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Aliases for TBXT Gene

Aliases for TBXT Gene

  • T-Box Transcription Factor T 2 3
  • T Brachyury Transcription Factor 2 3 5
  • Protein T 3 4
  • T 3 5
  • T, Brachyury Homolog (Mouse) 2
  • T, Brachyury Homolog 3
  • Brachyury Protein 3
  • SAVA 3
  • TFT 3

External Ids for TBXT Gene

Previous HGNC Symbols for TBXT Gene

  • T

Summaries for TBXT Gene

Entrez Gene Summary for TBXT Gene

  • The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for TBXT Gene

TBXT (T-Box Transcription Factor T) is a Protein Coding gene. Diseases associated with TBXT include Sacral Agenesis With Vertebral Anomalies and Neural Tube Defects. Among its related pathways are Cardiac Progenitor Differentiation and Regulation of Wnt-mediated beta catenin signaling and target gene transcription. An important paralog of this gene is TBX19.

UniProtKB/Swiss-Prot for TBXT Gene

  • Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation. Binds to a palindromic site (called T site) and activates gene transcription when bound to such a site.

Gene Wiki entry for TBXT Gene

Additional gene information for TBXT Gene

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

Genomics for TBXT Gene

GeneHancer (GH) Regulatory Elements for TBXT Gene

Promoters and enhancers for TBXT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I166170 Promoter 0.9 EPDnew 550.8 +0.0 25 0.1 ZNF777 ZEB2 ZNF335 ZNF341 ZNF600 NFE2 PRDM4 ZBTB26 EZH2 NFE2L2 TBXT ENSG00000276643
GH06I166169 Enhancer 0.7 ENCODE 550.8 +0.4 412 0.2 CTCF ZSCAN5A ZNF777 ZNF449 ZNF76 ZNF335 ZBTB48 PRDM10 ZNF600 ZBTB20 TBXT ENSG00000276643
GH06I166168 Enhancer 0.6 ENCODE 550.8 +0.7 712 0.2 MAZ ZNF189 SP2 EBF1 ZBTB8A ZNF335 PATZ1 ZBTB26 TCF7L2 EZH2 TBXT ENSG00000276643
GH06I166167 Enhancer 0.5 ENCODE 550.8 +1.1 1112 0.2 ZNF202 ZIC2 ZBTB20 EZH2 TBXT ENSG00000276643
GH06I166244 Enhancer 0.7 Ensembl ENCODE 11.6 -76.0 -75963 1.2 POLR2A IKZF1 NBN ATF7 MLLT1 RUNX3 SFT2D1 TBXT GNG5P1 LOC101929297 ENSG00000280850
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBXT on UCSC Golden Path with GeneCards custom track

Genomic Locations for TBXT Gene

Genomic Locations for TBXT Gene
chr6:166,157,656-166,168,700
(GRCh38/hg38)
Size:
11,045 bases
Orientation:
Minus strand
chr6:166,571,086-166,582,188
(GRCh37/hg19)

Genomic View for TBXT Gene

Genes around TBXT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for TBXT Gene

Proteins for TBXT Gene

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

    Protein Symbol:
    O15178-BRAC_HUMAN
    Recommended name:
    Brachyury protein
    Protein Accession:
    O15178
    Secondary Accessions:
    • E7ERD6
    • Q4KMP4

    Protein attributes for TBXT Gene

    Size:
    435 amino acids
    Molecular mass:
    47443 Da
    Quaternary structure:
    • Monomer.

    Alternative splice isoforms for TBXT Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBXT Gene

Post-translational modifications for TBXT Gene

No Post-translational modifications

Other Protein References for TBXT Gene

No data available for DME Specific Peptides for TBXT Gene

Domains & Families for TBXT Gene

Gene Families for TBXT Gene

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

Suggested Antigen Peptide Sequences for TBXT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

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

Function for TBXT Gene

Molecular function for TBXT Gene

UniProtKB/Swiss-Prot Function:
Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation. Binds to a palindromic site (called T site) and activates gene transcription when bound to such a site.

Phenotypes From GWAS Catalog for TBXT Gene

Gene Ontology (GO) - Molecular Function for TBXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding ISS --
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IDA 21632880
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IEA --
GO:0001085 RNA polymerase II transcription factor binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding IPI 22164283
genes like me logo Genes that share ontologies with TBXT: view
genes like me logo Genes that share phenotypes with TBXT: view

Human Phenotype Ontology for TBXT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for TBXT Gene

miRTarBase miRNAs that target TBXT

Inhibitory RNA Products

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

Localization for TBXT Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBXT 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 TBXT gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TBXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IEA --
GO:0000790 nuclear chromatin IDA 21632880
GO:0005634 nucleus IDA,IEA 22611028
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with TBXT: view

Pathways & Interactions for TBXT Gene

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

Gene Ontology (GO) - Biological Process for TBXT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0001570 vasculogenesis IEA --
GO:0001756 somitogenesis IEA --
GO:0001839 neural plate morphogenesis IEA --
GO:0001843 neural tube closure IEA --
genes like me logo Genes that share ontologies with TBXT: view

No data available for SIGNOR curated interactions for TBXT Gene

Drugs & Compounds for TBXT Gene

No Compound Related Data Available

Transcripts for TBXT Gene

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for TBXT Gene

GeneLoc Exon Structure for
TBXT
ECgene alternative splicing isoforms for
TBXT

Expression for TBXT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of TBXT Gene:

TBXT

mRNA Expression by UniProt/SwissProt for TBXT Gene:

O15178-BRAC_HUMAN
Tissue specificity: Detected in testis, but not in other, normal tissues. Detected in lung tumors (at protein level).

Evidence on tissue expression from TISSUES for TBXT Gene

  • Lung(4.4)
  • Nervous system(2.2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeleton
Organs:
Head and neck:
  • brain
  • forehead
  • head
  • skull
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TBXT: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for TBXT Gene

Orthologs for TBXT Gene

This gene was present in the common ancestor of animals.

Orthologs for TBXT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia T 34 33
  • 99.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia T 34 33
  • 89.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia T 34 33
  • 88.28 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia T 33
  • 86.64 (n)
mouse
(Mus musculus)
Mammalia T 34 16 33
  • 85.71 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia T 34
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia T 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves T 34 33
  • 81.05 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia T 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia t 33
  • 72.45 (n)
Str.10814 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.514 33
zebrafish
(Danio rerio)
Actinopterygii ntlb 34
  • 73 (a)
OneToOne
LOC100004296 33
  • 71.41 (n)
ntl 33
fruit fly
(Drosophila melanogaster)
Insecta byn 34
  • 31 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4353 34
  • 39 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14233 33
Species where no ortholog for TBXT 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)
  • worm (Caenorhabditis elegans)

Evolution for TBXT Gene

ENSEMBL:
Gene Tree for TBXT (if available)
TreeFam:
Gene Tree for TBXT (if available)

Paralogs for TBXT Gene

Paralogs for TBXT Gene

Pseudogenes.org Pseudogenes for TBXT Gene

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

Variants for TBXT Gene

Sequence variations from dbSNP and Humsavar for TBXT Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs3127334 risk-factor, Neural tube defects, susceptibility to 166,160,758(-) G/A intron_variant
rs587777303 pathogenic, Sacral agenesis with vertebral anomalies, Sacral agenesis with vertebral anomalies (SAVA) [MIM:615709] 166,165,800(-) T/C coding_sequence_variant, missense_variant
rs117097130 likely-benign, not provided 166,160,858(-) G/A coding_sequence_variant, missense_variant
rs182159312 uncertain-significance, not specified 166,158,436(-) G/A coding_sequence_variant, missense_variant
rs35292451 uncertain-significance, not specified 166,158,524(-) C/A/T coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv2733168 CNV deletion 23290073
esv2733169 CNV deletion 23290073
esv2733170 CNV deletion 23290073
nsv1121661 CNV deletion 24896259
nsv1142648 CNV deletion 24896259

Variation tolerance for TBXT Gene

Residual Variation Intolerance Score: 37% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.91; 89.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBXT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBXT

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

Disorders for TBXT Gene

MalaCards: The human disease database

(17) MalaCards diseases for TBXT Gene - From: OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
sacral agenesis with vertebral anomalies
  • sava
neural tube defects
  • neural tube defects, susceptibility to
chordoma
  • chordoma, susceptibility to
upper thoracic spina bifida cystica
cervicothoracic spina bifida cystica
- elite association - COSMIC cancer census association via MalaCards
Search TBXT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

BRAC_HUMAN
  • Chordoma (CHDM) [MIM:215400]: Rare, clinically malignant tumors derived from notochordal remnants. They occur along the length of the spinal axis, predominantly in the sphenooccipital, vertebral and sacrococcygeal regions. They are characterized by slow growth, local destruction of bone, extension into adjacent soft tissues and rarely, distant metastatic spread. {ECO:0000269 PubMed:19801981}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to development of chordomas is due to a T gene duplication.
  • Neural tube defects (NTD) [MIM:182940]: Congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components. {ECO:0000269 PubMed:15449172}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Sacral agenesis with vertebral anomalies (SAVA) [MIM:615709]: A disorder characterized by abnormalities of the spine, including sacral agenesis, abnormal ossification of all vertebral bodies, and a persistent notochordal canal during development. {ECO:0000269 PubMed:24253444}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBXT

genes like me logo Genes that share disorders with TBXT: view

No data available for Genatlas for TBXT Gene

Publications for TBXT Gene

  1. The human homolog T of the mouse T(Brachyury) gene; gene structure, cDNA sequence, and assignment to chromosome 6q27. (PMID: 8963900) Edwards YH … Sowden J (Genome research 1996) 2 3 4 22 58
  2. Mutations in the T (brachyury) gene cause a novel syndrome consisting of sacral agenesis, abnormal ossification of the vertebral bodies and a persistent notochordal canal. (PMID: 24253444) Postma AV … van Maarle MC (Journal of medical genetics 2014) 3 4 58
  3. Brachyury, a driver of the epithelial-mesenchymal transition, is overexpressed in human lung tumors: an opportunity for novel interventions against lung cancer. (PMID: 22611028) Roselli M … Palena C (Clinical cancer research : an official journal of the American Association for Cancer Research 2012) 3 4 58
  4. T (brachyury) gene duplication confers major susceptibility to familial chordoma. (PMID: 19801981) Yang XR … Kelley MJ (Nature genetics 2009) 3 4 58
  5. The human T locus and spina bifida risk. (PMID: 15449172) Jensen LE … Mitchell LE (Human genetics 2004) 4 22 58

Products for TBXT Gene

Sources for TBXT Gene

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