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Aliases for T Gene

Aliases for T Gene

  • T Brachyury Transcription Factor 2 3
  • Protein T 3 4
  • T, Brachyury Homolog (Mouse) 2
  • T, Brachyury Homolog 3
  • T Brachyury Homolog 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-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome and sacral agenesis with vertebral anomalies. Among its related pathways are Cardiac Progenitor Differentiation 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 TBX20.

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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for T Gene

Genomics for T Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for T Gene at MOPED

Post-translational modifications for T Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for T Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for T (Brachyury)

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

O15178

UniProtKB/Swiss-Prot:

BRAC_HUMAN :
  • Contains 1 T-box DNA-binding domain.
Domain:
  • Contains 1 T-box DNA-binding domain.
genes like me logo Genes that share domains with T: view

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

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
Jensen Localization Image for T Gene COMPARTMENTS Subcellular localization image for T gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for T Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin --
GO:0000790 nuclear chromatin IDA 21632880
GO:0005634 nucleus 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

PCR Array Products

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:

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 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



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).
genes like me logo Genes that share expression patterns with T: view

Protein tissue co-expression partners for T Gene

Primer Products

In Situ Assay Products

Orthologs for T Gene

This gene was present in the common ancestor of animals.

Orthologs for T Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia T 35
  • 88.28 (n)
  • 88.51 (a)
T 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia T 35
  • 89.43 (n)
  • 90.11 (a)
T 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia T 35
  • 85.71 (n)
  • 91.71 (a)
T 16
T 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia T 35
  • 99.77 (n)
  • 99.54 (a)
T 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia T 35
  • 86.64 (n)
  • 92.17 (a)
oppossum
(Monodelphis domestica)
Mammalia T 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia T 36
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves T 35
  • 81.05 (n)
  • 80.93 (a)
T 36
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia T 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10814 35
t 35
  • 72.45 (n)
  • 75 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.514 35
zebrafish
(Danio rerio)
Actinopterygii LOC100004296 35
  • 71.41 (n)
  • 75.18 (a)
ntl 35
ntlb 36
  • 73 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta byn 37
  • 68 (a)
byn 36
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tbx-8 37
  • 42 (a)
tbx-9 37
  • 41 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14233 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4353 36
  • 39 (a)
OneToMany
Species with no ortholog for T:
  • 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 MAF
rs920958 -- 166,166,976(-) CCCTC(G/T)GACGT intron-variant
rs920959 -- 166,166,897(-) CCTGG(G/T)CAGAG intron-variant
rs920960 -- 166,166,890(-) AGAGT(C/G)GGGGT intron-variant
rs920961 -- 166,166,769(-) GCGGA(C/T)AACCA reference, synonymous-codon
rs1056048 -- 166,166,700(-) CCCAG(C/T)TGCGT reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
nsv886933 CNV Loss 21882294
esv2733168 CNV Deletion 23290073
esv2733169 CNV Deletion 23290073
esv2733170 CNV Deletion 23290073

Variation tolerance for T Gene

Residual Variation Intolerance Score: 36.99% 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

HapMap Linkage Disequilibrium report
T
Human Gene Mutation Database (HGMD)
T

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

Disorders for T Gene

MalaCards: The human disease database

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

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 23 67
  2. Perforin and IL-2 upregulation define qualitative differences among highly functional virus-specific human CD8 T cells. (PMID: 20221423) Makedonas G. … Betts M.R. (PLoS Pathog. 2010) 23 67
  3. The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-gamma. (PMID: 20399120) Yagi R. … Zhu J. (Immunity 2010) 23 67
  4. Prognosis of hormone-dependent breast cancers: implications of the presence of dysfunctional transcriptional networks activated by insulin via the immune transcription factor T-bet. (PMID: 20068169) McCune K. … Nakshatri H. (Cancer Res. 2010) 23 67
  5. [Role of transcription factor T-bet and Eomes in IFN-gamma secretion of different human T cell subsets]. (PMID: 20056084) Wang H.T. … Li B.Q. (Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2010) 23 67

Products for T Gene

Sources for T Gene

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