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

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Suppressed Cellular Senescence Mediated by T-box3 in Aged Gastric Epithelial Cells may Contribute to Aging-related Carcinogenesis.
Title: Suppressed Cellular Senescence Mediated by T-box3 in Aged Gastric Epithelial Cells may Contribute to Aging-related Carcinogenesis.
Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments.
Title: Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments.
TBX3 Promotes Cervical Cancer Proliferation and Migration via HPV E6 and E7 Signaling.
Title: TBX3 Promotes Cervical Cancer Proliferation and Migration via HPV E6 and E7 Signaling.
TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration.
Title: TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration.
TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration.
Title: TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration.
TBX3 stimulates proliferation and stem cell self-renewal in bladder carcinoma.
Title: TBX3 stimulates proliferation and stem cell self-renewal in bladder carcinoma.
Hierarchical deployment of Tbx3 dictates the identity of hypothalamic KNDy neurons to control puberty onset.
Title: Hierarchical deployment of Tbx3 dictates the identity of hypothalamic KNDy neurons to control puberty onset.
TBX3 activating PVT1 accelerates proliferation, migration, and invasion by modulating the miR-30a/LOX axis in anaplastic thyroid carcinoma.
Title: TBX3 activating PVT1 accelerates proliferation, migration, and invasion by modulating the miR-30a/LOX axis in anaplastic thyroid carcinoma.
Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells.
Title: Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells.
A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells.
Title: A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells.

Submit: New GeneRIF Correction See all GeneRIFs (82)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S2090 (e-PCR)
- UniSTS:37516

RH102845 (e-PCR)
- UniSTS:97179

RH69906 (e-PCR)
- UniSTS:60321

TBX3_2272 (e-PCR)
- UniSTS:281044

STS-T94297 (e-PCR)
- UniSTS:81650

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

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

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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

NG_008315.1 RefSeqGene

Range

4990..18910

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_005996.4 → NP_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:303 → 391

TBX; T-box transcription factor

cd00182
Location:104 → 287

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 ...
NM_016569.4 → NP_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:323 → 411

TBX; T-box transcription factor

cd00182
Location:104 → 307

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 ...