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    Cbx1 chromobox 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360609, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Cbx1provided by RGD
    Official Full Name
    chromobox 1provided by RGD
    Primary source
    RGD:1310714
    See related
    EnsemblRapid:ENSRNOG00000008689 AllianceGenome:RGD:1310714
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including histone methyltransferase binding activity; identical protein binding activity; and methylated histone binding activity. Predicted to be involved in DNA damage response and heterochromatin formation. Predicted to act upstream of or within negative regulation of DNA-templated transcription. Predicted to be located in several cellular components, including chromocenter; chromosome; and pronucleus. Orthologous to human CBX1 (chromobox 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 331.2), Lung (RPKM 176.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cbx1 in Genome Data Viewer
    Location:
    10q31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (82266746..82286431)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (81770307..81789981)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (84656698..84677112)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene sorting nexin 11 Neighboring gene uncharacterized LOC134480860 Neighboring gene NFE2 like bZIP transcription factor 1 Neighboring gene uncharacterized LOC120095287

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. A mammalian homologue of Drosophila heterochromatin protein 1 (HP1) is a component of constitutive heterochromatin. Wreggett KA, et al. Cytogenet Cell Genet, 1994. PMID 8287692
    2. The heterochromatin protein 1 family is regulated in prostate development and cancer. Shapiro E, et al. J Urol, 2008 Jun. PMID 18436254
    3. Methylation-independent binding to histone H3 and cell cycle-dependent incorporation of HP1beta into heterochromatin. Dialynas GK, et al. J Biol Chem, 2006 May 19. PMID 16547356
    4. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. van der Heijden GW, et al. Mech Dev, 2005 Sep. PMID 15922569
    5. The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer. Brasher SV, et al. EMBO J, 2000 Apr 3. PMID 10747027, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. analysis of methylation-independent binding to histone H3 and cell cycle-dependent incorporation of HP1beta into heterochromatin
      Title: Methylation-independent binding to histone H3 and cell cycle-dependent incorporation of HP1beta into heterochromatin.
    Submit: New GeneRIF Correction

    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 RGD

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone methyltransferase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromocenter ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, centromeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in female pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in male pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in pericentric heterochromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in pericentric heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in spindle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chromobox protein homolog 1
    Names
    chromobox homolog 1 (HP1 beta homolog Drosophila )

    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_001398806.1 → NP_001385735.1  chromobox protein homolog 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A6HIG4
      Conserved Domains (2) summary
      cd18650
      Location:20 → 69
      CD_HP1beta_Cbx1; chromodomain of heterochromatin protein 1 homolog beta
      cd18654
      Location:112 → 169
      CSD_HP1beta_Cbx1; chromo shadow domain of heterochromatin protein 1 homolog beta

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      82266746..82286431
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006247233.5 → XP_006247295.1  chromobox protein homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_006247295.1

      UniProtKB/TrEMBL
      A0A8I5ZM96
      Related
      ENSRNOP00000078867.1, ENSRNOT00000094691.2
      Conserved Domains (2) summary
      pfam00385
      Location:27 → 70
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam01393
      Location:126 → 177
      Chromo_shadow; Chromo shadow domain

    2. XM_006247234.5 → XP_006247296.1  chromobox protein homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_006247296.1

      UniProtKB/TrEMBL
      A0A8I5ZM96
      Conserved Domains (2) summary
      pfam00385
      Location:27 → 70
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam01393
      Location:126 → 177
      Chromo_shadow; Chromo shadow domain

    3. XM_063269417.1 → XP_063125487.1  chromobox protein homolog 1 isoform X2

      UniProtKB/TrEMBL
      A6HIG4
    Nucleotide Protein Strain
    Heading Accession and Version

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