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    Tbr1 T-box brain transcription factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 21375, updated on 9-Dec-2024

    Summary

    Official Symbol
    Tbr1provided by MGI
    Official Full Name
    T-box brain transcription factor 1provided by MGI
    Primary source
    MGI:MGI:107404
    See related
    Ensembl:ENSMUSG00000035033 AllianceGenome:MGI:107404
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Enables DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin DNA binding activity. Involved in cerebral cortex development; chromatin remodeling; and gene expression. Acts upstream of or within several processes, including brain development; conditioned taste aversion; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart; and sensory organ. Used to study autism spectrum disorder. Orthologous to human TBR1 (T-box brain transcription factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in cortex adult (RPKM 13.7), CNS E14 (RPKM 13.4) and 4 other tissues See more
    Orthologs
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    Genomic context

    See Tbr1 in Genome Data Viewer
    Location:
    2 C1.3; 2 35.56 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (61633228..61644458)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (61802863..61814114)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E808 Neighboring gene STARR-positive B cell enhancer ABC_E5924 Neighboring gene STARR-positive B cell enhancer ABC_E506 Neighboring gene STARR-positive B cell enhancer ABC_E7821 Neighboring gene TRAF family member-associated Nf-kappa B activator Neighboring gene STARR-positive B cell enhancer mm9_chr2:61481154-61481454 Neighboring gene STARR-seq mESC enhancer starr_04632 Neighboring gene STARR-positive B cell enhancer ABC_E4457 Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 Neighboring gene STARR-seq mESC enhancer starr_04635 Neighboring gene predicted gene, 39837 Neighboring gene zinc finger protein 277 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within amygdala development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cerebral cortex development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within conditioned taste aversion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within hindbrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    T-box brain protein 1
    Names
    T-box brain gene 1
    T-brain-1
    TBR-1
    TES-56

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001418366.1NP_001405295.1  T-box brain protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL845291
      UniProtKB/TrEMBL
      A2AR81
      Related
      ENSMUSP00000099798.5, ENSMUST00000102737.5
    2. NM_001418367.1NP_001405296.1  T-box brain protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL845291
    3. NM_009322.4NP_033348.2  T-box brain protein 1 isoform 1

      See identical proteins and their annotated locations for NP_033348.2

      Status: VALIDATED

      Source sequence(s)
      AL845291
      Consensus CDS
      CCDS16063.1
      UniProtKB/Swiss-Prot
      Q64336, Q7TSY9
      Related
      ENSMUSP00000046787.9, ENSMUST00000048934.15
      Conserved Domains (2) summary
      pfam16176
      Location:418679
      T-box_assoc; T-box transcription factor-associated
      cd20204
      Location:203393
      T-box_TBR1; DNA-binding domain of T-box brain protein 1 and related T-box proteins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      61633228..61644458
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006499098.5XP_006499161.1  T-box brain protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006499161.1

      UniProtKB/Swiss-Prot
      Q64336, Q7TSY9
      Conserved Domains (2) summary
      pfam16176
      Location:418679
      T-box_assoc; T-box transcription factor-associated
      cd20204
      Location:203393
      T-box_TBR1; DNA-binding domain of T-box brain protein 1 and related T-box proteins