tbx16 T-box transcription factor 16 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: tbx16provided by ZNC
Official Full Name: T-box transcription factor 16provided by ZNC
Primary source: ZFIN:ZDB-GENE-990615-5
See related: Ensembl:ENSDARG00000007329 AllianceGenome:ZFIN:ZDB-GENE-990615-5
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: spt; cb103; spt-1; id:ibd2185; wu:fa17g07; zgc:109817
Summary: Enables transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including convergent extension; gastrulation; and tube morphogenesis. Located in chromatin and nucleus. Is expressed in several structures, including forerunner cell group; germ ring; mesoderm; presumptive mesoderm; and spinal cord. [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 8

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (51736296..51753588, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (51749767..51767059, complement)

Chromosome 8 - NC_007119.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

data demonstrate that tbx6l and tbx16 genes function redundantly to direct tail somite development
Title: tbx6l and tbx16 are redundantly required for posterior paraxial mesoderm formation during zebrafish embryogenesis.
The Tbx16 regulates the timing of collinear hox gene activation to coordinate the anterior-posterior fates and positions of paraxial Mesodermal progenitor cells (MPCs).
Title: Tbx16 regulates hox gene activation in mesodermal progenitor cells.
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.
Tbx16 and Msgn1 are required to establish directional cell migration of zebrafish mesodermal progenitors.
Title: Tbx16 and Msgn1 are required to establish directional cell migration of zebrafish mesodermal progenitors.
high levels of Wnt signaling induce a transition to mesoderm by directly activating tbx16, which in turn acts to irreversibly flip a bistable switch, leading to maintenance of the mesodermal fate and repression of the bipotential progenitor state
Title: Wnt signaling and tbx16 form a bistable switch to commit bipotential progenitors to mesoderm.
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.
Zebrafish Tbx16 regulates intermediate mesoderm cell fate by attenuating Fgf activity.
Title: Zebrafish Tbx16 regulates intermediate mesoderm cell fate by attenuating Fgf activity.
Results uncover a novel Sdc2-Tbx16-Fgf2 pathway that regulates epithelial cell morphogenesis.
Title: Sdc2 and Tbx16 regulate Fgf2-dependent epithelial cell morphogenesis in the ciliated organ of asymmetry.
These data suggest that spt expression and BMP inhibition are both required for somitic precursors to exit the tailbud.
Title: BMP signaling and spadetail regulate exit of muscle precursors from the zebrafish tailbud.
Through its combined effects on gene expression and cell movement, Msgn1 (with Spt) plays a key role both in genesis of the paraxial mesoderm and in maintenance of the progenitor population from which it derives.
Title: The differentiation and movement of presomitic mesoderm progenitor cells are controlled by Mesogenin 1.

Submit: New GeneRIF Correction See all GeneRIFs (20)

General gene information

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Markers

fa17g07.s1 (e-PCR)
- UniSTS:202420

spt/tbx16 (e-PCR)
- UniSTS:205500

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 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	IGI Inferred from Genetic Interaction 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 angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype 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 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 erythrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart jogging	IC Inferred by Curator 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 hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intermediate mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
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 mesodermal to mesenchymal transition involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myeloid cell development	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 paraxial mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within paraxial mesoderm formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in pattern specification process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pronephric duct 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 pronephros development	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 somatic muscle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somite development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somite specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somitogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in 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 16

Names: T-box 16; T-box gene 16; spadetail

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_131058.1 → NP_571133.1 T-box transcription factor 16

See identical proteins and their annotated locations for NP_571133.1

Status: PROVISIONAL

Source sequence(s)

AF077225

UniProtKB/TrEMBL

O93389

Related

ENSDARP00000003051.8, ENSDART00000007090.9

Conserved Domains (1) summary

cd00182
Location:30 → 217

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 ...