U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Cbx5 chromobox 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300266, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Cbx5provided by RGD
    Official Full Name
    chromobox 5provided by RGD
    Primary source
    RGD:1306619
    See related
    EnsemblRapid:ENSRNOG00000036841 AllianceGenome:RGD:1306619
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    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 deacetylase binding activity; identical protein binding activity; and methylated histone binding activity. Predicted to be involved in DNA damage response; heterochromatin formation; and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of DNA-templated transcription. Predicted to be located in several cellular components, including chromosomal region; nuclear lumen; and site of DNA damage. Predicted to be part of nucleoplasm; ribonucleoprotein complex; and transcription repressor complex. Orthologous to human CBX5 (chromobox 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 280.8), Thymus (RPKM 279.8) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Cbx5 in Genome Data Viewer
    Location:
    7q36
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (136203827..136254575, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (134333165..134376102, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (144819673..144865014, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120093746 Neighboring gene uncharacterized LOC103692988 Neighboring gene single-strand-selective monofunctional uracil-DNA glycosylase 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene nuclear factor, erythroid 2 Neighboring gene COPI coat complex subunit zeta 1 Neighboring gene microRNA 148b

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Network biology of tumor stem-like cells identified a regulatory role of CBX5 in lung cancer. Yu YH, et al. Sci Rep, 2012. PMID 22900142, Free PMC Article
    2. The heterochromatin protein 1 family is regulated in prostate development and cancer. Shapiro E, et al. J Urol, 2008 Jun. PMID 18436254
    3. Physical and functional interaction between heterochromatin protein 1alpha and the RNA-binding protein heterogeneous nuclear ribonucleoprotein U. Ameyar-Zazoua M, et al. J Biol Chem, 2009 Oct 9. PMID 19617346, Free PMC Article
    4. Cohesin acetyltransferase Esco2 is a cell viability factor and is required for cohesion in pericentric heterochromatin. Whelan G, et al. EMBO J, 2012 Jan 4. PMID 22101327, Free PMC Article
    5. JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Dawson MA, et al. Nature, 2009 Oct 8. PMID 19783980, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Homology

    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 chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone deacetylase 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 methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-macromolecule adaptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ribonucleoprotein complex 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 biological_process ND
    No biological Data available
    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
    		  
    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
    		  
    Component Evidence Code Pubs
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromocenter ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of histone deacetylase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of histone methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in kinetochore ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus 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
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription repressor complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    chromobox protein homolog 5
    Names
    chromobox homolog 5 (HP1 alpha homolog, Drosophila)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001106797.3 → NP_001100267.1  chromobox protein homolog 5

      See identical proteins and their annotated locations for NP_001100267.1

      Status: PROVISIONAL

      Source sequence(s)
      BC166908
      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Related
      ENSRNOP00000052163.2, ENSRNOT00000055289.4
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    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_086025.1 Reference GRCr8

      Range
      136203827..136254575 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078944.2 → XP_038934872.1  chromobox protein homolog 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    2. XM_008765707.4 → XP_008763929.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_008763929.1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    3. XM_039078942.2 → XP_038934870.1  chromobox protein homolog 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    4. XM_039078946.2 → XP_038934874.1  chromobox protein homolog 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    5. XM_006242391.5 → XP_006242453.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006242453.1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    6. XM_006242393.5 → XP_006242455.1  chromobox protein homolog 5 isoform X1

      See identical proteins and their annotated locations for XP_006242455.1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    7. XM_039078943.2 → XP_038934871.1  chromobox protein homolog 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    8. XM_017594793.3 → XP_017450282.1  chromobox protein homolog 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5J8, A0A8I6A5A0, A6KCZ7, A6KCZ8, B2RYU7
      Conserved Domains (2) summary
      cd18651
      Location:19 → 68
      CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
      cd18655
      Location:116 → 173
      CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

    9. XM_063263390.1 → XP_063119460.1  chromobox protein homolog 5 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous