T brachyury, T-box transcription factor T [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tprovided by MGI
Official Full Name: brachyury, T-box transcription factor Tprovided by MGI
Primary source: MGI:MGI:98472
See related: Ensembl:ENSMUSG00000062327 AllianceGenome:MGI:98472
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Lr; T1; Bra; Low; Tl2; Tl3; cou; Tbxt; me75; D17Mit170
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in negative regulation of DNA-binding transcription factor activity; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation. Acts upstream of or within several processes, including animal organ development; chordate embryonic development; and regulation of gene expression. Located in chromatin; cytoplasm; and nucleus. Is expressed in several structures, including egg cylinder; embryo mesenchyme; future spinal cord; heart; and mesoderm. Human ortholog(s) of this gene implicated in neural tube defect. Orthologous to human TBXT (T-box transcription factor T). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Low expression observed in reference dataset See more
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Genomic context

Location:: 17 A1; 17 4.92 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (8653255..8661328)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (8434423..8442496)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A 37 kb region upstream of brachyury comprising a notochord enhancer is essential for notochord and tail development.
Title: A 37 kb region upstream of brachyury comprising a notochord enhancer is essential for notochord and tail development.
Functionally distinct roles for T and Tbx6 during mouse development.
Title: Functionally distinct roles for T and Tbx6 during mouse development.
Aging aggravates intervertebral disc degeneration by regulating transcription factors toward chondrogenesis.
Title: Aging aggravates intervertebral disc degeneration by regulating transcription factors toward chondrogenesis.
Repressive functions of Eomes and Brachyury.
Title: Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state.
The data indicate that brachyury mediates acetylated H3K27 recruitment through a physical interaction with p300 during the mouse mesoderm development.
Title: BRACHYURY directs histone acetylation to target loci during mesoderm development.
we developed in vitro fertilization (IVF) methods for the BTBR mouse. We found low rates of fertilization and implantation in this strain, and identified the BTBR oocyte as the primary culprit of low success with BTBR IVF.
Title: Successful in vitro fertilization and generation of transgenics in Black and Tan Brachyury (BTBR) mice.
including Wnt and Fgf pathway components active in the axial progenitor niche. Our data demonstrate that integration of the Cdx2 and T Brachyury transcriptional networks controls differential axial growth during vertebrate trunk elongation
Title: Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche.
T, cooperatively with WNT signaling, controls the progenitor state and the switch toward the mesodermal fate. Sox2 acts antagonistically and promotes neural development.
Title: Antagonistic Activities of Sox2 and Brachyury Control the Fate Choice of Neuro-Mesodermal Progenitors.
T is required for correct axial positioning of the vessel of confluence.
Title: Brachyury drives formation of a distinct vascular branchpoint critical for fetal-placental arterial union in the mouse gastrula.
Wnt3a, which regulate cell growth, were also expressed strongly during E12.5-E13.5. On the other hand, cleft formation and branching morphogenesis was suppressed by knockdown of Brachyury gene, suggesting that Brachyury plays a central role in regulating cell growth and cleft formation in early-stage embryonic mouse salivary gland development
Title: Involvement of the T-box transcription factor Brachyury in early-stage embryonic mouse salivary gland.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (15) 1 citation
Transgenic (1) 1 citation
Chemically and radiation induced (6) 1 citation
Targeted (3) 1 citation
Radiation induced (11) 1 citation
Chemically induced (ENU) (6) 1 citation
Endonuclease-mediated (4) 1 citation

General gene information

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Markers

NoName (e-PCR)
- UniSTS:548391

T (e-PCR), detects polymorphism
- UniSTS:255285

T (e-PCR), detects polymorphism
- UniSTS:531514

NoName (e-PCR)
- UniSTS:492891

T (e-PCR), detects polymorphism
- UniSTS:144533

T (e-PCR), detects polymorphism
- UniSTS:144534

T (e-PCR), detects polymorphism
- UniSTS:144535

T (e-PCR), detects polymorphism
- UniSTS:144536

T (e-PCR), detects polymorphism
- UniSTS:463524

T (e-PCR), detects polymorphism
- UniSTS:525999

T (e-PCR), detects polymorphism
- UniSTS:526027

T (e-PCR), detects polymorphism
- UniSTS:532690

T (e-PCR), detects polymorphism
- UniSTS:265430

X51683 (e-PCR)
- UniSTS:180954

T (e-PCR), detects polymorphism
- UniSTS:536553

Homology

Homologs of the T gene: The T gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within SMAD protein signal transduction	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within anatomical structure morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cardiac muscle cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in cardiac muscle cell myoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle cell myoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of heart left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mesoderm formation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within mesoderm migration involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neural plate morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within notochord development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within notochord formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within penetration of zona pellucida	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-anal tail morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within post-anal tail morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	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	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within reproductive process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within signal transduction involved in regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in somitogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IMP Inferred from Mutant Phenotype more info	PubMed
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: T-box transcription factor T

Names: brachyury; brachyury protein; brachyury-like 2; brachyury-like 3; low ratio; protein T

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.

mRNA and Protein(s)

NM_009309.2 → NP_033335.1 T-box transcription factor T

See identical proteins and their annotated locations for NP_033335.1

Status: VALIDATED

Source sequence(s)

AC154579

Consensus CDS

CCDS28383.1

UniProtKB/Swiss-Prot

P20293

UniProtKB/TrEMBL

Q78ZW9

Related

ENSMUSP00000074236.3, ENSMUST00000074667.9

Conserved Domains (1) summary

cd20202
Location:41 → 219

T-box_TBXT; DNA-binding domain of T-box transcription factor T and related T-box proteins