TBR1 Gene (Protein Coding)

T-Box Brain Transcription Factor 1

GC02P161416
GIFtS:
41
This gene is a member of a conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of numerous developmental processes. In mouse, the ortholog of this gene is expressed in the cerebral cortex, hippocampus, amygdala and olfactory bulb and is thought to play an important role in neuronal migr... See more...

Aliases for TBR1 Gene

Aliases for TBR1 Gene

  • T-Box Brain Transcription Factor 1 2 3 5
  • T-Box Brain Protein 1 3 4
  • T-Box, Brain 1 2 3
  • T-Brain-1 3 4
  • TES-56 3 4
  • TBR-1 3 4
  • T-Box, Brain, 1 2
  • IDDAS 3
  • TBR1 5

External Ids for TBR1 Gene

Previous GeneCards Identifiers for TBR1 Gene

  • GC02P160326
  • GC02P160800
  • GC02P162236
  • GC02P162475
  • GC02P162098
  • GC02P161980
  • GC02P162272
  • GC02P154157

Summaries for TBR1 Gene

Entrez Gene Summary for TBR1 Gene

  • This gene is a member of a conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of numerous developmental processes. In mouse, the ortholog of this gene is expressed in the cerebral cortex, hippocampus, amygdala and olfactory bulb and is thought to play an important role in neuronal migration and axonal projection. In mouse, the C-terminal region of this protein was found to be necessary and sufficient for association with the guanylate kinase domain of calcium/calmodulin-dependent serine protein kinase. [provided by RefSeq, Dec 2015]

GeneCards Summary for TBR1 Gene

TBR1 (T-Box Brain Transcription Factor 1) is a Protein Coding gene. Diseases associated with TBR1 include Intellectual Developmental Disorder With Autism And Speech Delay and Pervasive Developmental Disorder. Among its related pathways are Neuroscience. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II core promoter sequence-specific DNA binding. An important paralog of this gene is EOMES.

UniProtKB/Swiss-Prot Summary for TBR1 Gene

  • Transcriptional repressor involved in multiple aspects of cortical development, including neuronal migration, laminar and areal identity, and axonal projection (PubMed:25232744, PubMed:30250039). As transcriptional repressor of FEZF2, it blocks the formation of the corticospinal (CS) tract from layer 6 projection neurons, thereby restricting the origin of CS axons specifically to layer 5 neurons (By similarity).

Gene Wiki entry for TBR1 Gene

Additional gene information for TBR1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBR1 Gene

Genomics for TBR1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TBR1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02J161416 Promoter 1 EPDnew Ensembl 600.7 -0.4 -396 1 RNF2 ZNF7 EZH2 CBX2 ZFHX2 TFDP1 NFYC ZNF384 TBR1 RNA5SP108 PSMD14
GH02J161414 Promoter 1 Ensembl 600.7 -1.6 -1596 1 HNRNPL ZNF692 ZIC2 RBFOX2 CTCF ZNF501 EZH2 GTF2F1 ZNF600 ZNF561 TBR1 LINC01806 RNA5SP108 PSMD14
GH02J161418 Promoter 0.4 Ensembl 600.7 +0.4 404 0.2 EZH2 TBR1 ENSG00000224076 SLC4A10
GH02J161238 Promoter/Enhancer 2.1 VISTA UCNEbase FANTOM5 ENCODE CraniofacialAtlas 13.6 -177.7 -177728 2.2 TEAD4 PRDM10 POLR2A BACH1 LARP7 ZIC2 SMAD5 ZNF600 YY1 ZNF341 lnc-RBMS1-10 lnc-RBMS1-9 TBR1 LINC01806 AHCTF1P1 SLC4A10 LOC101929512 PSMD14 ENSG00000235724 TANK
GH02J161417 Promoter 0.7 Ensembl 0.7 +2.8 2804 0.2 EZH2 MGA TFDP1 CBX2 POLR2A GABPB1 MXD4 SMARCA4 MXD3 ZNF580 ENSG00000224076 TBR1 SLC4A10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBR1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBR1

Top Transcription factor binding sites by QIAGEN in the TBR1 gene promoter:
  • E47
  • FAC1
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • NF-kappaB
  • NF-kappaB1
  • RelA
  • Tal-1beta

Genomic Locations for TBR1 Gene

Genomic Locations for TBR1 Gene
chr2:161,416,297-161,425,870
(GRCh38/hg38)
Size:
9,574 bases
Orientation:
Plus strand
chr2:162,272,605-162,282,381
(GRCh37/hg19)
Size:
9,777 bases
Orientation:
Plus strand

Genomic View for TBR1 Gene

Genes around TBR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBR1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TBR1 Gene

Proteins for TBR1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TBR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16650-TBR1_HUMAN
    Recommended name:
    T-box brain protein 1
    Protein Accession:
    Q16650
    Secondary Accessions:
    • B0AZS4
    • B2R6G5
    • Q14DC5
    • Q53TH0
    • Q56A81

    Protein attributes for TBR1 Gene

    Size:
    682 amino acids
    Molecular mass:
    74053 Da
    Quaternary structure:
    • Homodimer (PubMed:25232744). Part of a complex containing CASK, TBR1 and TSPYL2; may modulate gene expression in response to neuronal synaptic activity (By similarity). Interacts with FOXP2 (PubMed:25232744, PubMed:30250039). Interacts with FOXP1 (PubMed:30250039). Interacts with BCL11A (PubMed:30250039).

    Alternative splice isoforms for TBR1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBR1 Gene

Protein Expression for TBR1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TBR1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBR1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TBR1 Gene

Domains & Families for TBR1 Gene

Gene Families for TBR1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TBR1 Gene

InterPro:
Blocks:
  • Transcription factor, T-box
ProtoNet:

Suggested Antigen Peptide Sequences for TBR1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ79514, highly similar to T-brain-1 protein (B0AZS4_HUMAN)
  • TBR1 protein (Q56A81_HUMAN)
  • TES-56 (TBR1_HUMAN)
genes like me logo Genes that share domains with TBR1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TBR1 Gene

Function for TBR1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TBR1 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor involved in multiple aspects of cortical development, including neuronal migration, laminar and areal identity, and axonal projection (PubMed:25232744, PubMed:30250039). As transcriptional repressor of FEZF2, it blocks the formation of the corticospinal (CS) tract from layer 6 projection neurons, thereby restricting the origin of CS axons specifically to layer 5 neurons (By similarity).

Phenotypes From GWAS Catalog for TBR1 Gene

Gene Ontology (GO) - Molecular Function for TBR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001102 RNA polymerase II activating transcription factor binding IBA 21873635
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IBA 21873635
genes like me logo Genes that share ontologies with TBR1: view
genes like me logo Genes that share phenotypes with TBR1: view

Human Phenotype Ontology for TBR1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TBR1 Gene

MGI Knock Outs for TBR1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBR1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TBR1 Gene

Localization for TBR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBR1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBR1 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 2
cytoskeleton 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TBR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 25232744
genes like me logo Genes that share ontologies with TBR1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TBR1 Gene

Pathways & Interactions for TBR1 Gene

PathCards logo

SuperPathways for TBR1 Gene

SuperPathway Contained pathways
1 Neuroscience
Neuroscience
-
genes like me logo Genes that share pathways with TBR1: view

Pathways by source for TBR1 Gene

1 Cell Signaling Technology pathway for TBR1 Gene

Gene Ontology (GO) - Biological Process for TBR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0001661 conditioned taste aversion IEA --
GO:0001708 cell fate specification IBA 21873635
GO:0001947 heart looping IBA 21873635
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with TBR1: view

No data available for SIGNOR curated interactions for TBR1 Gene

Drugs & Compounds for TBR1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for TBR1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TBR1 Gene

1 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBR1

Alternative Splicing Database (ASD) splice patterns (SP) for TBR1 Gene

No ASD Table

Relevant External Links for TBR1 Gene

GeneLoc Exon Structure for
TBR1

Expression for TBR1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBR1 Gene

mRNA expression in normal human tissues for TBR1 Gene
mRNA expression by GTEx for TBR1 GenemRNA expression by BioGPS for TBR1 Gene

mRNA differential expression in normal tissues according to GTEx for TBR1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x17.7), Brain - Cortex (x13.1), Brain - Anterior cingulate cortex (BA24) (x11.3), and Brain - Amygdala (x4.6).

Protein differential expression in normal tissues from HIPED for TBR1 Gene

This gene is overexpressed in Pancreas (28.7), Breast (21.3), and Lung (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TBR1 Gene



Protein tissue co-expression partners for TBR1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBR1

SOURCE GeneReport for Unigene cluster for TBR1 Gene:

Hs.210862

mRNA Expression by UniProt/SwissProt for TBR1 Gene:

Q16650-TBR1_HUMAN
Tissue specificity: Brain.

Evidence on tissue expression from TISSUES for TBR1 Gene

  • Nervous system(5)
  • Skin(2.4)
  • Eye(2)
genes like me logo Genes that share expression patterns with TBR1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for TBR1 Gene

Orthologs for TBR1 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBR1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TBR1 30 31
  • 99.8 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TBR1 31
  • 99 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TBR1 31
  • 97 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TBR1 30 31
  • 96.68 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TBR1 30 31
  • 96.43 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Tbr1 30 17 31
  • 95.01 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Tbr1 30
  • 94.57 (n)
Chicken
(Gallus gallus)
 Aves TBR1 30 31
  • 89.59 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TBR1 31
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia tbr1 30
  • 80.38 (n)
Zebrafish
(Danio rerio)
 Actinopterygii tbr1b 30 31
  • 76.13 (n)
 OneToOne
tbr1 30
Worm
(Caenorhabditis elegans)
 Secernentea tbx-9 31 32
  • 31 (a)
 ManyToMany
tbx-8 31 32
  • 27 (a)
 ManyToMany
tbx-43 31
  • 27 (a)
 ManyToMany
tbx-37 31
  • 26 (a)
 ManyToMany
tbx-38 31
  • 24 (a)
 ManyToMany
tbx-11 31
  • 23 (a)
 ManyToMany
tbx-34 31
  • 22 (a)
 ManyToMany
tbx-35 31
  • 20 (a)
 ManyToMany
tbx-30 31
  • 18 (a)
 ManyToMany
tbx-42 31
  • 18 (a)
 ManyToMany
tbx-40 31
  • 17 (a)
 ManyToMany
tbx-39 31
  • 16 (a)
 ManyToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.7001 31
  • 15 (a)
 OneToMany
Species where no ortholog for TBR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TBR1 Gene

ENSEMBL:
Gene Tree for TBR1 (if available)
TreeFam:
Gene Tree for TBR1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBR1: view image

Paralogs for TBR1 Gene

Paralogs for TBR1 Gene

(8) SIMAP similar genes for TBR1 Gene using alignment to 4 proteins:

  • TBR1_HUMAN
  • B0AZS4_HUMAN
  • H7C0B1_HUMAN
  • Q56A81_HUMAN
genes like me logo Genes that share paralogs with TBR1: view

Variants for TBR1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBR1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
680335 Likely Benign: not provided 161,416,671(+) G/A SYNONYMOUS_VARIANT
745072 Likely Benign: not provided 161,418,909(+) C/T SYNONYMOUS_VARIANT
778013 Likely Benign: not provided 161,420,228(+) T/C SYNONYMOUS_VARIANT
791154 Benign: not provided 161,416,464(+) C/G SYNONYMOUS_VARIANT
801771 Likely Pathogenic: Autism 5 161,423,724(+) TA/T FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for TBR1 Gene

Structural Variations from Database of Genomic Variants (DGV) for TBR1 Gene

Variant ID Type Subtype PubMed ID
esv3593155 CNV loss 21293372
esv3593156 CNV gain 21293372
nsv1003307 CNV loss 25217958

Variation tolerance for TBR1 Gene

Residual Variation Intolerance Score: 11.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.08; 38.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBR1 Gene

Human Gene Mutation Database (HGMD)
TBR1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBR1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBR1 Gene

Disorders for TBR1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for TBR1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TBR1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TBR1_HUMAN
  • Intellectual developmental disorder with autism and speech delay (IDDAS) [MIM:606053]: An autosomal dominant neurodevelopmental disorder characterized by varying degrees of intellectual disability, autism spectrum disorder, and language deficits. {ECO:0000269 PubMed:14593429, ECO:0000269 PubMed:22495311, ECO:0000269 PubMed:23160955, ECO:0000269 PubMed:25232744, ECO:0000269 PubMed:25356899, ECO:0000269 PubMed:25363760, ECO:0000269 PubMed:25418537, ECO:0000269 PubMed:30250039}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBR1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with TBR1: view

No data available for Genatlas for TBR1 Gene

Publications for TBR1 Gene

  1. T-brain-1: a homolog of Brachyury whose expression defines molecularly distinct domains within the cerebral cortex. (PMID: 7619531) Bulfone A … Rubenstein JL (Neuron 1995) 2 3 4
  2. Functional characterization of TBR1 variants in neurodevelopmental disorder. (PMID: 30250039) den Hoed J … Fisher SE (Scientific reports 2018) 3 4
  3. Mutations in TBR1 gene leads to cortical malformations and intellectual disability. (PMID: 30268909) Vegas N … Bahi-Buisson N (European journal of medical genetics 2018) 3 4
  4. De novo TBR1 mutations in sporadic autism disrupt protein functions. (PMID: 25232744) Deriziotis P … Fisher SE (Nature communications 2014) 3 4
  5. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. (PMID: 23160955) O'Roak BJ … Shendure J (Science (New York, N.Y.) 2012) 3 4

ExternalLinks

View latest publications for TBR1 gene in Mastermind

Products for TBR1 Gene

  • Addgene plasmids for TBR1

Sources for TBR1 Gene