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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
  • Chromobox Protein Homolog 5 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 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 1. Among its related pathways are E2F transcription factor network and Chromatin Regulation / Acetylation. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for CBX5 Gene

Promoters and enhancers for CBX5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J054277 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 631.7 -4.2 -4197 13.6 HDGF MTA3 ZFX CC2D1A SP1 ZKSCAN8 MNT CBFA2T2 ZNF148 NKRF HNRNPA1 CBX5 MAP3K12 SP1 PCBP2 ATF7 ENSG00000258344 AAAS NPFF HOXC4
GH12J054256 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 600.4 +19.9 19895 6.9 SP1 CBFA2T2 ZNF148 MLLT1 CSDE1 ZNF384 ZSCAN21 BACH1 YY1 TRIM24 CBX5 GPR84 COPZ1 RNU6-950P MIR148B HNRNPA1 ENSG00000257534 FLJ12825 SMUG1 RN7SL390P
GH12J053971 Promoter/Enhancer 3 VISTA EPDnew FANTOM5 Ensembl ENCODE dbSUPER 30.8 +276.8 276821 63 ZNF652 ZFX SP1 CC2D1A CTCF ELF3 ZKSCAN8 CBFA2T2 ZNF148 NKRF HOXC8 HOXC11 HOXC4 HOXC9 HOXC6 HOXC10 HOXC5 GC12P054063 GC12P054146 GC12P054147
GH12J054354 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 31 -77.8 -77815 6.5 ZNF473 SP1 CC2D1A ZFX ELF3 CTCF CBFA2T2 ZNF148 MLLT1 ZNF121 SP1 PCBP2 ENSG00000258344 CBX5 GPR84 ZNF385A MAP3K12 ATF7 LOC100652999 HNRNPA1
GH12J053498 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 22.1 +779.6 779582 5.1 HDGF ZFX SP1 CC2D1A ELF3 MNT SIX5 CBFA2T2 ZNF148 NKRF MAP3K12 TARBP2 ENSG00000270175 KRT1 ATF7 HNRNPA1 ZNF740 ENSG00000258344 PCBP2 CBX5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CBX5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CBX5 gene promoter:
  • AML1a
  • C/EBPalpha
  • TBP

Genomic Locations for CBX5 Gene

Genomic Locations for CBX5 Gene
chr12:54,230,942-54,280,133
(GRCh38/hg38)
Size:
49,192 bases
Orientation:
Minus strand
chr12:54,624,724-54,673,915
(GRCh37/hg19)
Size:
49,192 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 (PubMed:20042602). Interacts directly with ATRX, CHAF1A, LBR, NIPBL, SP100, STAM2 and TRIM28 via the chromoshadow domain (PubMed:15882967, PubMed:9169472). Can interact directly with CBX3 via the chromoshadow domain (PubMed:9169472). Interacts with histone H3 methylated at 'Lys-9' (PubMed:11242053, PubMed:21047797). Interacts with BAHD1, MIS12 and DSN1 (PubMed:15502821, PubMed:19666599). Interacts with POGZ; POGZ and PXVXL motif-containing proteins such as INCENP and TRIM28 compete for interaction with CBX5 (PubMed:20562864, PubMed:20850016, PubMed:21346195). Interacts with INCENP and TRIM24 (PubMed:11313457). Interacts with CHAMP1 (PubMed:20850016). Interacts with PRR14 (via N-terminus) (PubMed:25906157). Interacts with RRP1B (PubMed:19710015). Interacts with HNRNPU (via C-terminus); this interaction is, at least in part, RNA-dependent (PubMed:19617346). Interacts with LRIF1 (via PxVxL motif) (PubMed:23542155).
    • (Microbial infection) Interacts with JC virus agnoprotein; this interaction induces the dissociation of CBX5 from LBR, resulting in destabilization of the nuclear envelope.

    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 isoforms=32, isoforms=143, isoforms=125, posLast=102102, isoforms=154, posLast=4242, isoforms=159, and isoforms=91
  • 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

GenScript: Design optimal peptide antigens:
  • Heterochromatin protein 1 homolog alpha (CBX5_HUMAN)
  • CBX5 protein (Q6I9T7_HUMAN)

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:0042802 identical protein binding IPI 18716626
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:
  • Cbx5 Cbx5<tm1a(EUCOMM)Wtsi>
  • Cbx5 Cbx5<tm1.1Ics>

Animal Model Products

  • Taconic Biosciences Mouse Models for CBX5

CRISPR Products

miRNA for CBX5 Gene

miRTarBase miRNAs that target CBX5

Clone Products

  • Applied Biological Materials (abm): Clones for CBX5 - Now 50% OFF >
  • * CBX5 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * CBX5 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for CBX5

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=Colocalizes with HNRNPU in the nucleus (PubMed:19617346). Component of centromeric and pericentromeric heterochromatin. Associates with chromosomes during mitosis. Associates specifically with chromatin during metaphase and anaphase. {ECO:0000269 PubMed:19617346}.

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 HDA 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 GeneGo (Thomson Reuters) pathway for CBX5 Gene
1 Cell Signaling Technology pathway 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 by RNA polymerase II IMP 19617346
GO:0006974 cellular response to DNA damage stimulus IMP 27248496
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 226

(6) 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

Clone Products

  • Applied Biological Materials (abm): Clones for CBX5 - Now 50% OFF >
  • * CBX5 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * CBX5 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for CBX5

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, 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

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 35 34
  • 99.65 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CBX5 35 34
  • 97.03 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CBX5 35 34
  • 96.68 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Cbx5 17 35 34
  • 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 35 34
  • 67.4 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Su(var)205 35
  • 40 (a)
ManyToMany
HP6 35
  • 38 (a)
ManyToMany
HP1b 35 36
  • 36 (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)
Aminode:
Evolutionary constrained regions (ECRs) for CBX5: view image

Paralogs for CBX5 Gene

Paralogs for CBX5 Gene

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

  • CBX5_HUMAN
  • F8VNY3_HUMAN
  • Q6I9T7_HUMAN

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 Variation AA Info Type
rs74625894 benign, not specified 54,281,778(-) A/G upstream_transcript_variant
rs1000095385 -- 54,246,496(-) G/A/T intron_variant
rs1000150733 -- 54,233,759(-) T/C 3_prime_UTR_variant
rs1000264281 -- 54,241,046(-) G/T 3_prime_UTR_variant
rs1000353290 -- 54,253,531(-) A/G 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)

Additional Variant Information for CBX5 Gene

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

SNP Genotyping and Copy Number Assay Products

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 1
  • icf1
- elite association - COSMIC cancer census association via MalaCards
Search CBX5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 23 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 23 58
  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 58
  4. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. (PMID: 23542155) Nozawa RS … Obuse C (Nature structural & molecular biology 2013) 3 4 58
  5. Recognition and specificity determinants of the human cbx chromodomains. (PMID: 21047797) Kaustov L … Arrowsmith CH (The Journal of biological chemistry 2011) 3 4 58

Products for CBX5 Gene