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CBX1 chromobox 1 [ Homo sapiens (human) ]

Gene ID: 10951, updated on 15-Jun-2019

Summary

Official Symbol
CBX1provided by HGNC
Official Full Name
chromobox 1provided by HGNC
Primary source
HGNC:HGNC:1551
See related
Ensembl:ENSG00000108468 MIM:604511
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
CBX; M31; MOD1; p25beta; HP1-BETA; HP1Hsbeta; HP1Hs-beta
Summary
This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family . The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The protein may play an important role in the epigenetic control of chromatin structure and gene expression. Several related pseudogenes are located on chromosomes 1, 3, and X. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 37.6), brain (RPKM 33.7) and 24 other tissues See more
Orthologs

Genomic context

See CBX1 in Genome Data Viewer
Location:
17q21.32
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (48070052..48101521, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46147414..46178883, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene coatomer protein complex subunit zeta 2 Neighboring gene microRNA 152 Neighboring gene nuclear factor, erythroid 2 like 1 Neighboring gene RNA, U6 small nuclear 1201, pseudogene Neighboring gene sorting nexin 11 Neighboring gene VISTA enhancer hs697 Neighboring gene src kinase associated phosphoprotein 1

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?

Phenotypes

NHGRI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
NHGRI GWA Catalog
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding TAS
Traceable Author Statement
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
chromocenter IEA
Inferred from Electronic Annotation
more info
 
chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
female pronucleus IEA
Inferred from Electronic Annotation
more info
 
male pronucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear chromosome, telomeric region HDA PubMed 
colocalizes_with nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nuclear heterochromatin TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
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 1
Names
HP1 beta homolog
chromobox homolog 1 (HP1 beta homolog Drosophila )
heterochromatin protein 1 homolog beta
heterochromatin protein 1-beta
heterochromatin protein p25 beta
modifier 1 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_001127228.2NP_001120700.1  chromobox protein homolog 1

    See identical proteins and their annotated locations for NP_001120700.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC002609, BC021302, DA020204, DB026977
    Consensus CDS
    CCDS11525.1
    UniProtKB/Swiss-Prot
    P83916
    UniProtKB/TrEMBL
    Q6IBN6
    Related
    ENSP00000225603.4, ENST00000225603.9
    Conserved Domains (2) summary
    pfam00385
    Location:2770
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:118170
    Chromo_shadow; Chromo shadow domain
  2. NM_006807.5NP_006798.1  chromobox protein homolog 1

    See identical proteins and their annotated locations for NP_006798.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC002609, BC021302, CB053834, DA689514
    Consensus CDS
    CCDS11525.1
    UniProtKB/Swiss-Prot
    P83916
    UniProtKB/TrEMBL
    Q6IBN6
    Related
    ENSP00000377060.3, ENST00000393408.7
    Conserved Domains (2) summary
    pfam00385
    Location:2770
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam01393
    Location:118170
    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.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    48070059..48101478 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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