Tbr1 MGI Mouse Gene Detail - MGI:107404 - T-box brain transcription factor 1

Symbol

Tbr1
Name

T-box brain transcription factor 1
Synonyms

T-box brain gene 1

Feature Type

protein coding gene
IDs

MGI:107404
NCBI Gene: 21375
Alliance

genome feature page
Transcription Start Sites

13 TSS

Sequence Map

Chr2:61633274-61644458 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 35.56 cM
Mapping Data

2 experiments

SNPs within 2kb

199 from dbSNP Build 142
Strain Annotations

19
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_107404	protein coding gene	Chr2:61633228-61644458 (+)
129S1/SvImJ	ENSMUSG00200002823	protein coding gene	Chr2:58704430-58714098 (+)
A/J	ENSMUSG00195004872	protein coding gene	Chr2:58823875-58833537 (+)
AKR/J	ENSMUSG00220007181	protein coding gene	Chr2:58925592-58935256 (+)
BALB/cJ	ENSMUSG00180020015	protein coding gene	Chr2:58779626-58789287 (+)
C3H/HeJ	ENSMUSG00175012703	protein coding gene	Chr2:58848382-58858044 (+)
C57BL/6NJ	ENSMUSG00215007776	protein coding gene	Chr2:58833123-58842784 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023589	protein coding gene	Chr2:56618068-56629246 (+)
CAST/EiJ	ENSTCUG00005022389	protein coding gene	Chr2:58202223-58211923 (+)
CBA/J	ENSMUSG00210033798	protein coding gene	Chr2:58874254-58883916 (+)
DBA/2J	ENSMUSG00185007963	protein coding gene	Chr2:58734407-58744077 (+)
FVB/NJ	ENSMUSG00205018429	protein coding gene	Chr2:58363075-58372743 (+)
JF1/MsJ	ENSUMUG00000018950	protein coding gene	Chr2:58440393-58450072 (+)
LP/J	ENSMUSG00230001042	protein coding gene	Chr2:60588033-60597697 (+)
NOD/ShiLtJ	ENSMUSG00190028567	protein coding gene	Chr2:58812551-58822216 (+)
NZO/HlLtJ	ENSMUSG00225000351	protein coding gene	Chr2:68300984-68310645 (+)
PWK/PhJ	ENSLUMG00010005378	protein coding gene	Chr2:58600211-58609852 (+)
SPRET/EiJ	ENSMSPG00010011536	protein coding gene	Chr2:59798354-59808015 (+)
WSB/EiJ	ENSIUOG00005027056	protein coding gene	Chr2:58917575-58927235 (+)

Human Ortholog

TBR1, T-box brain transcription factor 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

TBR1, T-box brain transcription factor 1
Synonyms

AUTS5, IDDAS, TBR-1, TES-56
Links

HGNC:11590

NCBI Gene ID: 10716

UniProt: Q16650
Chr Location

2q24.2; chr2:161416297-161425870 (+) GRCh38

MGI Vertebrate Homology

Tbr1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: TBR1
Gene Tree

Tbr1

Diseases

1 with Tbr1 mouse models

Human Disease

Mouse Models

autism spectrum disorder

IDs

View 2 models

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

2 with disease annotations

References

2 with disease annotations

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Phenotype Summary

41 phenotypes from 3 alleles in 4 genetic backgrounds
1 phenotype from multigenic genotypes
2 images
40 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

18
Chemically induced (other)

1
Endonuclease-mediated

7
Targeted

10
Genomic Mutations

1 involving Tbr1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

38 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for a targeted null allele fail to feed and die on the second postnatal day displaying disrupted forebrain morphology and a hypoplastic olfactory bulb that lacks normal mitral and tufted cells and shows a striking reduction in mature olfactory bulb projection neurons.

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All GO Annotations

45
GO References

18

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1595
Tissues

308
cDNA Data

17
Literature Summary

870

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase tbr1

ZFIN tbr1a, tbr1b

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All Sequences

45
RefSeq

8
UniProt

3
CCDS

CCDS16063.1

Ensembl

ENSMUSG00000035033 (Evidence)
NCBI Gene

21375

			Length	Strain/Species	Flank
genomic	ENSMUSG00000035033	Ensembl Gene Model \| MGI Sequence Detail	11185	C57BL/6J	± kb
transcript	ENSMUST00000048934	Ensembl \| MGI Sequence Detail	3977	Not Applicable
polypeptide	ENSMUSP00000046787	Ensembl \| MGI Sequence Detail	681	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000016140 T-box brain protein 1

(term hierarchy)
InterPro Domains

IPR008967 p53-like transcription factor, DNA-binding domain superfamily

IPR036960 T-box superfamily

IPR001699 T-box transcription factor

IPR032385 T-box transcription factor-associated

IPR046360 T-box transcription factor, DNA-binding domain

IPR018186 Transcription factor, T-box, conserved site
GlyGen

Q64336 4 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (2 sites)

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All nucleic 53

cDNA 20

Primer pair 14

Other 19

Antibodies 61

Microarray probesets 3

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MGD-MRK-35872

Summaries

All 935

Developmental Gene Expression 870

Diseases 2

Gene Ontology 18

Phenotypes 40
Earliest

J:27413 Bulfone A, et al., T-brain-1: a homolog of Brachyury whose expression defines molecularly distinct domains within the cerebral cortex. Neuron. 1995 Jul;15(1):63-78
Latest

J:391329 Duan CH, et al., Loss of Echs1 in neural stem and progenitor cells impairs neurogenesis via ER stress activation and lipid metabolic reprogramming. Nat Commun. 2026 Jul 1;17(1)

TSS for Tbr1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr17936	Chr2:61634845-61634882 (+)	1,590 bp
Tssr17937	Chr2:61634918-61634971 (+)	1,671 bp
Tssr17938	Chr2:61634982-61634989 (+)	1,712 bp
Tssr17939	Chr2:61635030-61635045 (+)	1,764 bp
Tssr17940	Chr2:61635101-61635110 (+)	1,832 bp
Tssr505	Chr2:61635121-61635131 (+)	1,852 bp
Tssr17941	Chr2:61635231-61635250 (+)	1,967 bp
Tssr17942	Chr2:61635320-61635340 (+)	2,056 bp
Tssr17943	Chr2:61635368-61635382 (+)	2,101 bp
Tssr17944	Chr2:61635384-61635397 (+)	2,117 bp
Tssr17945	Chr2:61642850-61642861 (+)	9,582 bp
Tssr17946	Chr2:61642900-61642919 (+)	9,636 bp
Tssr17947	Chr2:61643288-61643304 (+)	10,022 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/08/2026 MGI 6.24