U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 27324, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TOX3 in Genome Data Viewer
    Location:
    16q12.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (52436416..52547802, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (58234308..58345684, complement)
    RS_2024_09 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 uncharacterized LOC107984901 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:52331523-52332722 Neighboring gene VISTA enhancer hs161 Neighboring gene uncharacterized LOC105371262 Neighboring gene VISTA enhancer hs1300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:52472926-52473426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:52473427-52473927 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:52504393-52505003 Neighboring gene NANOG hESC enhancer GRCh37_chr16:52567073-52567576 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:52611160-52612359 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

    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 
    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

    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
      B4DRD0, 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: GCF_000001405.40-RS_2024_08

    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)

    mRNA and Protein(s)

    1. XM_054380038.1XP_054236013.1  TOX high mobility group box family member 3 isoform X1

    2. XM_054380039.1XP_054236014.1  TOX high mobility group box family member 3 isoform X2

    3. XM_054380040.1XP_054236015.1  TOX high mobility group box family member 3 isoform X3