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

Gene ID: 6862, updated on 12-Jan-2019

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
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

Genomic context

See TBXT in Genome Data Viewer
Location:
6q27
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (166157644..166168669, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (166571144..166582157, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 72 Neighboring gene uncharacterized LOC729681 Neighboring gene RNA, U6 small nuclear 153, pseudogene Neighboring gene uncharacterized LOC101929297 Neighboring gene G protein subunit gamma 5 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Neural tube defect
MedGen: C3891448 OMIM: 182940 GeneReviews: Not available
Compare labs
Sacral agenesis with vertebral anomalies
MedGen: C3810343 OMIM: 615709 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Pathways from BioSystems

General gene information

Markers

Homology

Clone Names

  • MGC104817

Gene Ontology Provided by GOA

Process Evidence Code Pubs
BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
 
SMAD protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
anterior/posterior axis specification, embryo TAS
Traceable Author Statement
more info
PubMed 
bone morphogenesis IEA
Inferred from Electronic Annotation
more info
 
canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
cellular response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
determination of heart left/right asymmetry IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
heart morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
mesoderm development TAS
Traceable Author Statement
more info
PubMed 
mesoderm migration involved in gastrulation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
neural plate morphogenesis IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
notochord formation IEA
Inferred from Electronic Annotation
more info
 
penetration of zona pellucida IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
post-anal tail morphogenesis IEA
Inferred from Electronic Annotation
more info
 
primitive streak formation NAS
Non-traceable Author Statement
more info
PubMed 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
signal transduction involved in regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
somitogenesis IEA
Inferred from Electronic Annotation
more info
 
vasculogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
T-box transcription factor T; brachyury protein
Names
T brachyury transcription factor
T, brachyury homolog
protein T

NCBI Reference Sequences (RefSeq)

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
    4975..15988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for NP_001257413.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL627443, BC098425, BE785653
    Consensus CDS
    CCDS59045.1
    UniProtKB/Swiss-Prot
    O15178
    Related
    ENSP00000355836.3, ENST00000366871.7
    Conserved Domains (2) summary
    PLN00217
    Location:171279
    PLN00217; predicted protein; Provisional
    pfam00907
    Location:44219
    T-box; T-box
  2. NM_001366285.1NP_001353214.1  T-box transcription factor T isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Conserved Domains (1) summary
    pfam00907
    Location:44219
    T-box; T-box
  3. NM_001366286.1NP_001353215.1  T-box transcription factor T isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL627443
    Conserved Domains (1) summary
    pfam00907
    Location:44219
    T-box; T-box
  4. NM_003181.3NP_003172.1  T-box transcription factor T isoform 1

    See identical proteins and their annotated locations for NP_003172.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ001699, AL627443, BC098425, BE785653, BU190437
    Consensus CDS
    CCDS5290.1
    UniProtKB/Swiss-Prot
    O15178
    Related
    ENSP00000296946.2, ENST00000296946.6
    Conserved Domains (1) summary
    smart00425
    Location:42223
    TBOX; Domain first found in the mice T locus (Brachyury) protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    166157644..166168669 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536080.2XP_011534382.1  brachyury protein isoform X1

    Related
    ENSP00000355841.2, ENST00000366876.6
    Conserved Domains (1) summary
    pfam00907
    Location:44219
    T-box; T-box
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