T T, brachyury homolog (mouse) [Homo sapiens (human)] - Gene

Summary

Go to the top of the page Help

Official Symbol: Tprovided by HGNC
Official Full Name: T, brachyury homolog (mouse)provided by HGNC
Primary source: HGNC:11515
Locus tag: RP11-459F1.1
See related: Ensembl:ENSG00000164458; HPRD:03236; MIM:601397; Vega:OTTHUMG00000015991
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: TFT
Summary: 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]

Genomic context

Go to the top of the page Help

Location :: 6q27

Sequence :: Chromosome: 6; NC_000006.11 (166571144..166582157, complement)

See T in Epigenomics, MapViewer

Chromosome 6 - NC_000006.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Our findings present clinical evidence for an important role of Brachyury in EMT in oral SCC, and suggest that Brachyury and EMT patterns are useful prognostic markers.
Title: T-box transcription factor Brachyury expression is correlated with epithelial-mesenchymal transition and lymph node metastasis in oral squamous cell carcinoma.
Data show a combination of only five genes (-BCL6, T (BRACHYURY), c-MYC, MITF and BAF60C (SMARCD3) rapidly and efficiently convert postnatal chorion and decidual cells into chondrocytes.
Title: Placenta to cartilage: direct conversion of human placenta to chondrocytes with transformation by defined factors.
Functional significance of Brachyury in the developmental program of hematopoietic differentiation from embryonic stem cells.
Title: Activin A promotes hematopoietic fated mesoderm development through upregulation of brachyury in human embryonic stem cells.
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Title: An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Propose the use of brachyury as an additional helpful immunohistochemical marker to resolve the differential diagnosis of hemangioblastoma and histologic mimics.
Title: Expression of brachyury in hemangioblastoma: potential use in differential diagnosis.
Genom-wide association identifies the T gene as a novel asthma pharmacogenetic locus.
Title: Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus.
Brachyury and related Tbx proteins interact with the Mixl1 homeodomain protein and negatively regulate Mixl1 transcriptional activity
Title: Brachyury and related Tbx proteins interact with the Mixl1 homeodomain protein and negatively regulate Mixl1 transcriptional activity.
BRACHYURY may regulate NANOG in mesenchymal-like CRC cells to impose a 'plastic-state', allowing competence of cells to respond to signals prompting invasion or metastasis.
Title: BRACHYURY confers cancer stem cell characteristics on colorectal cancer cells.
Loss of p27(Kip)(1) causes an elongated/scatter cell-like phenotype involving up-regulation of Brachyury and Twist gene expression.
Title: The cell cycle inhibitor p27Kip¹ controls self-renewal and pluripotency of human embryonic stem cells by regulating the cell cycle, Brachyury and Twist.
BRA was necessary for and preceded CDX2 expression.
Title: BRACHYURY and CDX2 mediate BMP-induced differentiation of human and mouse pluripotent stem cells into embryonic and extraembryonic lineages.

Submit: New GeneRIF Correction See all (23)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.

Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus.

Pathways from BioSystems

Go to the top of the page Help

Cardiac Progenitor Differentiation, organism-specific biosystem (from WikiPathways)
Cardiac Progenitor Differentiation, organism-specific biosystemFactors involved in the induction of cardiac differentiation in vitro and in vivo. This model was based on the below two review articles.
Regulation of Wnt-mediated beta catenin signaling and target gene transcription, organism-specific biosystem (from Pathway Interaction Database)
Regulation of Wnt-mediated beta catenin signaling and target gene transcription, organism-specific biosystem
Regulation of Wnt-mediated beta catenin signaling and target gene transcription
glycine cleavage, organism-specific biosystem (from BIOCYC)
glycine cleavage, organism-specific biosystemIn eukaryotes the mitochondrial glycine cleavage complex (glycine decarboxylase complex) is a loosely-associated multienzyme complex that catalyzes the oxidative cleavage of glycine to carbon dioxid...

General gene information

Go to the top of the page Help

Homology

Homologs of the T gene: The T gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, and mosquito.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA polymerase II activating transcription factor binding	IPI Inferred from Physical Interaction more info
RNA polymerase II core promoter proximal region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
RNA polymerase II distal enhancer sequence-specific DNA binding	IDA Inferred from Direct Assay more info
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity	IDA Inferred from Direct Assay more info
RNA polymerase II transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription	ISS Inferred from Sequence or Structural Similarity more info
sequence-specific DNA binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
BMP signaling pathway	IEA Inferred from Electronic Annotation more info
SMAD protein signal transduction	IEA Inferred from Electronic Annotation more info
anterior/posterior axis specification, embryo	TAS Traceable Author Statement more info	PubMed
bone morphogenesis	IEA Inferred from Electronic Annotation more info
canonical Wnt receptor signaling pathway	IEA Inferred from Electronic Annotation more info
determination of heart left/right asymmetry	IEA Inferred from Electronic Annotation more info
embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
heart morphogenesis	IDA Inferred from Direct Assay more info
mesoderm development	TAS Traceable Author Statement more info	PubMed
mesoderm migration involved in gastrulation	IEA Inferred from Electronic Annotation more info
negative regulation of transcription from RNA polymerase II promoter	ISS Inferred from Sequence or Structural Similarity more info
neural plate morphogenesis	IEA Inferred from Electronic Annotation more info
neural tube closure	IEA Inferred from Electronic Annotation more info
notochord formation	IEA Inferred from Electronic Annotation more info
penetration of zona pellucida	IEA Inferred from Electronic Annotation more info
positive regulation of cell proliferation	IEA Inferred from Electronic Annotation more info
positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation	IDA Inferred from Direct Assay more info
post-anal tail morphogenesis	IEA Inferred from Electronic Annotation more info
primitive streak formation	NAS Non-traceable Author Statement more info	PubMed
signal transduction	NAS Non-traceable Author Statement more info	PubMed
signal transduction involved in regulation of gene expression	IEA Inferred from Electronic Annotation more info
somitogenesis	IEA Inferred from Electronic Annotation more info
vasculogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytoplasm	IEA Inferred from Electronic Annotation more info
nuclear chromatin	IDA Inferred from Direct Assay more info

General protein information

Go to the top of the page Help

Preferred Names: brachyury protein

Names: brachyury protein; protein T; T brachyury homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_012135.1 RefSeqGene

Range

4975..15988

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270484.1 → NP_001257413.1 brachyury protein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL627443, BC098425, BE785653

Consensus CDS

CCDS59045.1

UniProtKB/Swiss-Prot

O15178

Related

ENSP00000355836, OTTHUMP00000248709, ENST00000366871, OTTHUMT00000043038

Conserved Domains (1) summary

cd00182
Location:41 – 223
Blast Score: 772

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_003181.3 → NP_003172.1 brachyury protein isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AJ001699, AL627443, BC098425, BE785653, BU190437

Consensus CDS

CCDS5290.1

UniProtKB/Swiss-Prot

O15178

Related

ENSP00000296946, OTTHUMP00000017588, ENST00000296946, OTTHUMT00000043037

Conserved Domains (1) summary

cd00182
Location:41 – 223
Blast Score: 769

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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000006.11 Reference GRCh37.p10 Primary Assembly

Range

166571144..166582157, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000138.1 Alternate HuRef

Range

164037863..164048876, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018917.1 Alternate CHM1_1.0

Range

166581205..166592218, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01015077.1 (20867..31880)	None
genomic	AL627443.6 (99897..110910)	None
genomic	AMYH01016846.1 (126603..137616)	None
genomic	CH471051.2	EAW47538.1
		EAW47539.1
genomic	HI638829.1	CBX55887.1
mRNA	AJ001699.1	CAA04938.1
mRNA	BC039877.1	None
mRNA	BC098425.1	AAH98425.1
mRNA	BE785653.1	None
mRNA	BG436736.1	None
mRNA	BU190437.1	None