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

Gene ID: 27324, updated on 17-Sep-2022

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
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Genomic context

See TOX3 in Genome Data Viewer
Location:
16q12.1
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (52436416..52547802, complement)
110 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_000016.10Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs161 Neighboring gene uncharacterized LOC105371262 Neighboring gene VISTA enhancer hs1300 Neighboring gene cancer susceptibility 16 Neighboring gene uncharacterized LOC105371265 Neighboring gene long intergenic non-protein coding RNA 3064

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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
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
PubMed 

General protein information

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)

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.

Genomic

  1. NG_012623.1 RefSeqGene

    Range
    5660..116386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080430.4NP_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
    B5MCW4, O15405
    Related
    ENSP00000219746.9, ENST00000219746.14
    Conserved Domains (1) summary
    cd00084
    Location:255320
    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 ...
  2. NM_001146188.2NP_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:250315
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    52436416..52547802 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255892.4XP_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:254319
    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 ...
  2. XM_047433909.1XP_047289865.1  TOX high mobility group box family member 3 isoform X2

  3. XM_011523002.3XP_011521304.1  TOX high mobility group box family member 3 isoform X3

    Conserved Domains (1) summary
    cd00084
    Location:232297
    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

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    58234308..58345684 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)