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    CBX3 chromobox 3 [ Homo sapiens (human) ]

    Gene ID: 11335, updated on 3-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
    mouse all
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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. Residues flanking the ARK(me3)T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Pokorná P, et al. Biochim Biophys Acta Gen Subj, 2021 Jan. PMID 33153976
    2. Nucleosome compaction facilitates HP1γ binding to methylated H3K9. Mishima Y, et al. Nucleic Acids Res, 2015 Dec 2. PMID 26319017, Free PMC Article
    3. CBX3 predicts an unfavorable prognosis and promotes tumorigenesis in osteosarcoma. Ma C, et al. Mol Med Rep, 2019 May. PMID 30942427, Free PMC Article
    4. Overexpression of HP1γ is associated with poor prognosis in non-small cell lung cancer cell through promoting cell survival. Zhou J, et al. Tumour Biol, 2014 Oct. PMID 24981246
    5. Evidence supporting a critical contribution of intrinsically disordered regions to the biochemical behavior of full-length human HP1γ. Velez G, et al. J Mol Model, 2016 Jan. PMID 26680990, Free PMC Article

    See all (317) 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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    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_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

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

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