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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-Centromeric Instability-Facial Anomalies Syndrome. Among its related pathways are E2F transcription factor network and E2F mediated regulation of DNA replication. GO annotations related to this gene include protein homodimerization activity and histone deacetylase binding. An important paralog of this gene is CBX1.

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

Additional gene information for CBX5 Gene

No data available for CIViC summary , 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
GH12H054354 2.1 FANTOM5 Ensembl ENCODE dbSUPER 31 -77.9 -77869 6 FEZF1 YBX1 YY1 ZNF143 SP3 MCM3 NFYC MEF2D ZNF610 GLIS1 SP1 PCBP2 ENSG00000258344 CBX5 GPR84 ZNF385A MAP3K12 ATF7 LOC100652999 HNRNPA1
GH12H054277 1.4 ENCODE dbSUPER 31.8 -0.9 -933 7 MLX DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A ZNF585B GLIS1 MAP3K12 CBX5 PCBP2 SP1 HNRNPA1 TARBP2 AAAS GPR84 COPZ1 RNU6-950P
GH12H053971 2 FANTOM5 Ensembl ENCODE dbSUPER 19.8 +289.9 289891 36 PKNOX1 FOXA2 ARNT SIN3A FEZF1 DMAP1 ZNF2 ZNF766 ZNF416 ZNF207 HNRNPA1 ZNF740 ENSG00000258344 ATF7 PCBP2 MAP3K12 LOC100652999 SP1 CALCOCO1 AAAS
GH12H054009 2.5 VISTA FANTOM5 Ensembl ENCODE dbSUPER 12.9 +258.0 258031 25 HDGF PKNOX1 ARNT SIN3A FEZF1 ZNF2 CBX5 ZNF143 ZNF207 DEK RARG AAAS ATF7 ENSG00000260470 LOC105378250 HOXC8 SMUG1 IGFBP6 HOXC-AS1 CBX5
GH12H053498 1.4 ENCODE dbSUPER 22.1 +779.5 779527 4 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ATF7 HNRNPA1 ZNF740 PCBP2 SP1 MAP3K12 CBX5 LOC100652999 ENSG00000258344 PRR13
- 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
ENSR00000052331 -367 4201 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D

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.

    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 posLast=3232, posLast=4242, Lys91, Lys102, posLast=125125, posLast=143143, posLast=154154, and posLast=159159
  • Modification sites at PhosphoSitePlus

Other Protein References for CBX5 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CBX5 (HP1 alpha)

No data available for DME Specific Peptides for CBX5 Gene

Domains & Families for CBX5 Gene

Gene Families for CBX5 Gene

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

Suggested Antigen Peptide Sequences for CBX5 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

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.

Phenotypes From GWAS Catalog for CBX5 Gene

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

CRISPR Products

miRNA for CBX5 Gene

miRTarBase miRNAs that target CBX5

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX5
  • Applied Biological Materials Clones for CBX5
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

Subcellular locations from the

Human Protein Atlas (HPA)

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

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:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 19617346
GO:0007596 blood coagulation TAS --
GO:0016032 viral process IEA --
GO:0045892 negative regulation of transcription, DNA-templated IMP 9636146
genes like me logo Genes that share ontologies with CBX5: view

Drugs & Compounds for CBX5 Gene

(6) Drugs for CBX5 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved Pharma Target 188

(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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CBX5
  • Applied Biological Materials Clones for CBX5
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 CGAP 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

Evidence on tissue expression from TISSUES for CBX5 Gene

  • Liver(4.6)
  • Nervous system(4.6)
  • Kidney(4.4)
  • Eye(3.2)
  • Intestine(2.2)
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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.65 (n)
cow
(Bos Taurus)
Mammalia CBX5 33 34
  • 97.03 (n)
dog
(Canis familiaris)
Mammalia CBX5 33 34
  • 96.68 (n)
mouse
(Mus musculus)
Mammalia Cbx5 33 16 34
  • 92.32 (n)
rat
(Rattus norvegicus)
Mammalia Cbx5 33
  • 91.8 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 36 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 34
  • 89 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia CBX5 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cbx5 33
  • 77.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia cbx5-prov 33
zebrafish
(Danio rerio)
Actinopterygii cbx5 33 34
  • 67.4 (n)
fruit fly
(Drosophila melanogaster)
Insecta HP1b 35 34
  • 52 (a)
Su(var)205 34
  • 40 (a)
ManyToMany
HP6 34
  • 38 (a)
ManyToMany
HP1e 34
  • 32 (a)
ManyToMany
HP1c 34
  • 27 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea hpl-1 34
  • 30 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3133 34
  • 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
rs1000095385 -- 54,246,496(+) ACTCC(A/G)GAGTC intron-variant
rs1000150733 -- 54,233,759(+) GACTG(C/T)CTCTA utr-variant-3-prime
rs1000264281 -- 54,241,046(+) AAGCA(G/T)AAGTG utr-variant-3-prime
rs1000353290 -- 54,253,531(+) AGACC(A/G)GCCTA intron-variant

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

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

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

(2) MalaCards diseases for CBX5 Gene - From: HGMD, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
reynolds syndrome
  • primary biliary cirrhosis, scleroderma, raynaud disease, and telangiectasia
immunodeficiency-centromeric instability-facial anomalies syndrome
  • icf syndrome
- 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 HJ (The Journal of biological chemistry 1996) 2 3 4 22 60
  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 60
  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 60
  4. 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 60
  5. Recognition and specificity determinants of the human cbx chromodomains. (PMID: 21047797) Kaustov L … Arrowsmith CH (The Journal of biological chemistry 2011) 3 4 60

Products for CBX5 Gene

  • Addgene plasmids for CBX5

Sources for CBX5 Gene

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