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    Cbx3 chromobox 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297093, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Cbx3provided by RGD
    Official Full Name
    chromobox 3provided by RGD
    Primary source
    RGD:1549705
    See related
    EnsemblRapid:ENSRNOG00000011814 AllianceGenome:RGD:1549705
    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
    Also known as
    Hp1-gamma
    Summary
    Predicted to enable several functions, including histone methyltransferase binding activity; identical protein binding activity; and transcription coregulator binding activity. Involved in cellular response to dexamethasone stimulus. Located in senescence-associated heterochromatin focus. Orthologous to human CBX3 (chromobox 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 493.3), Brain (RPKM 329.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cbx3 in Genome Data Viewer
    Location:
    4q24
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (81876155..81889912)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (80545450..80559284)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (81243809..81257898)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene NFE2 like bZIP transcription factor 3 Neighboring gene heterogeneous nuclear ribonucleoprotein A2/B1 Neighboring gene igE-binding protein-like Neighboring gene translocase of outer mitochondrial membrane 20 like 2 Neighboring gene MICOS complex subunit MIC13-like Neighboring gene sorting nexin 10

    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. Mechanisms Underlying the Regulation of HP1γ by the NGF-PKA Signaling Pathway. Seo S, et al. Sci Rep, 2018 Oct 10. PMID 30305677, Free PMC Article
    2. Granulocyte heterochromatin: defining the epigenome. Olins DE, et al. BMC Cell Biol, 2005 Nov 15. PMID 16287503, Free PMC Article
    3. HP1gamma associates with euchromatin and heterochromatin in mammalian nuclei and chromosomes. Minc E, et al. Cytogenet Cell Genet, 2000. PMID 11124534
    4. The heterochromatin protein 1 family is regulated in prostate development and cancer. Shapiro E, et al. J Urol, 2008 Jun. PMID 18436254
    5. Glucocorticoids induce long-lasting effects in neural stem cells resulting in senescence-related alterations. Bose R, et al. Cell Death Dis, 2010 Nov 4. PMID 21368868, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC94711, MGC105792, MGC105793, MGC156678

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to dexamethasone stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin lock complex 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 condensed chromosome, centromeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in euchromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear envelope 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 senescence-associated heterochromatin focus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 3
    Names
    HP1 gamma
    chromobox homolog 3 (HP1 gamma homolog, Drosophila)
    heterochromatin protein 1 gamma

    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_001008313.2 → NP_001008314.2  chromobox protein homolog 3

      See identical proteins and their annotated locations for NP_001008314.2

      Status: VALIDATED

      Source sequence(s)
      BC086601
      UniProtKB/TrEMBL
      A0JPM8, D3ZRS6, Q5RJK5
      Related
      ENSRNOP00000015828.5, ENSRNOT00000015828.9
      Conserved Domains (2) summary
      cd18652
      Location:29 → 78
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cd18656
      Location:116 → 173
      CSD_HP1gamma_Cbx3; chromo shadow domain of heterochromatin protein 1 gamma homolog gamma

    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_086022.1 Reference GRCr8

      Range
      81876155..81889912
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039107305.2 → XP_038963233.1  chromobox protein homolog 3 isoform X1

      UniProtKB/TrEMBL
      A0JPM8, D3ZRS6, Q5RJK5
      Conserved Domains (2) summary
      cd18652
      Location:29 → 78
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cd18656
      Location:116 → 173
      CSD_HP1gamma_Cbx3; chromo shadow domain of heterochromatin protein 1 gamma homolog gamma

    2. XM_063285770.1 → XP_063141840.1  chromobox protein homolog 3 isoform X2

      UniProtKB/TrEMBL
      D3ZRS6

    3. XM_039107306.2 → XP_038963234.1  chromobox protein homolog 3 isoform X2

      UniProtKB/TrEMBL
      D3ZRS6
      Conserved Domains (2) summary
      cd18652
      Location:19 → 68
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cl28914
      Location:106 → 163
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    4. XM_006236484.5 → XP_006236546.1  chromobox protein homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_006236546.1

      UniProtKB/TrEMBL
      A0JPM8, D3ZRS6, Q5RJK5
      Conserved Domains (2) summary
      cd18652
      Location:29 → 78
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cd18656
      Location:116 → 173
      CSD_HP1gamma_Cbx3; chromo shadow domain of heterochromatin protein 1 gamma homolog gamma

    5. XM_039107304.1 → XP_038963232.1  chromobox protein homolog 3 isoform X1

      UniProtKB/TrEMBL
      A0JPM8, D3ZRS6, Q5RJK5
      Conserved Domains (2) summary
      cd18652
      Location:29 → 78
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cd18656
      Location:116 → 173
      CSD_HP1gamma_Cbx3; chromo shadow domain of heterochromatin protein 1 gamma homolog gamma

    6. XM_039107302.2 → XP_038963230.1  chromobox protein homolog 3 isoform X1

      UniProtKB/TrEMBL
      A0JPM8, D3ZRS6, Q5RJK5
      Conserved Domains (2) summary
      cd18652
      Location:29 → 78
      CD_HP1gamma_Cbx3; chromodomain of heterochromatin protein 1 homolog gamma
      cd18656
      Location:116 → 173
      CSD_HP1gamma_Cbx3; chromo shadow domain of heterochromatin protein 1 gamma homolog gamma
    Nucleotide Protein Strain
    Heading Accession and Version

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