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brachyury transcription factor protein [ Ciona intestinalis (vase tunicate) ]

Gene ID: 778911, updated on 21-Dec-2023

Summary

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Gene symbol
brachyury
Gene description
transcription factor protein
See related
Ensembl:ENSCING00000000810
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Ciona intestinalis
Lineage
Eukaryota; Metazoa; Chordata; Tunicata; Ascidiacea; Phlebobranchia; Cionidae; Ciona
Also known as
bra
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Genomic context

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See brachyury in Genome Data Viewer
Location:
chromosome: Un
Exon count:
7
Annotation release Status Assembly Chr Location
104 current KH (GCF_000224145.3) Unplaced Scaffold NW_004190723.1 (6264..8022)

NW_004190723.1Genomic Context describing neighboring genes Neighboring gene interferon regulatory factor like protein Neighboring gene uncharacterized LOC108950622

Genomic regions, transcripts, and products

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Genomic Sequence:
NW_004190723 Unplaced Scaffold Reference KH Primary Assembly

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The brachyury Gly177Asp SNP is not associated with a risk of skull base chordoma in the Chinese population. Wu Z, et al. Int J Mol Sci, 2013 Oct 25. PMID 24232574, Free PMC Article
  2. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord. Katikala L, et al. PLoS Biol, 2013 Oct. PMID 24204212, Free PMC Article
  3. Brachyury null mutant-induced defects in juvenile ascidian endodermal organs. Chiba S, et al. Development, 2009 Jan. PMID 19019990, Free PMC Article
  4. Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Corbo JC, et al. Development, 1997 Feb. PMID 9043074
  5. Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. Wu Y, et al. Elife, 2022 Jan 20. PMID 35049502, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network.
    Title: Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network.
  2. Tbx2/3 (Ci-Tbx2/3) requires Ci-Bra for its role in Ciona notochord development
    Title: Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development.
  3. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another
    Title: Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.
  4. Our data suggest that the brachyury Gly177Asp SNP is not involved in the risks of skull-base chordoma, at least in the Chinese population
    Title: The brachyury Gly177Asp SNP is not associated with a risk of skull base chordoma in the Chinese population.
  5. Ciona Brachyury (Ci-Bra) controls most of its targets directly, through non-palindromic binding sites that function either synergistically or individually to activate early- and middle-onset genes, respectively.
    Title: Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.
  6. This work presents evidence of a synergistic interaction between Brachyury and FoxA in the activation of an individual notochord cis-regulatory modules, and highlights the importance of transcription factor binding site arrangement for its function.
    Title: Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis.
  7. Serial deletions of the 581-bp notochord CRM revealed that this sequence is also able to direct expression in muscle cells through the same T-box sites that are utilized by Ci-Bra in the notochord
    Title: The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord.
  8. The isolation of a recessive ethylnitrosourea-induced short-tailed mutant in the ascidian Ciona intestinalis that is the product of a premature stop in the brachyury gene, is reported.
    Title: Brachyury null mutant-induced defects in juvenile ascidian endodermal organs.
Submit: New GeneRIF Correction

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell fate specification IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in mesoderm formation IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
transcription factor protein

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_001078478.2 → NP_001071946.1  transcription factor protein

    See identical proteins and their annotated locations for NP_001071946.1

    Status: VALIDATED

    Source sequence(s)
    EAAA01004773
    UniProtKB/TrEMBL
    A0A1W2VP27, F6RP59, Q4H3U3
    Related
    ENSCINP00000001477, ENSCINT00000001477
    Conserved Domains (1) summary
    cd00182
    Location:22 → 206
    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: Ciona intestinalis Annotation Release 104 details...Open this link in a new tab

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

Reference KH Primary Assembly

Genomic

  1. NW_004190723.1 Reference KH Primary Assembly

    Range
    6264..8022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases
Research Materials