Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TBX3 Gene

Aliases for TBX3 Gene

  • T-Box 3 2 3 5
  • T-Box Protein 3 3 4
  • Bladder Cancer Related Protein XHL 3
  • T-Box Transcription Factor TBX3 3
  • Ulnar Mammary Syndrome 2
  • TBX3-ISO 3
  • XHL 3
  • UMS 3

External Ids for TBX3 Gene

Previous HGNC Symbols for TBX3 Gene

  • UMS

Previous GeneCards Identifiers for TBX3 Gene

  • GC12M114019
  • GC12M114628
  • GC12M114890
  • GC12M113520
  • GC12M113570
  • GC12M115108
  • GC12M112116

Summaries for TBX3 Gene

Entrez Gene Summary for TBX3 Gene

  • 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]

GeneCards Summary for TBX3 Gene

TBX3 (T-Box 3) is a Protein Coding gene. Diseases associated with TBX3 include Ulnar-Mammary Syndrome and Holt-Oram Syndrome. Among its related pathways are Preimplantation Embryo and Signaling pathways regulating pluripotency of stem cells. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is TBX2.

UniProtKB/Swiss-Prot for TBX3 Gene

  • Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation. Acts as a negative regulator of PML function in cellular senescence.

Gene Wiki entry for TBX3 Gene

Additional gene information for TBX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBX3 Gene

Genomics for TBX3 Gene

GeneHancer (GH) Regulatory Elements for TBX3 Gene

Promoters and enhancers for TBX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J114663 Promoter/Enhancer 3.1 VISTA EPDnew FANTOM5 Ensembl ENCODE dbSUPER 658.3 +7.4 7400 25.6 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 TBX3 RBM19 LOC105370000 GC12M114672 GC12P114687 PIR34512 GC12P114686 GC12P114684
GH12J114655 Enhancer 1.4 Ensembl ENCODE dbSUPER 11.7 +26.7 26731 4.7 PKNOX1 FOXA2 MLX ARNT ARID4B FEZF1 ZNF2 YY1 FOS SP5 GC12M114659 ENSG00000199220 RBM19 TBX3 GC12M114639
GH12J114690 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 8.7 -7.7 -7674 3.6 CTCF GATA3 L3MBTL2 SUZ12 ZNF133 BACH1 ZNF398 RAD21 EZH2 TBX3 LOC105370000 GC12P114686
GH12J114744 Enhancer 0.9 Ensembl ENCODE dbSUPER 10.8 -62.0 -62002 4.1 ZNF121 IKZF1 ZSCAN4 ZNF239 ZMYM3 PRDM10 KDM1A TBX3 GC12P114750 ENSG00000252459 LOC105370000
GH12J114625 Enhancer 0.7 ENCODE 10 +58.5 58526 0.7 CTCF IRF2 ARID4B THRB RBPJ RAD21 RARA ZFHX2 ZNF614 EGR1 TBX3 ENSG00000258254 GC12M114639
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBX3 gene promoter:
  • Nkx2-5
  • FOXF2
  • FAC1
  • Max1
  • HNF-4alpha1
  • HNF-4alpha2

Genomic Locations for TBX3 Gene

Genomic Locations for TBX3 Gene
13,911 bases
Minus strand
13,911 bases
Minus strand

Genomic View for TBX3 Gene

Genes around TBX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBX3 Gene

Proteins for TBX3 Gene

  • Protein details for TBX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    T-box transcription factor TBX3
    Protein Accession:
    Secondary Accessions:
    • Q8TB20
    • Q9UKF8

    Protein attributes for TBX3 Gene

    743 amino acids
    Molecular mass:
    79389 Da
    Quaternary structure:
    • Interacts with PML (isoform PML-4).

    Three dimensional structures from OCA and Proteopedia for TBX3 Gene

    Alternative splice isoforms for TBX3 Gene


neXtProt entry for TBX3 Gene

Post-translational modifications for TBX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TBX3 Gene

Domains & Families for TBX3 Gene

Gene Families for TBX3 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TBX3 Gene

Suggested Antigen Peptide Sequences for TBX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TBX3: view

No data available for UniProtKB/Swiss-Prot for TBX3 Gene

Function for TBX3 Gene

Molecular function for TBX3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation. Acts as a negative regulator of PML function in cellular senescence.
GENATLAS Biochemistry:
murine T-box gene Tbx3 (T,brachyury)homolog,putative transcription factor,pairing with TBX5,homolog to Drosophila optomotor-blind gene (omb),involved in optic lobe and wing development,involved in developmental regulation,expressed in anterior and posterior mouse limb buds,widely expressed in adults

Phenotypes From GWAS Catalog for TBX3 Gene

Gene Ontology (GO) - Molecular Function for TBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 11689487
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 11689487
GO:0001085 RNA polymerase II transcription factor binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding ISS --
genes like me logo Genes that share ontologies with TBX3: view
genes like me logo Genes that share phenotypes with TBX3: view

Human Phenotype Ontology for TBX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TBX3 Gene

MGI Knock Outs for TBX3:

Animal Model Products

miRNA for TBX3 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TBX3 Gene

Localization for TBX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBX3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBX3 gene
Compartment Confidence
nucleus 5
cytosol 3
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 11689487
genes like me logo Genes that share ontologies with TBX3: view

Pathways & Interactions for TBX3 Gene

genes like me logo Genes that share pathways with TBX3: view

Pathways by source for TBX3 Gene

Gene Ontology (GO) - Biological Process for TBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 11689487
GO:0001501 skeletal system development IMP 9207801
GO:0001568 blood vessel development IEA --
GO:0001701 in utero embryonic development IEA --
GO:0001947 heart looping IEA --
genes like me logo Genes that share ontologies with TBX3: view

No data available for SIGNOR curated interactions for TBX3 Gene

Drugs & Compounds for TBX3 Gene

No Compound Related Data Available

Transcripts for TBX3 Gene

mRNA/cDNA for TBX3 Gene

Unigene Clusters for TBX3 Gene

T-box 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBX3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP2: -

Relevant External Links for TBX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TBX3 Gene

This gene is overexpressed in Adrenal Gland (x9.8) and Prostate (x4.9).

Protein differential expression in normal tissues from HIPED for TBX3 Gene

This gene is overexpressed in Adrenal (27.1), Liver (20.7), and Placenta (18.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TBX3 Gene

Protein tissue co-expression partners for TBX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of TBX3 Gene:


SOURCE GeneReport for Unigene cluster for TBX3 Gene:


mRNA Expression by UniProt/SwissProt for TBX3 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for TBX3 Gene

  • Adrenal gland(4.4)
  • Liver(4.4)
  • Nervous system(4.4)
  • Kidney(4.3)
  • Heart(2.2)
  • Muscle(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBX3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • ear
  • face
  • forehead
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • pituitary gland
  • skull
  • tooth
  • breast
  • clavicle
  • heart
  • lung
  • scapula
  • abdominal wall
  • intestine
  • large intestine
  • stomach
  • anus
  • fallopian tube
  • ovary
  • penis
  • prostate
  • rectum
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • nail
  • radius
  • shoulder
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • hair
  • skin
  • sweat gland
genes like me logo Genes that share expression patterns with TBX3: view

Orthologs for TBX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TBX3 34 33
  • 99.55 (n)
(Bos Taurus)
Mammalia TBX3 34 33
  • 91.53 (n)
(Canis familiaris)
Mammalia TBX3 34 33
  • 91.38 (n)
(Rattus norvegicus)
Mammalia Tbx3 33
  • 87 (n)
(Mus musculus)
Mammalia Tbx3 16 34 33
  • 86.51 (n)
(Monodelphis domestica)
Mammalia TBX3 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia TBX3 34
  • 80 (a)
(Gallus gallus)
Aves TBX3 34 33
  • 77.34 (n)
(Anolis carolinensis)
Reptilia TBX3 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia tbx3 33
  • 72.65 (n)
Str.14358 33
African clawed frog
(Xenopus laevis)
Amphibia Tbx3 33
(Danio rerio)
Actinopterygii tbx3a 34 33
  • 71.35 (n)
fruit fly
(Drosophila melanogaster)
Insecta Doc3 35
  • 55 (a)
org-1 35
  • 55 (a)
Doc2 35
  • 54 (a)
Doc1 35
  • 50 (a)
bi 34 35
  • 27 (a)
(Caenorhabditis elegans)
Secernentea tbx-2 34 35
  • 43 (a)
tbx-9 35
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
Species where no ortholog for TBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TBX3 Gene

Gene Tree for TBX3 (if available)
Gene Tree for TBX3 (if available)
Evolutionary constrained regions (ECRs) for TBX3: view image

Paralogs for TBX3 Gene

Paralogs for TBX3 Gene

(2) SIMAP similar genes for TBX3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with TBX3: view

Variants for TBX3 Gene

Sequence variations from dbSNP and Humsavar for TBX3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1005098765 uncertain-significance, Ulnar-mammary syndrome 114,683,271(-) T/C 5_prime_UTR_variant
rs1011316812 uncertain-significance, Ulnar-mammary syndrome 114,671,826(-) G/C 3_prime_UTR_variant
rs104894376 pathogenic, Ulnar-mammary syndrome 114,677,644(-) T/A coding_sequence_variant, stop_gained
rs1050363151 uncertain-significance, Ulnar-mammary syndrome 114,683,578(-) A/T 5_prime_UTR_variant
rs1060505020 pathogenic, Ulnar-mammary syndrome 114,674,452(-) G/A coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for TBX3 Gene

Variant ID Type Subtype PubMed ID
nsv1136156 CNV deletion 24896259

Variation tolerance for TBX3 Gene

Residual Variation Intolerance Score: 23.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.30; 53.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBX3 Gene

Disorders for TBX3 Gene

MalaCards: The human disease database

(9) MalaCards diseases for TBX3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ulnar-mammary syndrome
  • ums
holt-oram syndrome
  • hos
murcs association
  • mullerian duct aplasia, unilateral renal agenesis, and cervicothoracic somite anomalies
  • achp
sinoatrial node disease
  • sa node
- elite association - COSMIC cancer census association via MalaCards
Search TBX3 in MalaCards View complete list of genes associated with diseases


  • Ulnar-mammary syndrome (UMS) [MIM:181450]: Characterized by ulnar ray defects, obesity, hypogenitalism, delayed puberty, hypoplasia of nipples and apocrine glands. {ECO:0000269 PubMed:10330342}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBX3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TBX3: view

No data available for Genatlas for TBX3 Gene

Publications for TBX3 Gene

  1. Structure of the DNA-bound T-box domain of human TBX3, a transcription factor responsible for ulnar-mammary syndrome. (PMID: 12005433) Coll M … Müller CW (Structure (London, England : 1993) 2002) 3 4 22 58
  2. Transcription repression by Xenopus ET and its human ortholog TBX3, a gene involved in ulnar-mammary syndrome. (PMID: 10468588) He Ml … Rao Y (Proceedings of the National Academy of Sciences of the United States of America 1999) 3 4 22 58
  3. The spectrum of mutations in TBX3: Genotype/Phenotype relationship in ulnar-mammary syndrome. (PMID: 10330342) Bamshad M … Jorde LB (American journal of human genetics 1999) 3 4 22 58
  4. Mutations in human TBX3 alter limb, apocrine and genital development in ulnar-mammary syndrome. (PMID: 9207801) Bamshad M … Jorde LB (Nature genetics 1997) 3 4 22 58
  5. Physical and functional interaction between PML and TBX2 in the establishment of cellular senescence. (PMID: 22002537) Martin N … Bischof O (The EMBO journal 2012) 3 4 58

Products for TBX3 Gene

Sources for TBX3 Gene

Loading form....