TOX3 TOX high mobility group box family member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TOX3provided by HGNC
Official Full Name: TOX high mobility group box family member 3provided by HGNC
Primary source: HGNC:HGNC:11972
See related: Ensembl:ENSG00000103460 MIM:611416; AllianceGenome:HGNC:11972
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CAGF9; TNRC9
Summary: The protein encoded by this gene contains an HMG-box, indicating that it may be involved in bending and unwinding of DNA and alteration of chromatin structure. The C-terminus of the encoded protein is glutamine-rich due to CAG repeats in the coding sequence. A minor allele of this gene has been implicated in an elevated risk of breast cancer. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2009]
Expression: Biased expression in stomach (RPKM 5.0), colon (RPKM 3.6) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q12.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (52436416..52547802, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (58234308..58345684, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (52470328..52581714, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

TOX3 regulates the proliferation and apoptosis of colorectal cancer by downregulating RhoB via the activation of the MAPK pathway.
Title: TOX3 regulates the proliferation and apoptosis of colorectal cancer by downregulating RhoB via the activation of the MAPK pathway.
Genetic polymorphism of fibroblast growth factor receptor 2 and trinucleotide repeat-containing 9 influence the susceptibility to HCV-induced hepatocellular carcinoma.
Title: Genetic polymorphism of fibroblast growth factor receptor 2 and trinucleotide repeat-containing 9 influence the susceptibility to HCV-induced hepatocellular carcinoma.
Risk Association of TOX3 and MMP7 Gene Polymorphisms with Sporadic Breast Cancer in Mexican Women.
Title: Risk Association of TOX3 and MMP7 Gene Polymorphisms with Sporadic Breast Cancer in Mexican Women.
Association between CASC16 rs4784227 polymorphism and breast cancer susceptibility: A meta-analysis.
Title: Association between CASC16 rs4784227 polymorphism and breast cancer susceptibility: A meta-analysis.
TOX3 Promotes Ovarian Estrogen Synthesis: An RNA-Sequencing and Network Study.
Title: TOX3 Promotes Ovarian Estrogen Synthesis: An RNA-Sequencing and Network Study.
TOX3 gene variant could be associated with painful restless legs.
Title: TOX3 gene variant could be associated with painful restless legs.
TOX high mobility group box family member 3 (TOX3) is one such gene, in which SNPs have been found to be associated with breast cancer. Found nine SNPs that may affect the gene regulation.
Title: An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene.
the TOX3 rs3803662 C>T polymorphism may not be associated with recurrent miscarriage in the southern Chinese population.
Title: Association between the TOX3 rs3803662 C>T polymorphism and recurrent miscarriage in a southern Chinese population.
Study identified TOX3 as a novel cancer suppressor gene in clear cell renal cell carcinoma (ccRCC). Hypermethylation in the promoter region was associated with its functional loss and poor outcome in ccRCC patients. Downregulation of TOX3 could accelerate the EMT by decreasing transcriptional repression of SNAI1 and SNAI2. Its overexpression inhibited RCC cell growth, migration and invasion.
Title: TOX3 inhibits cancer cell migration and invasion via transcriptional regulation of SNAI1 and SNAI2 in clear cell renal cell carcinoma.
TOX3-rs3803662, may confer some degrees of risk of breast cancer in Iranian population.
Title: Significant association of TOX3/LOC643714 locus-rs3803662 and breast cancer risk in a cohort of Iranian population.

Submit: New GeneRIF Correction See all GeneRIFs (53)

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

EBI GWAS Catalog

Description
A combined analysis of genome-wide association studies in breast cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. EBI GWAS Catalog EBI GWAS CatalogPubMed
A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies identify four ER negative-specific breast cancer risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies a common variant in RAD51B associated with male breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies five new breast cancer susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel breast cancer susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of breast cancer in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. EBI GWAS Catalog EBI GWAS CatalogPubMed

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	Depletion of TOX high mobility group box family member 3 (TOX3) by siRNA enhances HIV-1 Tat activation of HIV-1 LTR, which is not the results of increased Tat expression and release of CDK9/CCNT1 from 7SK snRNP, and activation of NF-kappaB	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH118810 (e-PCR)
- UniSTS:138791

D16S470E (e-PCR)
- UniSTS:181356

SHGC-154410 (e-PCR)
- UniSTS:178085

SHGC-148286 (e-PCR)
- UniSTS:176300

D16S2712 (e-PCR)
- UniSTS:153282

D16S783 (e-PCR)
- UniSTS:42208

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphoprotein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: TOX high mobility group box family member 3

Names: CAG trinucleotide repeat-containing gene F9 protein; trinucleotide repeat-containing gene 9 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.

Genomic

NG_012623.1 RefSeqGene

Range

5660..116386

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001080430.4 → NP_001073899.2 TOX high mobility group box family member 3 isoform 1

See identical proteins and their annotated locations for NP_001073899.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC007490, AI733227, AK299202, BE501808

Consensus CDS

CCDS54009.1

UniProtKB/Swiss-Prot

B4DRD0, B5MCW4, O15405

Related

ENSP00000219746.9, ENST00000219746.14

Conserved Domains (1) summary

cd00084
Location:255 → 320

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
NM_001146188.2 → NP_001139660.1 TOX high mobility group box family member 3 isoform 2

See identical proteins and their annotated locations for NP_001139660.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC007490, AI733227, AK299202

Consensus CDS

CCDS54008.1

UniProtKB/Swiss-Prot

O15405

Related

ENSP00000385705.3, ENST00000407228.7

Conserved Domains (1) summary

cd00084
Location:250 → 315

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

52436416..52547802 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005255892.4 → XP_005255949.1 TOX high mobility group box family member 3 isoform X1

See identical proteins and their annotated locations for XP_005255949.1

Conserved Domains (1) summary

cd00084
Location:254 → 319

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...
XM_047433909.1 → XP_047289865.1 TOX high mobility group box family member 3 isoform X2
XM_011523002.3 → XP_011521304.1 TOX high mobility group box family member 3 isoform X3

Conserved Domains (1) summary

cd00084
Location:232 → 297

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

58234308..58345684 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054380038.1 → XP_054236013.1 TOX high mobility group box family member 3 isoform X1
XM_054380039.1 → XP_054236014.1 TOX high mobility group box family member 3 isoform X2
XM_054380040.1 → XP_054236015.1 TOX high mobility group box family member 3 isoform X3