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Cbx3 chromobox 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 297093, updated on 10-Jul-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 nucleus and senescence-associated heterochromatin focus. Orthologous to human CBX3 (chromobox 3). [provided by Alliance of Genome Resources, Apr 2022]
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. 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
  4. The heterochromatin protein 1 family is regulated in prostate development and cancer. Shapiro E, et al. J Urol, 2008 Jun. PMID 18436254
  5. HP1gamma associates with euchromatin and heterochromatin in mammalian nuclei and chromosomes. Minc E, et al. Cytogenet Cell Genet, 2000. PMID 11124534

See all (22) 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
  
part_of 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
  
part_of euchromatin ISO
Inferred from Sequence Orthology
more info
  
part_of 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
  
part_of pericentric heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
  
part_of 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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