TBXT T-box transcription factor T [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBXTprovided by HGNC
Official Full Name: T-box transcription factor Tprovided by HGNC
Primary source: HGNC:HGNC:11515
See related: Ensembl:ENSG00000164458 MIM:601397; AllianceGenome:HGNC:11515
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: T; TFT; SAVA
Summary: The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Variation in this gene was associated with susceptibility to neural tube defects and chordoma. A mutation in this gene was found in a family with sacral agenesis with vertebral anomalies. [provided by RefSeq, Sep 2018]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 6q27

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (166157656..166168655, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (167527458..167538457, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (166571144..166582143, complement)

Chromosome 6 - NC_000006.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

On the genetic basis of tail-loss evolution in humans and apes.
Title: On the genetic basis of tail-loss evolution in humans and apes.
Association between TBXT rs2305089 polymorphism and chordoma in Iranian patients identified by a developed T-ARMS-PCR assay.
Title: Association between TBXT rs2305089 polymorphism and chordoma in Iranian patients identified by a developed T-ARMS-PCR assay.
Recurrent loss of chromosome 22 and SMARCB1 deletion in extra-axial chordoma: A clinicopathological and molecular analysis.
Title: Recurrent loss of chromosome 22 and SMARCB1 deletion in extra-axial chordoma: A clinicopathological and molecular analysis.
Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity.
Title: Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity.
miR-219-5p targets TBXT and inhibits breast cancer cell EMT and cell migration and invasion.
Title: miR-219-5p targets TBXT and inhibits breast cancer cell EMT and cell migration and invasion.
Machine learning based tissue analysis reveals Brachyury has a diagnosis value in breast cancer.
Title: Machine learning based tissue analysis reveals Brachyury has a diagnosis value in breast cancer.
Brachyury Is Associated with Glioma Differentiation and Response to Temozolomide.
Title: Brachyury Is Associated with Glioma Differentiation and Response to Temozolomide.
Genetic variants of TBX6 and TBXT identified in patients with congenital scoliosis in Southern China.
Title: Genetic variants of TBX6 and TBXT identified in patients with congenital scoliosis in Southern China.
Inhibition of Histone H3K27 Demethylases Inactivates Brachyury (TBXT) and Promotes Chordoma Cell Death.
Title: Inhibition of Histone H3K27 Demethylases Inactivates Brachyury (TBXT) and Promotes Chordoma Cell Death.
Signifying their developmental function, the key mesoderm specifier BRACHYURY (T) is accompanied by yylncT, which localizes to the active T locus during mesoderm commitment.
Title: yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs.

Submit: New GeneRIF Correction See all GeneRIFs (70)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neural tube defect MedGen: C0027794 OMIM: 182940 GeneReviews: Not available	Compare labs
Sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome MedGen: C3810343 OMIM: 615709 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment 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	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in anterior/posterior axis specification, embryo	TAS Traceable Author Statement more info	PubMed
involved_in cardiac muscle cell myoblast differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart morphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in mesoderm development	TAS Traceable Author Statement more info	PubMed
involved_in mesoderm formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in primitive streak formation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed
involved_in somitogenesis	IBA Inferred from Biological aspect of Ancestor 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
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: T-box transcription factor T

Names: T brachyury transcription factor; T, brachyury homolog; brachyury protein; protein T

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.

Genomic

NG_012135.1 RefSeqGene

Range

5793..15988

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270484.2 → NP_001257413.1 T-box transcription factor T isoform 2

See identical proteins and their annotated locations for NP_001257413.1

Status: REVIEWED

Source sequence(s)

AL627443

Consensus CDS

CCDS59045.1

UniProtKB/Swiss-Prot

O15178

Related

ENSP00000355836.3, ENST00000366871.7

Conserved Domains (2) summary

PLN00217
Location:171 → 279

PLN00217; predicted protein; Provisional

pfam00907
Location:44 → 219

T-box; T-box
NM_001366285.2 → NP_001353214.1 T-box transcription factor T isoform 3

Status: REVIEWED

Source sequence(s)

AL627443

Consensus CDS

CCDS94030.1

UniProtKB/TrEMBL

J3KP65

Related

ENSP00000355841.3, ENST00000366876.7

Conserved Domains (1) summary

pfam00907
Location:44 → 219

T-box; T-box
NM_001366286.2 → NP_001353215.1 T-box transcription factor T isoform 3

Status: REVIEWED

Source sequence(s)

AL627443

Consensus CDS

CCDS94030.1

UniProtKB/TrEMBL

J3KP65

Conserved Domains (1) summary

pfam00907
Location:44 → 219

T-box; T-box
NM_003181.4 → NP_003172.1 T-box transcription factor T isoform 1

See identical proteins and their annotated locations for NP_003172.1

Status: REVIEWED

Source sequence(s)

AL627443

Consensus CDS

CCDS5290.1

UniProtKB/Swiss-Prot

E7ERD6, O15178, Q4KMP4

Related

ENSP00000296946.2, ENST00000296946.6

Conserved Domains (1) summary

smart00425
Location:42 → 223

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