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CBX5 chromobox 5 [ Homo sapiens (human) ]

Gene ID: 23468, updated on 11-Apr-2024

Summary

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Official Symbol
CBX5provided by HGNC
Official Full Name
chromobox 5provided by HGNC
Primary source
HGNC:HGNC:1555
See related
Ensembl:ENSG00000094916 MIM:604478; AllianceGenome:HGNC:1555
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HP1; HP1A; HEL25; HP1alpha
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 15.3), thyroid (RPKM 14.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.13
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54230942..54280122, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54197516..54246699, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54624726..54673906, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54556725-54557225 Neighboring gene uncharacterized LOC102724030 Neighboring gene single-strand-selective monofunctional uracil-DNA glycosylase 1 Neighboring gene uncharacterized LOC105369777 Neighboring gene Sharpr-MPRA regulatory region 1888 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:54609784-54609969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4524 Neighboring gene microRNA 3198-2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:54642790-54642989 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:54650247-54650908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6436 Neighboring gene RNA, 7SL, cytoplasmic 390, pseudogene Neighboring gene S-phase cancer associated transcript 2 Neighboring gene CRISPRi-FlowFISH-validated NFE2 regulatory element 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated COPZ1 and HNRNPA1 regulatory element Neighboring gene nuclear factor, erythroid 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. HP1α promotes the progression of prostate cancer. Zhang S, et al. Mol Biol Rep, 2023 May. PMID 37014569
  2. Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding. Her C, et al. Nucleic Acids Res, 2022 Dec 9. PMID 36537242, Free PMC Article
  3. Changes in the properties of membrane tethers in response to HP1α depletion in MCF7 cells. Pradhan S, et al. Biochem Biophys Res Commun, 2022 Jan 8. PMID 34872000
  4. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. Strom AR, et al. Elife, 2021 Jun 9. PMID 34106828, Free PMC Article
  5. Depletion of HP1α alters the mechanical properties of MCF7 nuclei. Pradhan S, et al. Biophys J, 2021 Jul 6. PMID 34087208, Free PMC Article

See all (286) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. How to evict HP1 from H3: Using a complex salt bridge.
    Title: How to evict HP1 from H3: Using a complex salt bridge.
  2. HP1alpha promotes the progression of prostate cancer.
    Title: HP1α promotes the progression of prostate cancer.
  3. Molecular interactions underlying the phase separation of HP1alpha: role of phosphorylation, ligand and nucleic acid binding.
    Title: Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding.
  4. Circ_0037866 Contributes to the Tumorigenesis of Renal Cell Carcinoma by Sequestering miR-384 to Elevate Chromobox 5 Expression.
    Title: Circ_0037866 Contributes to the Tumorigenesis of Renal Cell Carcinoma by Sequestering miR-384 to Elevate Chromobox 5 Expression.
  5. Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.
    Title: Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.
  6. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
    Title: HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
  7. Changes in the properties of membrane tethers in response to HP1alpha depletion in MCF7 cells.
    Title: Changes in the properties of membrane tethers in response to HP1α depletion in MCF7 cells.
  8. HP1alpha is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
    Title: HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
  9. Structural dynamics of the chromo-shadow domain and chromodomain of HP1 bound to histone H3K9 methylated peptide, as measured by site-directed spin-labeling EPR spectroscopy.
    Title: Structural dynamics of the chromo-shadow domain and chromodomain of HP1 bound to histone H3K9 methylated peptide, as measured by site-directed spin-labeling EPR spectroscopy.
  10. Depletion of HP1alpha alters the mechanical properties of MCF7 nuclei.
    Title: Depletion of HP1α alters the mechanical properties of MCF7 nuclei.
Submit: New GeneRIF Correction See all GeneRIFs (102)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat is recruited by CTIP2 into a complex with HP1alpha, leading to the relocalization of Tat and inactivation of Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
Vpr vpr HIV-1 Vpr actively recruits p300/HAT to a range of chromatin regions including the centromere, resulting in the displacement of HP1-alpha PubMed
vpr HIV-1 Vpr interferes with the heterochromatin structure by displacing HP1-alpha and HP1-gamma proteins in interphase, which leads to relocalization of the centromere chromatin proteins Mis12, Sgo1, and CPC after prophase PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-macromolecule adaptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with PML body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in chromocenter IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome, telomeric region HDA PubMed 
part_of heterochromatin TAS
Traceable Author Statement
more info
 PubMed 
part_of histone deacetylase complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of histone methyltransferase complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in kinetochore IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear envelope TAS
Traceable Author Statement
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of pericentric heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of pericentric heterochromatin NAS
Non-traceable Author Statement
more info
 PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of DNA damage IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of transcription repressor complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
chromobox protein homolog 5
Names
HP1 alpha homolog
HP1-ALPHA
HP1Hs alpha
antigen p25
chromobox homolog 5 (HP1 alpha homolog, Drosophila)
epididymis luminal protein 25
heterochromatin protein 1 homolog alpha
heterochromatin protein 1-alpha

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001127321.1 → NP_001120793.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_001120793.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC078778, BC006821, BC030149, BP236173
    Consensus CDS
    CCDS8875.1
    UniProtKB/Swiss-Prot
    B2R8T9, P45973
    UniProtKB/TrEMBL
    Q6I9T7, V9HWG0
    Related
    ENSP00000401009.2, ENST00000439541.6
    Conserved Domains (2) summary
    cd18651
    Location:19 → 68
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116 → 173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

  2. NM_001127322.1 → NP_001120794.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_001120794.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC078778, AK313506, BC030149, DT217255
    Consensus CDS
    CCDS8875.1
    UniProtKB/Swiss-Prot
    B2R8T9, P45973
    UniProtKB/TrEMBL
    Q6I9T7, V9HWG0
    Related
    ENSP00000449207.1, ENST00000550411.5
    Conserved Domains (2) summary
    cd18651
    Location:19 → 68
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116 → 173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

  3. NM_012117.3 → NP_036249.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_036249.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC078778, BC030149, BP336150
    Consensus CDS
    CCDS8875.1
    UniProtKB/Swiss-Prot
    B2R8T9, P45973
    UniProtKB/TrEMBL
    Q6I9T7, V9HWG0
    Related
    ENSP00000209875.4, ENST00000209875.9
    Conserved Domains (2) summary
    cd18651
    Location:19 → 68
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116 → 173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    54230942..54280122 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    54197516..54246699 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P45973.1 GenPept UniProtKB/Swiss-Prot:P45973

Gene LinkOut

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