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

Gene ID: 6926, updated on 16-Aug-2021

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
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
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Genomic context

See TBX3 in Genome Data Viewer
Location:
12q24.21
Exon count:
8
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (114670255..114684175, complement)
105.20201022 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 RN7SK pseudogene 216 Neighboring gene osteoclast stimulating factor 1 pseudogene 1 Neighboring gene TBX3 promoter region Neighboring gene VISTA enhancer hs483 Neighboring gene TBX3 antisense RNA 1

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
Genetic correction of PSA values using sequence variants associated with PSA levels.
GeneReviews: Not available
Genetic determinants of P wave duration and PR segment.
GeneReviews: Not available
Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
GeneReviews: Not available
Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
GeneReviews: Not available
Genome-wide association study of blood pressure and hypertension.
GeneReviews: Not available
Genome-wide association study of PR interval.
GeneReviews: Not available
Identification of a novel percent mammographic density locus at 12q24.
GeneReviews: Not available
Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis.
GeneReviews: Not available
Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
GeneReviews: Not available
Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians.
GeneReviews: Not available
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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
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 chamber development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 aging IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell fate specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular senescence IDA
Inferred from Direct Assay
more info
PubMed 
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 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 negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
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 IBA
Inferred from Biological aspect of Ancestor
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 transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 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
located_in chromatin ISA
Inferred from Sequence Alignment
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)

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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

  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
    UniProtKB/Swiss-Prot
    O15119
    UniProtKB/TrEMBL
    A0A024RBQ4
    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
    UniProtKB/TrEMBL
    A0A024RBL6
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

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