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 AllianceGenome:RGD:1310141
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable 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 cellular response to retinoic acid. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in chromatin and nucleus. 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, Jun 2025]
Expression: Biased expression in Lung (RPKM 9.3), Thymus (RPKM 6.6) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q12

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (54845674..54859340, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (52298104..52309813, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (52887067..52900691, complement)

Chromosome 1 - NC_086019.1 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: 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 Functions

What's a GeneRIF?

Brachyury promotes extracellular matrix synthesis through transcriptional regulation of Smad3 in nucleus pulposus.
Title: Brachyury promotes extracellular matrix synthesis through transcriptional regulation of Smad3 in nucleus pulposus.
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

General gene information

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Markers

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

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

Gene Ontology Provided by RGD

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	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within anatomical structure morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anatomical structure morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle cell myoblast differentiation	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within determination of heart left/right asymmetry	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within determination of heart left/right asymmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic skeletal system development	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mesoderm development	ISO Inferred from Sequence Orthology more info
involved_in mesoderm formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mesoderm migration involved in gastrulation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mesoderm migration involved in gastrulation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural plate morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural plate morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within notochord development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within notochord development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within notochord formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within notochord formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within penetration of zona pellucida	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within penetration of zona pellucida	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-anal tail morphogenesis	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within signal transduction involved in regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within signal transduction involved in regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in somitogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within somitogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within somitogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within vasculogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within vasculogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: T-box transcription factor T

Names: T brachyury transcription factor; brachyury homolog; brachyury 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)

NM_001106209.2 → NP_001099679.1 T-box transcription factor T

See identical proteins and their annotated locations for NP_001099679.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A6KK19, A6KK20

Conserved Domains (1) summary

cd20202
Location:41 → 219

T-box_TBXT; DNA-binding domain of T-box transcription factor T and related T-box proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

54845674..54859340 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039103475.2 → XP_038959403.1 T-box transcription factor T isoform X3

UniProtKB/TrEMBL

A0A8I6AEA5, A6KK20

Related

ENSRNOP00000092633.1, ENSRNOT00000110131.2

Conserved Domains (1) summary

cl00145
Location:42 → 178

T-box; DNA-binding domain of the T-box transcription factor family
XM_039103470.2 → XP_038959398.1 T-box transcription factor T isoform X2

UniProtKB/TrEMBL

A6KK19, A6KK20

Conserved Domains (1) summary

cd20202
Location:41 → 219

T-box_TBXT; DNA-binding domain of T-box transcription factor T and related T-box proteins
XM_017588873.3 → XP_017444362.1 T-box transcription factor T isoform X1

UniProtKB/TrEMBL

A6KK20, D4A4W8

Related

ENSRNOP00000016471.3, ENSRNOT00000016471.5

Conserved Domains (1) summary

smart00425
Location:42 → 224

TBOX; Domain first found in the mice T locus (Brachyury) protein
XM_063282870.1 → XP_063138940.1 T-box transcription factor T isoform X1

UniProtKB/TrEMBL

A6KK20, D4A4W8