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

Gene ID: 6862, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See TBXT in Genome Data Viewer
Location:
6q27
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (166157656..166168655, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (167527458..167538457, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (166571144..166582143, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901524 Neighboring gene uncharacterized LOC729681 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:166525837-166527036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:166581481-166582075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17773 Neighboring gene lncRNA divergent activator of TBXT Neighboring gene NANOG hESC enhancer GRCh37_chr6:166610696-166611243 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:166618881-166620080 Neighboring gene RNA, U6 small nuclear 153, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:166637642-166637828 Neighboring gene uncharacterized LOC101929297 Neighboring gene G protein subunit gamma 5 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Brachyury Is Associated with Glioma Differentiation and Response to Temozolomide.
    Title: Brachyury Is Associated with Glioma Differentiation and Response to Temozolomide.
  7. 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.
  8. 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.
  9. 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.
  10. hordomas can be primarily diagnosed by fine needle aspiration cytology in a typical clinicoradiological setting with a combination of key cytomorphological features...An exact diagnosis has treatment implications and requires confirmation by brachyury immunostaining.
    Title: Clinicocytopathological spectrum, including uncommon forms, of nine cases of chordomas with immunohistochemical results, including brachyury immunostaining: A single institutional experience.
Submit: New GeneRIF Correction See all GeneRIFs (69)

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 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
Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC104817

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
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in 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

  1. NG_012135.1 RefSeqGene

    Range
    5793..15988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    166157656..166168655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419269.1 → XP_047275225.1  T-box transcription factor T isoform X1

    UniProtKB/Swiss-Prot
    E7ERD6, O15178, Q4KMP4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    167527458..167538457 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356267.1 → XP_054212242.1  T-box transcription factor T isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15178.1 GenPept UniProtKB/Swiss-Prot:O15178

Gene LinkOut

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