CBX3 chromobox 3 [Homo sapiens (human)] - Gene

Summary

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

Location:: 7p15.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (26201443..26213607)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (26337121..26349288)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (26241063..26253227)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

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

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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

CBX3 (e-PCR)
- UniSTS:503620

HSC11F052 (e-PCR)
- UniSTS:60487

D7S2103E (e-PCR)
- UniSTS:151124

STS-H78370 (e-PCR)
- UniSTS:68958

RH24974 (e-PCR)
- UniSTS:85612

SHGC-83036 (e-PCR)
- UniSTS:96139

SHGC-57830 (e-PCR)
- UniSTS:22730

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
part_of 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 more info	PubMed
located_in condensed chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
part_of euchromatin	IDA Inferred from Direct Assay more info	PubMed
part_of 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
part_of pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of 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)

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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

26201443..26213607

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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