tbxta T-box transcription factor Ta [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: tbxtaprovided by ZNC
Official Full Name: T-box transcription factor Taprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-437
See related: Ensembl:ENSDARG00000101576 AllianceGenome:ZFIN:ZDB-GENE-980526-437
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ta; ntl; zft; ZF-T; ntla; cb240; ZF-NTL; Zf-T-A; id:ibd5074; wu:fc80a01
Summary: Enables transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including Kupffer's vesicle development; animal organ development; and post-anal tail morphogenesis. Located in chromatin and nucleus. Is expressed in several structures, including blastoderm; germ ring; mesoderm; presumptive structure; and tail bud. 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]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: 19

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (14187540..14191592, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	19	NC_007130.6 (14325345..14329397, complement)

Chromosome 19 - NC_007130.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ntla and Spt do not differentially regulate medial floor plate (MPF) induction along the anterior-posterior axis; rather, the T-box genes act redundantly within margin derived cells to promote the posterior extension of MFP progenitors.
Title: Optochemical dissection of T-box gene-dependent medial floor plate development.
observed normal cardiac convergence in spt(-/-) and ntl(-/-) embryos implying that these novel roles of spt and ntl in PGP migration cannot be explained simply by generalised effects on midline convergence
Title: Sequential effects of spadetail, one-eyed pinhead and no tail on midline convergence of nephric primordia during zebrafish embryogenesis.
As a proof of principle, it has dynamically profiled No tail a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering discrete sets of transcripts.
Title: Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development.
embryonic mesodermal progenitors uniquely establish their own niche--with Brachyury being essential for creating a domain of high Wnt and low RA signaling--rather than having a niche created by separate support cells.
Title: Brachyury establishes the embryonic mesodermal progenitor niche.
Data demonstrate that the nodal-independent regulation of ntl is essential for tail formation in zebrafish.
Title: no tail integrates two modes of mesoderm induction.
Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies.
Title: A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
no tail gene (ntl), a key gene participating in the formation of normal tail, was used as a target for ribonuclease (RNase) P-mediated gene disruption in zebrafish in vivo.
Title: Inhibition of no tail (ntl) gene expression in zebrafish by external guide sequence (EGS) technique.
the endoplasmic reticulum Ca(2+) pump has a role in expression of no tail (ntl) and left-right dynein related (lrdr) in the dorsal forerunner cells during gastrulation
Title: Suppression of the endoplasmic reticulum calcium pump during zebrafish gastrulation affects left-right asymmetry of the heart and brain.
Regulation of canonical Wnt signaling by ntl is essential for posterior mesoderm formation.
Title: Regulation of canonical Wnt signaling by Brachyury is essential for posterior mesoderm formation.
Ntl is necessary for KV lumen formation.
Title: Two T-box genes play independent and cooperative roles to regulate morphogenesis of ciliated Kupffer's vesicle in zebrafish.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ntl (e-PCR), detects polymorphism
- UniSTS:205417

fc80a01.x1 (e-PCR)
- UniSTS:188297

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
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 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	IEA Inferred from Electronic Annotation 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 transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Kupffer's vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within Spemann organizer formation at the embryonic shield	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within convergent extension involved in axis elongation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in nephron morphogenesis	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 determination of left/right asymmetry in diencephalon	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right asymmetry in lateral mesoderm	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive tract development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic heart tube morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within liver development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mesoderm development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mesoderm development	IMP Inferred from Mutant Phenotype more info
involved_in mesoderm formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mesoderm formation	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within notochord cell differentiation	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 pancreas development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-anal tail morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephric glomerulus morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of BMP signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of endodermal cell fate specification	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within somite development	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within somite development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somite specification	IMP Inferred from Mutant Phenotype 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_or_within specification of animal organ position	IMP Inferred from Mutant Phenotype more info

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
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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: T-box transcription factor T-A

Names: T, brachyury homolog a; T-box protein ZfT; T-box protein ZfT-A; brachyury protein homolog A; no tail a; no tail protein A; no tail protein A-A; protein T homolog A; t protein homolog A

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_131162.1 → NP_571237.1 T-box transcription factor T-A

See identical proteins and their annotated locations for NP_571237.1

Status: PROVISIONAL

Source sequence(s)

S57147

UniProtKB/Swiss-Prot

B3DG73, Q07998

Related

ENSDARP00000141934.1, ENSDART00000164594.2

Conserved Domains (1) summary

cd00182
Location:34 → 216

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 ...