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    TBX3 T-box transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 6926, updated on 1-Mar-2024

    Summary

    Official Symbol
    TBX3provided by HGNC
    Official Full Name
    T-box transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:11602
    See related
    Ensembl:ENSG00000135111 MIM:601621; AllianceGenome:HGNC:11602
    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
    UMS; XHL; TBX3-ISO
    Summary
    This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This protein is a transcriptional repressor and is thought to play a role in the anterior/posterior axis of the tetrapod forelimb. Mutations in this gene cause ulnar-mammary syndrome, affecting limb, apocrine gland, tooth, hair, and genital development. Alternative splicing of this gene results in three transcript variants encoding different isoforms; however, the full length nature of one variant has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in adrenal (RPKM 89.8), prostate (RPKM 51.1) and 11 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TBX3 in Genome Data Viewer
    Location:
    12q24.21
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (114670255..114684175, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (114647343..114661251, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (115108060..115121980, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene osteoclast stimulating factor 1 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:115056546-115056730 Neighboring gene uncharacterized LOC124903026 Neighboring gene NANOG hESC enhancer GRCh37_chr12:115079511-115080012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:115109316-115109876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:115109877-115110436 Neighboring gene NANOG hESC enhancer GRCh37_chr12:115113537-115114038 Neighboring gene TBX3 promoter region Neighboring gene VISTA enhancer hs483 Neighboring gene TBX3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115134740-115135593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115135594-115136448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115136449-115137301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115138140-115138949 Neighboring gene uncharacterized LOC105369999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115173261-115174104 Neighboring gene small nucleolar RNA SNORA27

    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

    Associated conditions

    Description Tests
    Ulnar-mammary syndrome
    MedGen: C1866994 OMIM: 181450 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-09-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-23)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genetic correction of PSA values using sequence variants associated with PSA levels.
    EBI GWAS Catalog
    Genetic determinants of P wave duration and PR segment.
    EBI GWAS Catalog
    Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
    EBI GWAS Catalog
    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
    EBI GWAS Catalog
    Genome-wide association study of blood pressure and hypertension.
    EBI GWAS Catalog
    Genome-wide association study of PR interval.
    EBI GWAS Catalog
    Identification of a novel percent mammographic density locus at 12q24.
    EBI GWAS Catalog
    Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis.
    EBI GWAS Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within animal organ morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in anterior/posterior axis specification, embryo IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in atrioventricular bundle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in atrioventricular canal development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in atrioventricular canal morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branching involved in mammary gland duct morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cardiac jelly development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cardiac muscle cell fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cellular senescence IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in embryonic digit morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endocardial cushion formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in female genitalia development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in follicle-stimulating hormone secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forelimb morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in heart looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hepatoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limbic system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in luteinizing hormone secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in male genitalia development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mammary gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mammary placode formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesoderm morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell proliferation involved in heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of myoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in outflow tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell cycle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein complex stability IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of protein stability IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in semicircular canal morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sinoatrial node cell development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in specification of animal organ position IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ureteric peristalsis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular septum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cilium IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    T-box transcription factor TBX3
    Names
    T-box 3
    T-box protein 3
    bladder cancer related protein XHL

    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_008315.1 RefSeqGene

      Range
      4990..18910
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005996.4NP_005987.3  T-box transcription factor TBX3 isoform 1

      See identical proteins and their annotated locations for NP_005987.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the shorter isoform (1) of this protein.
      Source sequence(s)
      AC026765, AF140240, AK054604, BC025258
      Consensus CDS
      CCDS9175.1
      Related
      ENSP00000257567.2, ENST00000349155.7
      Conserved Domains (2) summary
      pfam12598
      Location:303391
      TBX; T-box transcription factor
      cd00182
      Location:104287
      TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
    2. NM_016569.4NP_057653.3  T-box transcription factor TBX3 isoform 2

      See identical proteins and their annotated locations for NP_057653.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini and is longer compared to isoform 1.
      Source sequence(s)
      AC026765, AF140240, AK054604, BC025258
      Consensus CDS
      CCDS9176.1
      UniProtKB/Swiss-Prot
      O15119, Q8TB20, Q9UKF8
      Related
      ENSP00000257566.3, ENST00000257566.7
      Conserved Domains (2) summary
      pfam12598
      Location:323411
      TBX; T-box transcription factor
      cd00182
      Location:104307
      TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

    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

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      114670255..114684175 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      114647343..114661251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)