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CBX5 chromobox 5 [ Homo sapiens (human) ]

Gene ID: 23468, updated on 6-Sep-2021

Summary

Official Symbol
CBX5provided by HGNC
Official Full Name
chromobox 5provided by HGNC
Primary source
HGNC:HGNC:1555
See related
Ensembl:ENSG00000094916 MIM:604478
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
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

See CBX5 in Genome Data Viewer
Location:
12q13.13
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (54230942..54280122, complement)
105.20201022 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 single-strand-selective monofunctional uracil-DNA glycosylase 1 Neighboring gene uncharacterized LOC102724030 Neighboring gene Sharpr-MPRA regulatory region 1237 Neighboring gene uncharacterized LOC105369777 Neighboring gene microRNA 3198-2 Neighboring gene RNA, 7SL, cytoplasmic 390, pseudogene Neighboring gene CRISPRi-FlowFISH-validated NFE2 regulatory element Neighboring gene S-phase cancer associated transcript 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 regulatory element Neighboring gene nuclear factor, erythroid 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
New gene functions in megakaryopoiesis and platelet formation.
GeneReviews: Not available

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
Component Evidence Code Pubs
colocalizes_with PML body IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in chromosome, telomeric region HDA PubMed 
located_in 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 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 
located_in pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in 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

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_001127321.1NP_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
    P45973
    UniProtKB/TrEMBL
    V9HWG0
    Related
    ENSP00000401009.2, ENST00000439541.6
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  2. NM_001127322.1NP_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
    P45973
    UniProtKB/TrEMBL
    V9HWG0
    Related
    ENSP00000449207.1, ENST00000550411.5
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  3. NM_012117.3NP_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
    P45973
    UniProtKB/TrEMBL
    V9HWG0
    Related
    ENSP00000209875.4, ENST00000209875.9
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

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