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CBX5 chromobox 5 [ Homo sapiens (human) ]

Gene ID: 23468, updated on 18-Jun-2019

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

Genomic context

See CBX5 in Genome Data Viewer
Location:
12q13.13
Exon count:
6
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (54230942..54280122, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54624730..54673915, 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 S-phase cancer associated transcript 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 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 FunctionsWhat's a GeneRIF?

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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging ISS
Inferred from Sequence or Structural Similarity
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
repressing transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
blood coagulation TAS
Traceable Author Statement
more info
 
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with PML body IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromocenter IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
histone methyltransferase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
kinetochore IEA
Inferred from Electronic Annotation
more info
 
nuclear chromosome, telomeric region HDA PubMed 
nuclear envelope TAS
Traceable Author Statement
more info
PubMed 
nuclear heterochromatin TAS
Traceable Author Statement
more info
PubMed 
nuclear pericentric heterochromatin NAS
Non-traceable Author Statement
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
site of DNA damage IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcriptional 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)

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
    pfam00385
    Location:2069
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain
  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
    pfam00385
    Location:2069
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain
  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
    pfam00385
    Location:2069
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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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