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Aliases for T Gene

Aliases for T Gene

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

External Ids for T Gene

Previous GeneCards Identifiers for T Gene

  • GC06M165924
  • GC06M166444
  • GC06M166481
  • GC06M166482
  • GC06M166541
  • GC06M164037

Summaries for T Gene

Entrez Gene Summary for T 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 T Gene

T (T Brachyury Transcription Factor) is a Protein Coding gene. Diseases associated with T include Sacral Agenesis With Vertebral Anomalies and Neural Tube Defects. Among its related pathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and Regulation of Wnt-mediated beta catenin signaling and target gene transcription. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II core promoter proximal region sequence-specific DNA binding. An important paralog of this gene is TBX19.

UniProtKB/Swiss-Prot for T 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 T Gene

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

Genomics for T Gene

Regulatory Elements for T Gene

Enhancers for T Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G166244 0.9 Ensembl ENCODE 11.6 -76.0 -75963 1.2 MXI1 MTA2 BHLHE40 CBX2 TBX21 POLR2A IKZF1 NBN RELB MLLT1 SFT2D1 T GNG5P1 ENSG00000280850
GH06G166004 1.7 FANTOM5 Ensembl ENCODE 2.8 +161.6 161628 4.8 PKNOX1 FOXA2 SIN3A FEZF1 ZNF2 FOS ZNF263 REST TBX21 KAT8 T PRR18 LINC00473 LOC105378117
GH06G166169 0.7 ENCODE 0.7 +0.4 413 0.2 CTCF ZSCAN5A ZNF777 SUZ12 ZNF76 RBBP5 ZBTB48 ZNF600 PRDM10 ZBTB20 T ENSG00000276643
GH06G166167 0.6 ENCODE 0.7 +1.1 1113 0.2 ZNF202 SUZ12 CHD1 CBX2 RBBP5 ZIC2 EZH2 ZBTB20 T ENSG00000276643
GH06G166168 0.6 ENCODE 0.7 +0.7 713 0.2 MAZ SP2 ZBTB8A PATZ1 ZBTB26 EZH2 TCF7L2 ZBTB20 T ENSG00000276643
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around T on UCSC Golden Path with GeneCards custom track

Genomic Location for T Gene

Chromosome:
6
Start:
166,157,656 bp from pter
End:
166,168,700 bp from pter
Size:
11,045 bases
Orientation:
Minus strand

Genomic View for T Gene

Genes around T on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for T Gene

Proteins for T Gene

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

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

    Protein attributes for T Gene

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

    Alternative splice isoforms for T Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for T Gene

Post-translational modifications for T Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for T Gene

No data available for DME Specific Peptides for T Gene

Domains & Families for T Gene

Gene Families for T Gene

Suggested Antigen Peptide Sequences for T Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

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

Function for T Gene

Molecular function for T Gene

GENATLAS Biochemistry:
murine T-box gene Tbx (T,brachyury) homolog,expressed in cells derived from the notochord,crucial for mesoderm formation,no evidence of association with neural tube defects (NTD) in Netherlands and U.K.
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.

Gene Ontology (GO) - Molecular Function for T Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region 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 T: view
genes like me logo Genes that share phenotypes with T: view

Human Phenotype Ontology for T Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Targeted motifs for T Gene
HOMER Transcription Factor Regulatory Elements motif T
  • Consensus sequence: ANTTMRCASBNNNGTGYKAAN Submotif: canonical Cell Type: Mesoendoderm GEO ID: GSE54963

Inhibitory RNA Products

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

Localization for T Gene

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

Gene Ontology (GO) - Cellular Components for T Gene

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

Pathways & Interactions for T Gene

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

Gene Ontology (GO) - Biological Process for T Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter 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 T: view

No data available for SIGNOR curated interactions for T Gene

Drugs & Compounds for T Gene

(1) Drugs for T Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Flunisolide Approved, Investigational Pharma 6
genes like me logo Genes that share compounds with T: view

Transcripts for T Gene

Unigene Clusters for T Gene

T, brachyury homolog (mouse):
Representative Sequences:

Inhibitory RNA Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b
SP1: - - - -
SP2:
SP3:
SP4: - - -
SP5:

Relevant External Links for T Gene

GeneLoc Exon Structure for
T
ECgene alternative splicing isoforms for
T

Expression for T Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Pituitary (x8.0).

Protein differential expression in normal tissues from HIPED for T Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (69.0).

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



Protein tissue co-expression partners for T Gene

NURSA nuclear receptor signaling pathways regulating expression of T Gene:

T

SOURCE GeneReport for Unigene cluster for T Gene:

Hs.389457

mRNA Expression by UniProt/SwissProt for T 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 T Gene

  • Lung(4.4)
  • Nervous system(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for T 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 T: view

Orthologs for T Gene

This gene was present in the common ancestor of animals.

Orthologs for T Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia T 34 35
  • 99.77 (n)
dog
(Canis familiaris)
Mammalia T 34 35
  • 89.43 (n)
cow
(Bos Taurus)
Mammalia T 34 35
  • 88.28 (n)
rat
(Rattus norvegicus)
Mammalia T 34
  • 86.64 (n)
mouse
(Mus musculus)
Mammalia T 34 16 35
  • 85.71 (n)
oppossum
(Monodelphis domestica)
Mammalia T 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia T 35
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves T 34 35
  • 81.05 (n)
lizard
(Anolis carolinensis)
Reptilia T 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia t 34
  • 72.45 (n)
Str.10814 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.514 34
zebrafish
(Danio rerio)
Actinopterygii ntlb 35
  • 73 (a)
OneToOne
LOC100004296 34
  • 71.41 (n)
ntl 34
fruit fly
(Drosophila melanogaster)
Insecta byn 36 35
  • 68 (a)
worm
(Caenorhabditis elegans)
Secernentea tbx-8 36
  • 42 (a)
tbx-9 36
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4353 35
  • 39 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14233 34
Species where no ortholog for T 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 T Gene

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

Paralogs for T Gene

Paralogs for T Gene

(14) SIMAP similar genes for T Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for T Gene

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

Variants for T Gene

Sequence variations from dbSNP and Humsavar for T Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs587777303 Pathogenic, Sacral agenesis with vertebral anomalies (SAVA) [MIM:615709] 166,165,800(+) CTATG(C/T)GGATT reference, missense
rs182159312 Uncertain significance 166,158,436(+) ATCCC(A/G)AGGAA reference, missense
rs3127334 other 166,160,758(+) TAAGG(A/G)CCTAT intron-variant
rs1000362183 -- 166,160,280(+) CATTG(C/T)TTACC intron-variant
rs1000457722 -- 166,157,220(+) TTTTG(C/T)TTTTG downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for T 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 T 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)

Relevant External Links for T Gene

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

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

Disorders for T Gene

MalaCards: The human disease database

(21) MalaCards diseases for T Gene - From: OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
sacral agenesis with vertebral anomalies
  • sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome
neural tube defects
  • spina bifida
chordoma
  • chordoma, susceptibility to
upper thoracic spina bifida aperta
upper thoracic spina bifida cystica
- elite association - COSMIC cancer census association via MalaCards
Search T 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.

Relevant External Links for T

Genetic Association Database (GAD)
T
Human Genome Epidemiology (HuGE) Navigator
T
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
T
genes like me logo Genes that share disorders with T: view

No data available for Genatlas for T Gene

Publications for T Gene

  1. The human homolog T of the mouse T(Brachyury) gene; gene structure, cDNA sequence, and assignment to chromosome 6q27. (PMID: 8963900) Edwards Y.H. … Sowden J. (Genome Res. 1996) 2 3 4 22 64
  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 A.V. … van Maarle M.C. (J. Med. Genet. 2014) 3 4 64
  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. (Clin. Cancer Res. 2012) 3 4 64
  4. T (brachyury) gene duplication confers major susceptibility to familial chordoma. (PMID: 19801981) Yang X.R. … Kelley M.J. (Nat. Genet. 2009) 3 4 64
  5. A missense T (Brachyury) mutation contributes to vertebral malformations. (PMID: 18466071) Ghebranious N. … Giampietro P.F. (J. Bone Miner. Res. 2008) 3 46 64

Products for T Gene

  • Addgene plasmids for T

Sources for T Gene

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