Tbxt T-box transcription factor T [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tbxtprovided by RGD
Official Full Name: T-box transcription factor Tprovided by RGD
Primary source: RGD:1310141
See related: Ensembl:ENSRNOG00000012229
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: T
Expression: Biased expression in Lung (RPKM 9.3), Thymus (RPKM 6.6) and 4 other tissues See more
Orthologs: human mouse all

Genomic context

Location:: 1q12

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (52887067..52900691, complement)
104	previous assembly	Rnor_5.0 (GCF_000001895.4)	1	NC_005100.3 (54139554..54147385, complement)

Chromosome 1 - NC_005100.4 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

The mutation of Brachyury protein is a result of a deletion in exon 2 causing the early termination and loss of function of protein encoded by the T gene, manifesting as a short tail phenotype.
Title: Identification of a novel mouse brachyury (T) allele causing a short tail mutation in mice.

Submit: New GeneRIF Correction

Variation

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Pathways from BioSystems

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Folic Acid Network, organism-specific biosystem (from WikiPathways)
Folic Acid Network, organism-specific biosystemThe folic acid-centred micronutrient biological network. The most relevant biochemical processes related to folic acid in the context of metabolism, oxidation and inflammation are represented. Also, ...
Selenium Micronutrient Network, organism-specific biosystem (from WikiPathways)
Selenium Micronutrient Network, organism-specific biosystemThe selenium-centred micronutrient biological network. The most relevant biochemical processes related to selenium in the context of metabolism, oxidation and inflammation are represented. Also, the ...

General gene information

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Markers

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

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

Homology

Homologs of the Tbxt gene: The Tbxt gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, mouse, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 245 organisms have orthologs with human gene Tbxt
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
RNA polymerase II activating transcription factor binding	IEA Inferred from Electronic Annotation more info
RNA polymerase II activating transcription factor binding	ISO Inferred from Sequence Orthology more info
RNA polymerase II distal enhancer sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
RNA polymerase II distal enhancer sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
RNA polymerase II proximal promoter sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
RNA polymerase II proximal promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
RNA polymerase II transcription factor binding	ISO Inferred from Sequence Orthology more info
molecular_function	ND No biological Data available more info
sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
BMP signaling pathway	IEA Inferred from Electronic Annotation more info
BMP signaling pathway	ISO Inferred from Sequence Orthology more info
SMAD protein signal transduction	IEA Inferred from Electronic Annotation more info
SMAD protein signal transduction	ISO Inferred from Sequence Orthology more info
anatomical structure morphogenesis	ISO Inferred from Sequence Orthology more info
anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
bone morphogenesis	IEA Inferred from Electronic Annotation more info
bone morphogenesis	ISO Inferred from Sequence Orthology more info
canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
determination of heart left/right asymmetry	IEA Inferred from Electronic Annotation more info
determination of heart left/right asymmetry	ISO Inferred from Sequence Orthology more info
embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
embryonic skeletal system development	ISO Inferred from Sequence Orthology more info
heart morphogenesis	IEA Inferred from Electronic Annotation more info
heart morphogenesis	ISO Inferred from Sequence Orthology more info
mesoderm development	ISO Inferred from Sequence Orthology more info
mesoderm migration involved in gastrulation	IEA Inferred from Electronic Annotation more info
mesoderm migration involved in gastrulation	ISO Inferred from Sequence Orthology more info
negative regulation of DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
neural plate morphogenesis	IEA Inferred from Electronic Annotation more info
neural plate morphogenesis	ISO Inferred from Sequence Orthology more info
neural tube closure	IEA Inferred from Electronic Annotation more info
neural tube closure	ISO Inferred from Sequence Orthology more info
notochord development	ISO Inferred from Sequence Orthology more info
notochord formation	IEA Inferred from Electronic Annotation more info
notochord formation	ISO Inferred from Sequence Orthology more info
penetration of zona pellucida	IEA Inferred from Electronic Annotation more info
penetration of zona pellucida	ISO Inferred from Sequence Orthology more info
positive regulation of cell proliferation	IEA Inferred from Electronic Annotation more info
positive regulation of cell proliferation	ISO Inferred from Sequence Orthology more info
positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation	IEA Inferred from Electronic Annotation more info
positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation	ISO Inferred from Sequence Orthology more info
post-anal tail morphogenesis	IEA Inferred from Electronic Annotation more info
post-anal tail morphogenesis	ISO Inferred from Sequence Orthology more info
regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
reproductive process	ISO Inferred from Sequence Orthology more info
signal transduction involved in regulation of gene expression	IEA Inferred from Electronic Annotation more info
signal transduction involved in regulation of gene expression	ISO Inferred from Sequence Orthology more info
somitogenesis	IEA Inferred from Electronic Annotation more info
somitogenesis	ISO Inferred from Sequence Orthology more info
vasculogenesis	IEA Inferred from Electronic Annotation more info
vasculogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
cellular_component	ND No biological Data available more info
chromatin	ISO Inferred from Sequence Orthology more info
cytoplasm	IEA Inferred from Electronic Annotation more info
cytoplasm	ISO Inferred from Sequence Orthology more info
nuclear chromatin	IEA Inferred from Electronic Annotation more info
nuclear chromatin	ISO Inferred from Sequence Orthology more info
nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: brachyury protein

Names: T brachyury transcription factor; brachyury homolog

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_001106209.1 → NP_001099679.1 brachyury protein

See identical proteins and their annotated locations for NP_001099679.1

Status: PROVISIONAL

Source sequence(s)

CH474059

UniProtKB/TrEMBL

D4A4W8

Related

ENSRNOP00000016471.2, ENSRNOT00000016471.3

Conserved Domains (1) summary

smart00425
Location:42 → 224

TBOX; Domain first found in the mice T locus (Brachyury) protein

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...

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

Reference Rnor_6.0 Primary Assembly

Genomic

NC_005100.4 Reference Rnor_6.0 Primary Assembly

Range

52887067..52900691 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017588873.1 → XP_017444362.1 brachyury protein isoform X1

Conserved Domains (1) summary

smart00425
Location:42 → 224

TBOX; Domain first found in the mice T locus (Brachyury) protein