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

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 and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including brain development; conditioned taste aversion; and specification of animal organ identity. Located in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart; and sensory organ. Used to study autism spectrum disorder. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human TBR1 (T-box brain transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in cortex adult (RPKM 13.7), CNS E14 (RPKM 13.4) and 4 other tissues See more
Orthologs: human all
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Genomic context

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Tbr1 Misexpression Alters Neuronal Development in the Cerebral Cortex.
Title: Tbr1 Misexpression Alters Neuronal Development in the Cerebral Cortex.
Enhancing WNT Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants.
Title: Enhancing WNT Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants.
Tbr1 is genetically ablated during retinal development, these two RGC groups cannot develop. Ectopically expressing Tbr1 in M4 ipRGCs during development alters dendritic branching and density but not the inner plexiform layer stratification level.
Title: Essential Roles of Tbr1 in the Formation and Maintenance of the Orientation-Selective J-RGCs and a Group of OFF-Sustained RGCs in Mouse.
Tbr1 gene dosage regulates neocortex layer 6 connectivity.
Title: Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity.
Two transmembrane molecules, Sorcs3 and Cdh8, act as effectors of the Tbr1-controlled lamination program
Title: Tbr1 instructs laminar patterning of retinal ganglion cell dendrites.
Tbr1 haploinsufficiency specifically impaired olfactory discrimination but not olfactory sensation. Tbr1+/- mice exhibited abnormal olfactory bulbs.
Title: Haploinsufficiency of autism causative gene Tbr1 impairs olfactory discrimination and neuronal activation of the olfactory system in mice.
Study induced neuronal differentiation of mouse bone mesenchymal stem cells (bMSCs) into neuron-like cells in vitro. miR-122-5p was well complementary with the target site of Tbr1 mRNA3'UTR and could inhibit Tbr1 expression by binding to its 3'UTR. Expressions of Tbr1 mRNA and protein were decreased. Overexpression of miR-122-5p downregulated the expressions of Tbr1, NSE, and TAU.
Title: The role of miR-122-5p in negatively regulating T-box brain 1 expression on the differentiation of mouse bone mesenchymal stem cells.
CASK T740A mutation attenuated the interaction between CASK and TBR1 in the brain. However, CASK T740A mice were generally healthy, without obvious defects in brain morphology. The most dramatic defect among the mutant mice was in extinction of associative memory, though acquisition was normal.
Title: Calcium/calmodulin-dependent serine protein kinase (CASK), a protein implicated in mental retardation and autism-spectrum disorders, interacts with T-Brain-1 (TBR1) to control extinction of associative memory in male mice.
Mice lacking Tbr1 have Ca2+ waves in the cortex at normal frequencies and with normal neurotransmitter dependencies.
Title: Distinct calcium signals in developing cortical interneurons persist despite disorganization of cortex by Tbr1 KO.
Our findings highlight a TBR1-regulated network of autism spectrum disorders genes in the developing neocortex that are relatively intolerant to loss-of-function mutations, indicating that these genes may play critical roles in normal cortical development.
Title: TBR1 regulates autism risk genes in the developing neocortex.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Variation

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Alleles

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

Targeted (8) 1 citation
Endonuclease-mediated (5) 1 citation

General gene information

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Markers

Tbr1 (e-PCR), detects polymorphism
- UniSTS:507271

Tbr1 (e-PCR), detects polymorphism
- UniSTS:144548

TBR1 (e-PCR)
- UniSTS:513741

Tbr1 (e-PCR), detects polymorphism
- UniSTS:546541

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info

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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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
part_of 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

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Preferred Names: T-box brain protein 1

Names: T-box brain gene 1; T-brain-1; TBR-1; TES-56

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)

NM_001418366.1 → NP_001405295.1 T-box brain protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL845291

UniProtKB/TrEMBL

A2AR81

Related

ENSMUSP00000099798.5, ENSMUST00000102737.5
NM_001418367.1 → NP_001405296.1 T-box brain protein 1 isoform 3

Status: VALIDATED

Source sequence(s)

AL845291
NM_009322.4 → NP_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: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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

61633228..61644458

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499098.5 → XP_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: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