PhosphoSitePlus

Other Protein References for CBX5 Gene

No data available for DME Specific Peptides for CBX5 Gene

Domains & Families for CBX5 Gene

Gene Families for CBX5 Gene

Suggested Antigen Peptide Sequences for CBX5 Gene

Graphical View of Domain Structure for InterPro Entry

P45973

UniProtKB/Swiss-Prot:

CBX5_HUMAN :
  • Contains 2 chromo domains.
Domain:
  • Contains 2 chromo domains.
genes like me logo Genes that share domains with CBX5: view

Function for CBX5 Gene

Molecular function for CBX5 Gene

UniProtKB/Swiss-Prot Function:
Component of heterochromatin that recognizes and binds histone H3 tails methylated at Lys-9 (H3K9me), leading to epigenetic repression. In contrast, it is excluded from chromatin when Tyr-41 of histone H3 is phosphorylated (H3Y41ph). Can interact with lamin-B receptor (LBR). This interaction can contribute to the association of the heterochromatin with the inner nuclear membrane. Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins.

Gene Ontology (GO) - Molecular Function for CBX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 8663349
GO:0030674 protein binding, bridging ISS --
GO:0035064 methylated histone binding IDA 19783980
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with CBX5: view
genes like me logo Genes that share phenotypes with CBX5: view

Animal Models for CBX5 Gene

MGI Knock Outs for CBX5:

Animal Model Products

  • Taconic Biosciences Mouse Models for CBX5

miRNA for CBX5 Gene

miRTarBase miRNAs that target CBX5

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CBX5 Gene

Localization for CBX5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CBX5 Gene

Nucleus. Chromosome. Chromosome, centromere. Note=Component of centromeric and pericentromeric heterochromatin. Associates with chromosomes during mitosis. Associates specifically with chromatin during metaphase and anaphase.

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 CBX5 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for CBX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex ISS --
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IEA --
GO:0000784 nuclear chromosome, telomeric region IDA 19135898
GO:0000792 heterochromatin IEA --
genes like me logo Genes that share ontologies with CBX5: view

Pathways & Interactions for CBX5 Gene

genes like me logo Genes that share pathways with CBX5: view

Pathways by source for CBX5 Gene

1 Cell Signaling Technology pathway for CBX5 Gene
2 BioSystems pathways for CBX5 Gene

Interacting Proteins for CBX5 Gene

SIGNOR curated interactions for CBX5 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CBX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007596 blood coagulation TAS --
GO:0016032 viral process IEA --
GO:0045892 negative regulation of transcription, DNA-templated IMP,IDA 9636146
genes like me logo Genes that share ontologies with CBX5: view

Drugs & Compounds for CBX5 Gene

(5) Drugs for CBX5 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(8) Additional Compounds for CBX5 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CBX5: view

Transcripts for CBX5 Gene

Unigene Clusters for CBX5 Gene

Chromobox homolog 5:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CBX5 Gene

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

Relevant External Links for CBX5 Gene

GeneLoc Exon Structure for
CBX5
ECgene alternative splicing isoforms for
CBX5

Expression for CBX5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CBX5 Gene

Protein differential expression in normal tissues from HIPED for CBX5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CBX5 Gene



Protein tissue co-expression partners for CBX5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CBX5 Gene:

CBX5

SOURCE GeneReport for Unigene cluster for CBX5 Gene:

Hs.349283
genes like me logo Genes that share expression patterns with CBX5: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CBX5 Gene

Orthologs for CBX5 Gene

This gene was present in the common ancestor of animals.

Orthologs for CBX5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CBX5 34 35
  • 99.65 (n)
cow
(Bos Taurus)
Mammalia CBX5 34 35
  • 97.03 (n)
dog
(Canis familiaris)
Mammalia CBX5 34 35
  • 96.68 (n)
mouse
(Mus musculus)
Mammalia Cbx5 34 16 35
  • 92.32 (n)
rat
(Rattus norvegicus)
Mammalia Cbx5 34
  • 91.8 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 36 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 35
  • 89 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia CBX5 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx5 34
  • 77.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia cbx5-prov 34
zebrafish
(Danio rerio)
Actinopterygii cbx5 34 35
  • 67.4 (n)
fruit fly
(Drosophila melanogaster)
Insecta HP1b 36 35
  • 52 (a)
Su(var)205 35
  • 40 (a)
ManyToMany
HP6 35
  • 38 (a)
ManyToMany
HP1e 35
  • 32 (a)
ManyToMany
HP1c 35
  • 27 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea hpl-1 35
  • 30 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3133 35
  • 45 (a)
OneToMany
Species where no ortholog for CBX5 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 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 CBX5 Gene

ENSEMBL:
Gene Tree for CBX5 (if available)
TreeFam:
Gene Tree for CBX5 (if available)

Paralogs for CBX5 Gene

Paralogs for CBX5 Gene

(16) SIMAP similar genes for CBX5 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for CBX5 Gene

genes like me logo Genes that share paralogs with CBX5: view

Variants for CBX5 Gene

Sequence variations from dbSNP and Humsavar for CBX5 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs74625894 Benign 54,281,778(+) CATAA(A/G)TTAAC intron-variant, upstream-variant-2KB
rs10219739 -- 54,258,870(+) GGAGG(A/G)CCCAC intron-variant
rs1056010 -- 54,232,968(-) CCACC(A/G)CTGGG upstream-variant-2KB, utr-variant-3-prime
rs1056138 -- 54,231,097(-) TGTTC(A/C)CCTTT downstream-variant-500B, utr-variant-3-prime
rs1056162 -- 54,231,040(-) GACAT(C/T)TGATG downstream-variant-500B, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for CBX5 Gene

Variant ID Type Subtype PubMed ID
nsv976626 CNV duplication 23825009
nsv832420 CNV loss 17160897
nsv832419 CNV loss 17160897
nsv509467 CNV insertion 20534489
nsv1122737 CNV deletion 24896259
nsv1049160 CNV gain 25217958
esv25123 CNV loss 19812545

Variation tolerance for CBX5 Gene

Residual Variation Intolerance Score: 49.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.06; 1.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CBX5 Gene

Human Gene Mutation Database (HGMD)
CBX5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CBX5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CBX5 Gene

Disorders for CBX5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CBX5 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
reynolds syndrome
  • primary biliary cirrhosis, scleroderma, raynaud disease, and telangiectasia
immunodeficiency, centromere instability and facial anomalies syndrome
  • icf syndrome
axenfeld-rieger syndrome, type 3
  • anterior segment mesenchymal dysgenesis
- elite association - COSMIC cancer census association via MalaCards
Search CBX5 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CBX5

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CBX5
genes like me logo Genes that share disorders with CBX5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CBX5 Gene

Publications for CBX5 Gene

  1. Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1. (PMID: 8663349) Ye Q. … Worman H.J. (J. Biol. Chem. 1996) 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. 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
  4. Recognition and specificity determinants of the human cbx chromodomains. (PMID: 21047797) Kaustov L. … Arrowsmith C.H. (J. Biol. Chem. 2011) 3 4 64
  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. (Mol. Biol. Cell 2011) 3 4 64

Products for CBX5 Gene

Sources for CBX5 Gene

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