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    CBX5 chromobox 5 [ Homo sapiens (human) ]

    Gene ID: 23468, updated on 15-Jul-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CBX5 in Genome Data Viewer
    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

    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?

    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

    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 
    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

    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)

    NEW Try the new Transcript table

    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
      B2R8T9, P45973
      UniProtKB/TrEMBL
      Q6I9T7, 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
      B2R8T9, P45973
      UniProtKB/TrEMBL
      Q6I9T7, 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
      B2R8T9, P45973
      UniProtKB/TrEMBL
      Q6I9T7, 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: 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)