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Cbx5 chromobox 5 [ Rattus norvegicus (Norway rat) ]

Gene ID: 300266, updated on 18-Sep-2024

Summary

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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 cellular response to DNA damage stimulus; chromatin organization; and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription, DNA-templated. Predicted to be located in chromocenter; chromosome; and nuclear lumen. Predicted to be part of nucleoplasm; ribonucleoprotein complex; and transcription repressor complex. Predicted to be active in pericentric heterochromatin. Predicted to colocalize with PML body. Orthologous to human CBX5 (chromobox 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 280.8), Thymus (RPKM 279.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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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

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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 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. 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. Involvement of ZFPIP/Zfp462 in chromatin integrity and survival of P19 pluripotent cells. Massé J, et al. Exp Cell Res, 2010 Apr 15. PMID 20219459

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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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

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Preferred Names
chromobox protein homolog 5
Names
chromobox homolog 5 (HP1 alpha 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_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

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