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 uln... See more...

Aliases for TBX3 Gene

Aliases for TBX3 Gene

  • T-Box Transcription Factor 3 2 3 5
  • T-Box Transcription Factor TBX3 3 4
  • T-Box Protein 3 3 4
  • TBX3-ISO 2 3
  • T-Box 3 2 3
  • XHL 2 3
  • Bladder Cancer Related Protein XHL 3
  • Ulnar Mammary Syndrome 2
  • TBX3 5
  • 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 Transcription Factor 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 Mesodermal Commitment Pathway. 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBX3 Gene

Genomics for TBX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TBX3 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBX3

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

Genomic Locations for TBX3 Gene

Genomic Locations for TBX3 Gene
chr12:114,670,255-114,684,175
(GRCh38/hg38)
Size:
13,921 bases
Orientation:
Minus strand
chr12:115,108,059-115,121,969
(GRCh37/hg19)
Size:
13,911 bases
Orientation:
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:
    O15119-TBX3_HUMAN
    Recommended name:
    T-box transcription factor TBX3
    Protein Accession:
    O15119
    Secondary Accessions:
    • Q8TB20
    • Q9UKF8

    Protein attributes for TBX3 Gene

    Size:
    743 amino acids
    Molecular mass:
    79389 Da
    Quaternary structure:
    • Interacts with PML (isoform PML-4).
    Miscellaneous:
    • [Isoform II]: Contains an interrupted T-box domain.
    • [Isoform III]: Contains an interrupted T-box domain.
    • [Isoform IV]: May be produced by joining exon 1 to exon 7 thereby eliminating the T-box.

    Three dimensional structures from OCA and Proteopedia for TBX3 Gene

    Alternative splice isoforms for TBX3 Gene

    UniProtKB/Swiss-Prot:

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

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

Protein Domains for TBX3 Gene

InterPro:
Blocks:
  • Transcription factor, T-box
ProtoNet:

Suggested Antigen Peptide Sequences for TBX3 Gene

GenScript: Design optimal peptide antigens:
  • T-box transcription factor TBX3 (TBX3_HUMAN)
genes like me logo Genes that share domains with TBX3: view

No data available for Graphical View of Domain Structure and 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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 11689487
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001085 RNA polymerase II transcription factor binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding IBA,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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX3

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

COMPARTMENTS
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
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA,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

SIGNOR curated interactions for TBX3 Gene

Inactivates:
Is activated by:

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:0001708 cell fate specification IBA 21873635
genes like me logo Genes that share ontologies with TBX3: view

Drugs & Compounds for TBX3 Gene

No Compound Related Data Available

Transcripts for TBX3 Gene

mRNA/cDNA for TBX3 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX3

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b
SP1:
SP2: -

Relevant External Links for TBX3 Gene

GeneLoc Exon Structure for
TBX3

Expression for TBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBX3

SOURCE GeneReport for Unigene cluster for TBX3 Gene:

Hs.744016

mRNA Expression by UniProt/SwissProt for TBX3 Gene:

O15119-TBX3_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for TBX3 Gene

  • Liver(4.6)
  • Nervous system(4.5)
  • Adrenal gland(4.5)
  • Kidney(4.5)
  • Heart(2.7)
  • Muscle(2.7)
  • Thyroid gland(2.6)
  • Blood(2.5)
  • Lung(2.5)
  • Skin(2.4)
  • Intestine(2.4)
  • Pancreas(2.3)
  • Bone marrow(2.1)
  • Lymph node(2.1)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • face
  • forehead
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • pituitary gland
  • skull
  • tooth
Thorax:
  • breast
  • clavicle
  • heart
  • lung
  • scapula
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • stomach
Pelvis:
  • anus
  • fallopian tube
  • ovary
  • penis
  • prostate
  • rectum
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • nail
  • radius
  • shoulder
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • 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
Chimpanzee
(Pan troglodytes)
Mammalia TBX3 30 31
  • 99.55 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TBX3 30 31
  • 91.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TBX3 30 31
  • 91.38 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tbx3 30
  • 87 (n)
Mouse
(Mus musculus)
Mammalia Tbx3 30 17 31
  • 86.51 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TBX3 31
  • 84 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TBX3 31
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TBX3 30 31
  • 77.34 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TBX3 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tbx3 30
  • 72.65 (n)
Str.14358 30
African clawed frog
(Xenopus laevis)
Amphibia Tbx3 30
Zebrafish
(Danio rerio)
Actinopterygii tbx3a 30 31
  • 71.35 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Doc3 32
  • 55 (a)
org-1 32
  • 55 (a)
Doc2 32
  • 54 (a)
Doc1 32
  • 50 (a)
bi 31 32
  • 27 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea tbx-2 31 32
  • 43 (a)
OneToMany
tbx-9 32
  • 39 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 32 (a)
OneToMany
Species where no ortholog for TBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

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

Paralogs for TBX3 Gene

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

  • TBX3_HUMAN
genes like me logo Genes that share paralogs with TBX3: view

Variants for TBX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBX3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
707158 Likely Benign: not provided 114,682,985(-) G/A SYNONYMOUS_VARIANT
711210 Likely Benign: Ulnar-mammary syndrome 114,672,213(-) G/A SYNONYMOUS_VARIANT
716572 Likely Benign: not provided 114,683,105(-) C/A SYNONYMOUS_VARIANT
718181 Likely Benign: not provided 114,683,129(-) C/T SYNONYMOUS_VARIANT
719198 Likely Benign: not provided 114,672,186(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for TBX3 Gene

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)
TBX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBX3

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

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

Disorder Aliases PubMed IDs
ulnar-mammary syndrome
  • ums
holt-oram syndrome
  • hos
breast liposarcoma
  • liposarcoma of the breast
mayer-rokitansky-kuster-hauser syndrome
  • mrkh syndrome
digeorge syndrome
  • cayler cardiofacial syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TBX3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TBX3_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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 23
  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 23
  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 23
  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

Products for TBX3 Gene

Sources for TBX3 Gene