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    Cbx5 chromobox 5 [ Mus musculus (house mouse) ]

    Gene ID: 12419, updated on 9-Dec-2024

    Summary

    Official Symbol
    Cbx5provided by MGI
    Official Full Name
    chromobox 5provided by MGI
    Primary source
    MGI:MGI:109372
    See related
    Ensembl:ENSMUSG00000009575 AllianceGenome:MGI:109372
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    HP1; Hp1a; Hp1alpha; 2610029O15Rik
    Summary
    Enables several functions, including histone deacetylase binding activity; identical protein binding activity; and methylated histone binding activity. Acts upstream of or within negative regulation of DNA-templated transcription. Located in chromocenter; chromosomal region; and nucleolus. Part of histone deacetylase complex; histone methyltransferase complex; and transcription repressor complex. Is expressed in several structures, including alimentary system; early embryo; genitourinary system; nervous system; and sensory organ. Orthologous to human CBX5 (chromobox 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 47.5), whole brain E14.5 (RPKM 29.9) and 22 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Cbx5 in Genome Data Viewer
    Location:
    15 F3; 15 58.34 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (103099973..103148337, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (103191546..103239904, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene Riken cDNA D930007P13 gene Neighboring gene STARR-positive B cell enhancer mm9_chr15:102993642-102993943 Neighboring gene single-strand selective monofunctional uracil DNA glycosylase Neighboring gene STARR-seq mESC enhancer starr_39867 Neighboring gene STARR-seq mESC enhancer starr_39868 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene STARR-seq mESC enhancer starr_39872 Neighboring gene nuclear factor, erythroid derived 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

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

    General protein information

    Preferred Names
    chromobox protein homolog 5
    Names
    HP1 alpha
    chromobox homolog 5
    heterochromatin protein 1 alpha
    heterochromatin protein 1 homolog alpha
    mHP1(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_001076789.2NP_001070257.1  chromobox protein homolog 5

      See identical proteins and their annotated locations for NP_001070257.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC162693, AC164069
      Consensus CDS
      CCDS37231.1
      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      Related
      ENSMUSP00000113157.2, ENSMUST00000118152.8
      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_001110216.1NP_001103686.1  chromobox protein homolog 5

      See identical proteins and their annotated locations for NP_001103686.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC162693, AC164069, AK030366, AK030442, BM247903
      Consensus CDS
      CCDS37231.1
      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      Related
      ENSMUSP00000113158.2, ENSMUST00000122182.2
      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_001358950.1NP_001345879.1  chromobox protein homolog 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC162693, AC164069
      Consensus CDS
      CCDS37231.1
      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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
    4. NM_007626.3NP_031652.1  chromobox protein homolog 5

      See identical proteins and their annotated locations for NP_031652.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the same protein as variants 2, 3 and 4.
      Source sequence(s)
      AC162693, AC164069
      Consensus CDS
      CCDS37231.1
      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      Related
      ENSMUSP00000104441.4, ENSMUST00000108813.10
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000081.7 Reference GRCm39 C57BL/6J

      Range
      103099973..103148337 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006520372.5XP_006520435.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006520435.1

      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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. XM_006520374.4XP_006520437.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006520437.1

      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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. XM_006520376.4XP_006520439.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006520439.1

      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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
    4. XM_030248308.2XP_030104168.1  chromobox protein homolog 5 isoform X1

      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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
    5. XM_006520375.5XP_006520438.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006520438.1

      UniProtKB/Swiss-Prot
      Q61686, Q9CS35, Q9CXD1
      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
    6. XM_006520377.3XP_006520440.1  chromobox protein homolog 5 isoform X2

      Conserved Domains (2) summary
      cd18651
      Location:1968
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cl28914
      Location:116142
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains