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    Tbr1 T-box brain transcription factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 680427, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Tbr1provided by RGD
    Official Full Name
    T-box brain transcription factor 1provided by RGD
    Primary source
    RGD:1591773
    See related
    EnsemblRapid:ENSRNOG00000005049 AllianceGenome:RGD:1591773
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables protein kinase binding activity. Involved in cerebral cortex development. Predicted to be located in chromatin. Predicted to be active in nucleus. Orthologous to human TBR1 (T-box brain transcription factor 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward (RPKM 43.2) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tbr1 in Genome Data Viewer
    Location:
    3q21
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (66758805..66769626)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (46350237..46368397)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (47677720..47685902)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene TRAF family member-associated NFKB activator Neighboring gene cation-dependent mannose-6-phosphate receptor pseudogene Neighboring gene proteasome 26S subunit, non-ATPase 14 Neighboring gene RNA, U6 small nuclear 249 Neighboring gene ribosomal protein L9, pseudogene 12

    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 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. N-acetylcysteine attenuates lipopolysaccharide-induced impairment in lamination of Ctip2-and Tbr1- expressing cortical neurons in the developing rat fetal brain. Chao MW, et al. Sci Rep, 2016 Aug 31. PMID 27577752, Free PMC Article
    2. De novo TBR1 mutations in sporadic autism disrupt protein functions. Deriziotis P, et al. Nat Commun, 2014 Sep 18. PMID 25232744, Free PMC Article
    3. Nuclear translocation and transcription regulation by the membrane-associated guanylate kinase CASK/LIN-2. Hsueh YP, et al. Nature, 2000 Mar 16. PMID 10749215
    4. Identification of Tbr-1/CASK complex target genes in neurons. Wang TF, et al. J Neurochem, 2004 Dec. PMID 15584924
    5. Cortical and thalamic axon pathfinding defects in Tbr1, Gbx2, and Pax6 mutant mice: evidence that cortical and thalamic axons interact and guide each other. Hevner RF, et al. J Comp Neurol, 2002 May 20. PMID 11967891

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An increase in fetal cortical thickness was noted in the LPS-treated group. In the enlarged fetal cortex, laminar positioning of the early born cortical cells expressing Tbr1 and Ctip2 was disrupted, with a scattered distribution
      Title: N-acetylcysteine attenuates lipopolysaccharide-induced impairment in lamination of Ctip2-and Tbr1- expressing cortical neurons in the developing rat fetal brain.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 chromatin DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within amygdala development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cerebral cortex development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cerebral cortex development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in commitment of neuronal cell to specific neuron type in forebrain IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within commitment of neuronal cell to specific neuron type in forebrain ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within conditioned taste aversion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hindbrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron differentiation 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
    		  
    acts_upstream_of_or_within regulation of axon guidance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of neuron projection development 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 specification of animal organ identity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    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 brain protein 1
    Names
    T-box brain gene 1
    T-box, brain, 1
    T-box, brain, 1-like

    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_001191070.2 → NP_001177999.2  T-box brain protein 1

      Status: VALIDATED

      Source sequence(s)
      BF281828, JAXUCZ010000003
      UniProtKB/TrEMBL
      D4A6N8
      Related
      ENSRNOP00000059530.4, ENSRNOT00000065340.5
      Conserved Domains (2) summary
      pfam16176
      Location:418 → 679
      T-box_assoc; T-box transcription factor-associated
      cd20204
      Location:203 → 393
      T-box_TBR1; DNA-binding domain of T-box brain protein 1 and related T-box proteins

    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_086021.1 Reference GRCr8

      Range
      66758805..66769626
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105842.2 → XP_038961770.1  T-box brain protein 1 isoform X1

      Conserved Domains (2) summary
      pfam16176
      Location:186 → 447
      T-box_assoc; T-box transcription factor-associated
      cl00145
      Location:1 → 161
      T-box; DNA-binding domain of the T-box transcription factor family
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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