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    Tbx6 T-box transcription factor 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 365371, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Tbx6provided by RGD
    Official Full Name
    T-box transcription factor 6provided by RGD
    Primary source
    RGD:1307716
    See related
    EnsemblRapid:ENSRNOG00000019771 AllianceGenome:RGD:1307716
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    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. Predicted to be involved in cell fate specification; negative regulation of DNA-binding transcription factor activity; and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of neuron maturation; regulation of gene expression; and somite rostral/caudal axis specification. Predicted to be located in chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spondylocostal dysostosis 5. Orthologous to human TBX6 (T-box transcription factor 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 16.7), Spleen (RPKM 9.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tbx6 in Genome Data Viewer
    Location:
    1q36
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (190818397..190823824)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (181387851..181392762)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (198214797..198218706)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene glycerophosphodiester phosphodiesterase domain containing 3 Neighboring gene yippee-like 3 Neighboring gene protein phosphatase 4, catalytic subunit Neighboring gene uncharacterized LOC103691235 Neighboring gene aldolase, fructose-bisphosphate A Neighboring gene U6 spliceosomal RNA

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Regulation of Tbx6 expression by Notch signaling. White PH, et al. Genesis, 2005 Jun. PMID 15864811
    2. Dll1 is a downstream target of Tbx6 in the paraxial mesoderm. White PH, et al. Genesis, 2005 Jul. PMID 15986483
    3. Spatially coordinated kinase signaling regulates local axon degeneration. Chen M, et al. J Neurosci, 2012 Sep 26. PMID 23015435, Free PMC Article
    4. Defective somite patterning in mouse embryos with reduced levels of Tbx6. White PH, et al. Development, 2003 Apr. PMID 12620991
    5. Three neural tubes in mouse embryos with mutations in the T-box gene Tbx6. Chapman DL, et al. Nature, 1998 Feb 12. PMID 9490412

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mesoderm formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within mesodermal cell fate specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    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 signal transduction involved in regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within somite rostral/caudal axis specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    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 TBX6
    Names
    T-box 6
    T-box protein 6

    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)

    1. NM_001108920.1 → NP_001102390.1  T-box transcription factor TBX6

      See identical proteins and their annotated locations for NP_001102390.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473956
      UniProtKB/Swiss-Prot
      D3ZJK7
      Related
      ENSRNOP00000060687.1, ENSRNOT00000068543.3
      Conserved Domains (1) summary
      cd00182
      Location:90 → 277
      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 ...

    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

    1. NC_086019.1 Reference GRCr8

      Range
      190818397..190823824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085289.2 → XP_038941217.1  T-box transcription factor TBX6 isoform X1

      Conserved Domains (2) summary
      PHA03247
      Location:293 → 453
      PHA03247; large tegument protein UL36; Provisional
      cd20196
      Location:91 → 273
      T-box_TBX6; DNA-binding domain of T-box transcription factor 6, and related T-box proteins

    2. XM_039085290.2 → XP_038941218.1  T-box transcription factor TBX6 isoform X2

      Conserved Domains (1) summary
      cl00145
      Location:91 → 273
      T-box; DNA-binding domain of the T-box transcription factor family

    RNA

    1. XR_005489694.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3ZJK7.1 GenPept UniProtKB/Swiss-Prot:D3ZJK7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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