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

Gene ID: 20997, updated on 12-May-2024

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
Orthologs
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Genomic context

Location:
17 A1; 17 4.92 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 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_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_41764 Neighboring gene predicted gene, 16702 Neighboring gene STARR-seq mESC enhancer starr_41765 Neighboring gene T (brachyury) promoter Neighboring gene ribosomal protein L15 pseudogene Neighboring gene brachyury 2 Neighboring gene predicted gene, 34036 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:8661752-8661935 Neighboring gene STARR-seq mESC enhancer starr_41767 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:8755802-8755955 Neighboring gene phosphodiesterase 10A Neighboring gene predicted gene 15425 Neighboring gene predicted gene 17087

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

General gene information

Markers

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
 
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
 
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 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
 
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
 
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
 
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
 
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
 
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
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 
part_of 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
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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

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)

  1. NM_009309.2NP_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:41219
    T-box_TBXT; DNA-binding domain of T-box transcription factor T and related T-box proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    8653255..8661328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)