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    T T brachyury transcription factor [ Homo sapiens (human) ]

    Gene ID: 6862, updated on 22-Apr-2017
    Official Symbol
    Tprovided by HGNC
    Official Full Name
    T brachyury transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:11515
    See related
    Ensembl:ENSG00000164458 MIM:601397; Vega:OTTHUMG00000015991
    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
    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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]
    Orthologs
    Location:
    6q27
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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 uncharacterized LOC105378117 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 72 Neighboring gene RNA, U6 small nuclear 153, pseudogene Neighboring gene uncharacterized LOC101929297 Neighboring gene G protein subunit gamma 5 pseudogene 1

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Neural tube defect
    MedGen: C0027794 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

    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 transcription from RNA polymerase II promoter 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
     
    transcription, DNA-templated 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 
    Preferred Names
    brachyury protein
    Names
    T, brachyury homolog
    protein T

    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  brachyury protein 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, OTTHUMP00000248709, ENST00000366871.7, OTTHUMT00000043038
      Conserved Domains (2) summary
      PLN00217
      Location:171279
      PLN00217; predicted protein; Provisional
      cd00182
      Location:42223
      TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
    2. NM_003181.3NP_003172.1  brachyury protein 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, OTTHUMP00000017588, ENST00000296946.6, OTTHUMT00000043037
      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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 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, OTTHUMP00000248710, ENST00000366876.6, OTTHUMT00000419145
      Conserved Domains (1) summary
      cd00182
      Location:42223
      TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      166835290..166846303 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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