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CBX3 chromobox 3 [ Homo sapiens (human) ]

Gene ID: 11335, updated on 2-Nov-2024

Summary

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Official Symbol
CBX3provided by HGNC
Official Full Name
chromobox 3provided by HGNC
Primary source
HGNC:HGNC:1553
See related
Ensembl:ENSG00000122565 MIM:604477; AllianceGenome:HGNC:1553
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HECH; HP1gamma; HP1-GAMMA; HP1Hs-gamma
Summary
At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.[provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in lymph node (RPKM 47.3), testis (RPKM 43.1) and 25 other tissues See more
Orthologs
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Genomic context

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See CBX3 in Genome Data Viewer
Location:
7p15.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (26201443..26213607)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (26337121..26349288)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (26241063..26253227)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:26191778-26192572 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr7:26192573-26193366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26197976-26198476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26198477-26198977 Neighboring gene Sharpr-MPRA regulatory region 12991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25783 Neighboring gene NFE2 like bZIP transcription factor 3 Neighboring gene Sharpr-MPRA regulatory region 4449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25785 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:26227891-26228415 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26238808-26239781 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26239782-26240754 Neighboring gene heterogeneous nuclear ribonucleoprotein A2/B1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18035 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:26262791-26262893 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26302097-26302746 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:26311265-26311466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18037 Neighboring gene ribosomal protein L23 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26341907-26342408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26342409-26342908 Neighboring gene sorting nexin 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26375053-26375568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26385227-26386154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25789 Neighboring gene SNX10 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Overexpression of CBX3 in Pancreatic Adenocarcinoma Promotes Cell Cycle Transition-Associated Tumor Progression. Chen LY, et al. Int J Mol Sci, 2018 Jun 14. PMID 29903985, Free PMC Article
  2. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Saint-André V, et al. Nat Struct Mol Biol, 2011 Mar. PMID 21358630
  3. A role for heterochromatin protein 1γ at human telomeres. Canudas S, et al. Genes Dev, 2011 Sep 1. PMID 21865325, Free PMC Article
  4. Heterochromatin protein 1γ overexpression in P19 embryonal carcinoma cells elicits spontaneous differentiation into the three germ layers. Morikawa K, et al. Biochem Biophys Res Commun, 2013 Feb 8. PMID 23313480
  5. Comprehensive pan-cancer analysis on CBX3 as a prognostic and immunological biomarker. Niu H, et al. BMC Med Genomics, 2022 Feb 16. PMID 35172803, Free PMC Article

See all (313) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CBX3 promotes clear cell renal carcinoma through PI3K/AKT activation and aberrant immunity.
    Title: CBX3 promotes clear cell renal carcinoma through PI3K/AKT activation and aberrant immunity.
  2. PSMC4 promotes prostate carcinoma progression by regulating the CBX3-EGFR-PI3K-AKT-mTOR pathway.
    Title: PSMC4 promotes prostate carcinoma progression by regulating the CBX3-EGFR-PI3K-AKT-mTOR pathway.
  3. CBX3 promotes breast cancer progression and high level of CBX3 predicts poor prognosis in patients.
    Title: CBX3 promotes breast cancer progression and high level of CBX3 predicts poor prognosis in patients.
  4. The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis.
    Title: The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis.
  5. CBX3 regulated by miR-139 promotes the development of HCC by regulating cell cycle progression.
    Title: CBX3 regulated by miR-139 promotes the development of HCC by regulating cell cycle progression.
  6. CBX3 Regulated By YBX1 Promotes Smoking-induced Pancreatic Cancer Progression via Inhibiting SMURF2 Expression.
    Title: CBX3 Regulated By YBX1 Promotes Smoking-induced Pancreatic Cancer Progression via Inhibiting SMURF2 Expression.
  7. CBX3 accelerates the malignant progression of glioblastoma multiforme by stabilizing EGFR expression.
    Title: CBX3 accelerates the malignant progression of glioblastoma multiforme by stabilizing EGFR expression.
  8. Comprehensive pan-cancer analysis on CBX3 as a prognostic and immunological biomarker.
    Title: Comprehensive pan-cancer analysis on CBX3 as a prognostic and immunological biomarker.
  9. Clinicopathological significance of CBX3 in colorectal cancer: An intensive expression study based on formalin-fixed and paraffin-embedded tissues.
    Title: Clinicopathological significance of CBX3 in colorectal cancer: An intensive expression study based on formalin-fixed and paraffin-embedded tissues.
  10. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
    Title: HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
Submit: New GeneRIF Correction See all GeneRIFs (63)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Expression of HIV-1 Tat upregulates the abundance of chromobox homolog 3 (CBX3) in the nucleoli of Jurkat T-cells PubMed
Vpr vpr HIV-1 Vpr interferes with the heterochromatin structure by displacing HP1-alpha and HP1-gamma proteins in interphase, which leads to relocalization of the centromere chromatin proteins Mis12, Sgo1, and CPC after prophase PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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 GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heterochromatin formation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in rhythmic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin lock complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in chromosome, centromeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region HDA PubMed 
located_in condensed chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in euchromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear envelope ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear inner membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in pericentric heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in site of DNA damage IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in spindle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
chromobox protein homolog 3
Names
HP1 gamma homolog
chromobox homolog 3 (HP1 gamma homolog, Drosophila)
heterochromatin protein 1 homolog gamma
heterochromatin protein HP1 gamma
heterochromatin-like protein 1
modifier 2 protein

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_001410866.1 → NP_001397795.1  chromobox protein homolog 3 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC010677
    Consensus CDS
    CCDS94069.1
    UniProtKB/TrEMBL
    A0A024RA30, B8ZZ43
    Related
    ENSP00000387348.1, ENST00000409747.5

  2. NM_007276.5 → NP_009207.2  chromobox protein homolog 3 isoform a

    See identical proteins and their annotated locations for NP_009207.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains an alternate 5' exon but encodes the same isoform (a) as transcript variant 2.
    Source sequence(s)
    BC000954, BX648807, CV575477, DB565723
    Consensus CDS
    CCDS5398.1
    UniProtKB/Swiss-Prot
    Q13185, Q96CD7, Q99409, Q9BVS3, Q9P0Z6
    UniProtKB/TrEMBL
    A4D177
    Related
    ENSP00000336687.4, ENST00000337620.8
    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

  3. NM_016587.4 → NP_057671.2  chromobox protein homolog 3 isoform a

    See identical proteins and their annotated locations for NP_057671.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon but encodes the same isoform (a) as transcript variant 1.
    Source sequence(s)
    BX648807, CD514780, DB565723
    Consensus CDS
    CCDS5398.1
    UniProtKB/Swiss-Prot
    Q13185, Q96CD7, Q99409, Q9BVS3, Q9P0Z6
    UniProtKB/TrEMBL
    A4D177
    Related
    ENSP00000379670.2, ENST00000396386.7
    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_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    26201443..26213607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249611.5 → XP_005249668.1  chromobox protein homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_005249668.1

    UniProtKB/Swiss-Prot
    Q13185, Q96CD7, Q99409, Q9BVS3, Q9P0Z6
    UniProtKB/TrEMBL
    A4D177
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    26337121..26349288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357182.1 → XP_054213157.1  chromobox protein homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    Q13185, Q96CD7, Q99409, Q9BVS3, Q9P0Z6
    UniProtKB/TrEMBL
    A4D177
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13185.4 GenPept UniProtKB/Swiss-Prot:Q13185

Gene LinkOut

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