Format

Send to:

Choose Destination

CBX3 chromobox 3 [ Homo sapiens (human) ]

Gene ID: 11335, updated on 6-Jan-2019

Summary

Official Symbol
CBX3provided by HGNC
Official Full Name
chromobox 3provided by HGNC
Primary source
HGNC:HGNC:1553
See related
Ensembl:ENSG00000122565 MIM:604477
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; 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

Genomic context

See CBX3 in Genome Data Viewer
Location:
7p15.2
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (26201211..26213607)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (26240831..26253227)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene nuclear factor, erythroid 2 like 3 Neighboring gene heterogeneous nuclear ribonucleoprotein A2/B1 Neighboring gene ribosomal protein L23 pseudogene 7 Neighboring gene sorting nexin 10 Neighboring gene uncharacterized LOC105375304

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin remodeling NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
condensed chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromosome, telomeric region HDA PubMed 
nuclear envelope ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear euchromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear inner membrane NAS
Non-traceable Author Statement
more info
PubMed 
nuclear pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
site of DNA damage IMP
Inferred from Mutant Phenotype
more info
PubMed 
spindle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_007276.4NP_009207.2  chromobox protein homolog 3

    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 protein as transcript variant 2.
    Source sequence(s)
    BC000954, BX648807, CV575477, DB565723
    Consensus CDS
    CCDS5398.1
    UniProtKB/Swiss-Prot
    Q13185
    UniProtKB/TrEMBL
    A4D177
    Related
    ENSP00000336687.4, ENST00000337620.8
    Conserved Domains (2) summary
    pfam00385
    Location:3079
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain
  2. NM_016587.4NP_057671.2  chromobox protein homolog 3

    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 protein as transcript variant 1.
    Source sequence(s)
    BX648807, CD514780, DB565723
    Consensus CDS
    CCDS5398.1
    UniProtKB/Swiss-Prot
    Q13185
    UniProtKB/TrEMBL
    A4D177
    Related
    ENSP00000379670.2, ENST00000396386.6
    Conserved Domains (2) summary
    pfam00385
    Location:3079
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    26201211..26213607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249611.4XP_005249668.1  chromobox protein homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_005249668.1

    UniProtKB/Swiss-Prot
    Q13185
    UniProtKB/TrEMBL
    A4D177
    Conserved Domains (2) summary
    pfam00385
    Location:3079
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:122174
    Chromo_shadow; Chromo shadow domain
Support Center