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Gene: Tbr1 (T-box brain transcription factor 1) Rattus norvegicus

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Symbol:

Tbr1

Name:

T-box brain transcription factor 1

RGD ID:

1591773

Description:

Enables protein kinase binding activity. Involved in cerebral cortex development. Predicted to be active in chromatin and nucleus. Orthologous to human TBR1 (T-box brain transcription factor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bis(2-ethylhexyl) phthalate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC680427; similar to T-box brain gene 1; T-box brain gene 1; T-box brain protein 1; T-box, brain, 1; T-box, brain, 1-like

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	TBR1 (T-box brain transcription factor 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Tbr1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Tbr1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TBR1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TBR1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tbr1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TBR1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TBR1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tbr1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Tbr1 (T-box brain transcription factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TBR1 (T-box brain transcription factor 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tbr1 (T-box brain transcription factor 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tbr1b (T-box, brain, 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	tbx-38	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	tbx-40	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	tbx-37	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	sea-1	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	tbr1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	66,758,805 - 66,769,626 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	66,759,803 - 66,769,626 (+)	Ensembl				GRCr8
mRatBN7.2	3	46,350,237 - 46,368,397 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	46,351,213 - 46,361,041 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	49,696,902 - 49,706,651 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	58,280,420 - 58,290,169 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	56,063,000 - 56,072,814 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	47,677,720 - 47,685,902 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	47,677,720 - 47,685,902 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	54,349,276 - 54,356,654 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	43,647,046 - 43,655,746 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	46,019,111 - 46,026,902 (+)	NCBI		Celera
Cytogenetic Map	3	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISS)

autistic disorder (ISO)

complex cortical dysplasia with other brain malformations (ISO)

epilepsy (ISO)

genetic disease (ISO)

hereditary spastic paraplegia 11 (ISO)

Intellectual Developmental Disorder with Autism and Speech Delay (ISO)

intellectual disability (ISO)

Marfanoid Mental Retardation Syndrome, Autosomal (ISO)

Muscle Hypotonia (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amosite asbestos (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

colforsin daropate hydrochloride (EXP)

crocidolite asbestos (ISO)

diiodine (ISO)

Diisodecyl phthalate (ISO)

enzyme inhibitor (ISO)

epoxiconazole (ISO)

genistein (ISO)

Licochalcone B (ISO)

lipopolysaccharide (ISO)

maneb (ISO)

methylmercury chloride (ISO)

paracetamol (ISO)

paraquat (ISO)

PCB138 (EXP)

pentanal (ISO)

potassium chromate (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

serpentine asbestos (ISO)

testosterone (ISO)

titanium dioxide (ISO)

valproic acid (ISO)

zinc atom (EXP)

zinc(0) (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

amygdala development (ISO)

cell fate specification (IBA)

cerebral cortex development (IEA,IEP,ISO)

chromatin remodeling (IEA,ISO)

commitment of neuronal cell to specific neuron type in forebrain (IBA,ISO)

conditioned taste aversion (ISO)

DNA-templated transcription (IEA)

forebrain neuron differentiation (IEA)

gene expression (IEA,ISO)

hindbrain development (ISO)

negative regulation of DNA-templated transcription (IEA,ISO)

neuron differentiation (ISO)

positive regulation of DNA-templated transcription (IEA)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of axon guidance (ISO)

regulation of DNA-templated transcription (IEA)

regulation of gene expression (ISO)

regulation of neuron projection development (IBA,ISO)

regulation of transcription by RNA polymerase II (IBA)

specification of animal organ identity (ISO)

Cellular Component

chromatin (IBA)

nucleus (IBA,IEA,ISO)

Molecular Function

chromatin DNA binding (IEA,ISO)

DNA binding (IEA,ISO)

DNA-binding transcription factor activity (IEA,ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

protein binding (ISO)

protein kinase binding (IPI)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Nuclear translocation and transcription regulation by the membrane-associated guanylate kinase CASK/LIN-2.	Hsueh YP, etal., Nature. 2000 Mar 16;404(6775):298-302.
3.	GOA pipeline	RGD automated data pipeline
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11967891	PMID:14999075	PMID:15584924	PMID:16202707	PMID:16540585	PMID:20615956	PMID:23144223	PMID:24441682	PMID:25232744	PMID:25931508	PMID:27577752

Genomics

Comparative Map Data

Tbr1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	66,758,805 - 66,769,626 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	66,759,803 - 66,769,626 (+)	Ensembl				GRCr8
mRatBN7.2	3	46,350,237 - 46,368,397 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	46,351,213 - 46,361,041 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	49,696,902 - 49,706,651 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	58,280,420 - 58,290,169 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	56,063,000 - 56,072,814 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	47,677,720 - 47,685,902 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	47,677,720 - 47,685,902 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	54,349,276 - 54,356,654 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	43,647,046 - 43,655,746 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	46,019,111 - 46,026,902 (+)	NCBI		Celera
Cytogenetic Map	3	q21	NCBI

TBR1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	161,416,297 - 161,425,870 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	161,416,297 - 161,425,870 (+)	Ensembl			hg38	GRCh38
GRCh37	2	162,272,808 - 162,282,381 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	161,980,866 - 161,989,819 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	162,098,126 - 162,107,080	NCBI
Celera	2	155,884,680 - 155,893,641 (+)	NCBI		Celera
Cytogenetic Map	2	q24.2	NCBI
HuRef	2	154,157,074 - 154,166,003 (+)	NCBI		HuRef
CHM1_1	2	162,278,783 - 162,287,744 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	161,874,640 - 161,884,225 (+)	NCBI		T2T-CHM13v2.0

Tbr1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	61,633,228 - 61,644,458 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	61,633,274 - 61,644,458 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	61,802,863 - 61,814,114 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	61,802,930 - 61,814,114 (+)	Ensembl			mm10	GRCm38
MGSCv37	2	61,642,510 - 61,652,171 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	61,605,292 - 61,614,953 (+)	NCBI		MGSCv36	mm8
Celera	2	63,506,383 - 63,516,091 (+)	NCBI		Celera
Cytogenetic Map	2	C1.3	NCBI
cM Map	2	35.56	NCBI

Tbr1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955449	12,293,601 - 12,301,272 (-)	Ensembl
ChiLan1.0	NW_004955449	12,293,534 - 12,301,440 (-)	NCBI	ChiLan1.0	ChiLan1.0

TBR1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	13	64,104,948 - 64,117,914 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	64,119,913 - 64,132,886 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	48,709,687 - 48,719,382 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	166,079,344 - 166,089,098 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

TBR1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	36	6,989,644 - 6,997,916 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	6,989,488 - 6,997,900 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	7,126,869 - 7,135,163 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	36	7,114,027 - 7,122,334 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	36	7,113,967 - 7,124,104 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	36	7,130,436 - 7,138,715 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	36	7,174,694 - 7,183,004 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	36	7,282,621 - 7,290,907 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Tbr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	124,127,933 - 124,137,660 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936469	17,479,842 - 17,490,710 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936469	17,481,049 - 17,489,535 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TBR1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	68,213,562 - 68,222,990 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	15	68,208,884 - 68,222,993 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	75,711,701 - 75,721,764 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TBR1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	46,819,396 - 46,831,590 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	46,819,393 - 46,828,008 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	152,709,778 - 152,727,689 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tbr1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624732	4,043,867 - 4,052,551 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624732	4,043,867 - 4,052,621 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Tbr1
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	5	39,447,955 - 39,459,135 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Tbr1
54 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	56
Count of miRNA genes:	44
Interacting mature miRNAs:	52
Transcripts:	ENSRNOT00000065340
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	28625339	67641995	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	35403199	97383526	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	58601291	153936591	Rat
631832	Sach1	Saccharin preference QTL 1	2.7	0.02	consumption behavior trait (VT:0002069)	calculated saccharin drink intake volume (CMO:0001600)	3	47904172	92904172	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	49872657	138829559	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	48657744	93657744	Rat
10450816	Scl75	Serum cholesterol level QTL 75	4.4	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	58601291	71157804	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	37796919	82796919	Rat
2313093	Bmd77	Bone mineral density QTL 77	2.2	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	3	47904172	70710963	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	38708931	67641995	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	38708931	67641995	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	38708931	67641995	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	36721849	110333156	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	38708931	67641995	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	38708931	67641995	Rat
2313101	Bmd76	Bone mineral density QTL 76	3.6	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	3	47904172	70710963	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	38708931	67641995	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	67641995	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	48657744	93657744	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	1	141509147	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	36101403	81101403	Rat
10450852	Stl33	Serum triglyceride level QTL 33	3.4	0.05	blood LDL triglyceride amount (VT:0010699)	blood lipoprotein triglyceride level (CMO:0002685)	3	58601291	71157804	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	5675975	141509147	Rat
4889975	Bmd81	Bone mineral density QTL 81	4.3		tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	3	59119402	70710963	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	51490129	111359995	Rat
634317	Bw117	Body weight QTL 117	3.58		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	59863663	73704481	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	59863663	87321459	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	51581665	184004958	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	53651826	98651826	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	48876619	93876619	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	48876619	93876619	Rat
2313079	Bss73	Bone structure and strength QTL 73	1.5		tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	3	47904172	70710963	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	87321459	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
2313076	Bss74	Bone structure and strength QTL 74	2	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	3	47904172	70710963	Rat
1300169	Bp177	Blood pressure QTL 177	2.96		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	3	36425116	81425116	Rat
10450813	Scl74	Serum cholesterol level QTL 74	5.8	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	58601291	71157804	Rat
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	83358329	Rat
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	58925062	103925062	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	48657744	93657744	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	50766145	95766145	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	50766145	95766145	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	42158111	124558371	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	83708931	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	48657744	93657744	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	37363734	82363734	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	48657744	93657744	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	42158111	124558371	Rat
2313049	Bss72	Bone structure and strength QTL 72	2.6	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	3	47904172	70710963	Rat

Markers in Region

TBR1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	3	66,762,109 - 66,762,807 (+)	Marker Load Pipeline
Rnor_6.0	3	47,679,772 - 47,680,465	NCBI	Rnor6.0
Rnor_5.0	3	54,351,328 - 54,352,021	UniSTS	Rnor5.0
RGSC_v3.4	3	43,653,001 - 43,653,694	UniSTS	RGSC3.4
Celera	3	46,021,163 - 46,021,856	UniSTS
Cytogenetic Map	3	q21	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
13	3	39	147	40	42	19	60	19	6	185	116	4	138	35	84	23	15	15

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191070	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105842	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BF281828	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212619	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000065340 ⟹ ENSRNOP00000059530

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	66,759,803 - 66,769,626 (+)	Ensembl
mRatBN7.2 Ensembl	3	46,351,213 - 46,361,041 (+)	Ensembl
Rnor_6.0 Ensembl	3	47,677,720 - 47,685,902 (+)	Ensembl

RefSeq Acc Id:

NM_001191070 ⟹ NP_001177999

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	66,759,803 - 66,769,626 (+)	NCBI
mRatBN7.2	3	46,351,213 - 46,361,041 (+)	NCBI
Rnor_6.0	3	47,677,720 - 47,685,902 (+)	NCBI
Rnor_5.0	3	54,349,276 - 54,356,654 (+)	NCBI
Celera	3	46,019,111 - 46,026,902 (+)	NCBI

Sequence:

show sequence

ATGCAGCTGGAGCATTGCCTCTCTCCTTCTATCATGCTCTCCAAGAAATTTCTCAATGTGAGCA
GCAGCTACCCACATTCGGGCGGATCTGAGCTTGTCTTGCATGATCATCCCATTATCTCGACCAC
TGACAACCTGGAGAGAAGTTCACCTTTGAAAAAAATTACCAGGGGGATGACGAATCAGTCAGAT
ACAGACAATTTTCCTGACTCCAAGGACTCACCAGGGGACGTCCAGAGAAGTAAACTCTCTCCTG
TCTTGGACGGGGTCTCTGAGCTTCGTCACAGTTTCGATGGCTCTGCTGCAGATCGTTACCTCCT
CTCTCAGTCCAGCCAGCCACAGTCTGCGGCCACCGCTCCCAGTGCCATGTTCCCGTACCCCGGC
CAGCACGGACCGGCGCATCCCGCCTTCTCCATCGGCAGCCCCAGTCGCTACATGGCCCACCACC
CGGTCATCACCAACGGAGCTTACAACAGCCTGCTGTCCAACTCTTCGCCGCAGGGCTACCCCAC
CGCCGGCTACCCCTACCCACAGCAGTACGGCCACTCCTACCAAGGAGCCCCATTCTACCAGTTC
TCCTCCACCCAGCCCGGGTTGGTGCCCGGCAAGGCGCAGGTATACCTGTGCAACAGGCCACTTT
GGCTGAAATTTCATCGGCATCAAACGGAGATGATCATCACTAAACAGGGAAGGCGCATGTTTCC
CTTTTTGAGTTTTAACATTTCTGGTCTCGATCCCACCGCTCATTACAATATTTTTGTGGATGTG
ATTTTGGCGGATCCCAATCACTGGAGGTTTCAAGGAGGCAAATGGGTTCCTTGTGGCAAAGCGG
ACACCAATGTGCAAGGAAACCGGGTCTATATGCATCCGGATTCCCCCAACACTGGGGCTCACTG
GATGCGGCAAGAAATCTCGTTTGGAAAATTAAAACTTACCAACAACAAGGGAGCATCAAACAAC
AATGGGCAGATGGTGGTTTTACAGTCCCTGCACAAGTACCAGCCCCGTCTGCACGTGGTGGAAG
TGAATGAGGACGGCACAGAGGACACCAGCCAGCCAGGCCGCGTCCAGACGTTCACTTTCCCAGA
GACTCAGTTCATCGCTGTCACCGCCTATCAGAACACCGATGTACAACAACTAAAAATAGATCAT
AACCCCTTTGCAAAAGGATTTCGAGATAACTATGACACGATCTACACGGGCTGCGACATGGACC
GCTTGACCCCGTCGCCCAACGACTCTCCGCGCTCTCAGATCGTGCCCGGCGCTCGCTACGCCAT
GGCCGGCTCTTTCCTGCAAGATCAATTCGTGAGCAACTACGCCAAGGCCCGCTTCCACCCGGGC
GCCGGCGCGGGCCCCGGGCCTGGCACGGACCGCAGCGTGCCGCACACCAACGGGCTACTGTCCC
CGCAACAGGCCGAGGACCCGGGCGCGCCGTCGCCGCAGCGCTGGTTCGTGACGCCGGCCAACAA
CCGGCTGGACTTCGCGGCCTCGGCCTACGATACGGCCACGGACTTCGCCGGCAACGCGGCCACG
CTGCTGTCGTACGCGGCCGCGGGCGTGAAGGCGCTGCCGCTGCAGGCCGCGGGCTGCACGGGCC
GCCCGCTCGGCTACTACGCCGACCCTTCCGGCTGGGGCGCGCGCAGCCCTCCGCAGTACTGCGG
CGCCAAGTCGGGCTCCGTGCTCCCCTGCTGGCCCAACAGCGCTGCGGCCGCCGCGCGCATGGCG
GGCGCCAACCCCTACTTAGGCGAGGAGGCCGAGGGCCTGGCGGCCGAGCGCTCTCCGCTGGCGC
CCGCCGCCGAGGACGCCAAGCCCAAGGACCTGTCCGACTCCAGCTGGATCGAGACGCCCTCCTC
GATCAAGTCCATCGACTCGAGCGACTCGGGGATTTACGAGCAGGCCAAGCGGAGGCGGATCTCT
CCGGCCGACACGCCGGTGTCCGAGAGCTCGTCCCCACTCAAGAGCGAGGTGCTGGCCCAGCGGG
ACTGCGAGAAGAACTGCGCCAAGGACATAGGCGGCTACTATGGCTTCTACTCGCACAGCTAG

hide sequence

RefSeq Acc Id:

XM_039105842 ⟹ XP_038961770

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	66,758,805 - 66,769,626 (+)	NCBI
mRatBN7.2	3	46,350,237 - 46,368,397 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001177999	(Get FASTA)	NCBI Sequence Viewer
	XP_038961770	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000059530
	ENSRNOP00000059530.4

RefSeq Acc Id:

NP_001177999 ⟸ NM_001191070

- UniProtKB:

D4A6N8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MQLEHCLSPSIMLSKKFLNVSSSYPHSGGSELVLHDHPIISTTDNLERSSPLKKITRGMTNQSD
TDNFPDSKDSPGDVQRSKLSPVLDGVSELRHSFDGSAADRYLLSQSSQPQSAATAPSAMFPYPG
QHGPAHPAFSIGSPSRYMAHHPVITNGAYNSLLSNSSPQGYPTAGYPYPQQYGHSYQGAPFYQF
SSTQPGLVPGKAQVYLCNRPLWLKFHRHQTEMIITKQGRRMFPFLSFNISGLDPTAHYNIFVDV
ILADPNHWRFQGGKWVPCGKADTNVQGNRVYMHPDSPNTGAHWMRQEISFGKLKLTNNKGASNN
NGQMVVLQSLHKYQPRLHVVEVNEDGTEDTSQPGRVQTFTFPETQFIAVTAYQNTDVQQLKIDH
NPFAKGFRDNYDTIYTGCDMDRLTPSPNDSPRSQIVPGARYAMAGSFLQDQFVSNYAKARFHPG
AGAGPGPGTDRSVPHTNGLLSPQQAEDPGAPSPQRWFVTPANNRLDFAASAYDTATDFAGNAAT
LLSYAAAGVKALPLQAAGCTGRPLGYYADPSGWGARSPPQYCGAKSGSVLPCWPNSAAAAARMA
GANPYLGEEAEGLAAERSPLAPAAEDAKPKDLSDSSWIETPSSIKSIDSSDSGIYEQAKRRRIS
PADTPVSESSSPLKSEVLAQRDCEKNCAKDIGGYYGFYSHS

hide sequence

Ensembl Acc Id:

ENSRNOP00000059530 ⟸ ENSRNOT00000065340

RefSeq Acc Id:	XP_038961770 ⟸ XM_039105842
- Peptide Label:	isoform X1

Protein Domains

T-box

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A6N8-F1-model_v2	AlphaFold	D4A6N8	1-680	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1591773	AgrOrtholog
BioCyc Gene	G2FUF-49598	BioCyc
Ensembl Genes	ENSRNOG00000005049	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000065340	ENTREZGENE
	ENSRNOT00000065340.5	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.820	UniProtKB/TrEMBL
InterPro	p53-like_TF_DNA-bd	UniProtKB/TrEMBL
	T-box_assoc	UniProtKB/TrEMBL
	T-box_DNA-bd	UniProtKB/TrEMBL
	T-box_sf	UniProtKB/TrEMBL
	TF_T-box	UniProtKB/TrEMBL
	TF_T-box_CS	UniProtKB/TrEMBL
KEGG Report	rno:680427	UniProtKB/TrEMBL
NCBI Gene	680427	ENTREZGENE
PANTHER	PTHR11267	UniProtKB/TrEMBL
	T-BOX BRAIN PROTEIN 1	UniProtKB/TrEMBL
Pfam	T-box	UniProtKB/TrEMBL
	T-box_assoc	UniProtKB/TrEMBL
PhenoGen	Tbr1	PhenoGen
PRINTS	TBOX	UniProtKB/TrEMBL
PROSITE	TBOX_1	UniProtKB/TrEMBL
	TBOX_2	UniProtKB/TrEMBL
	TBOX_3	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000005049	RatGTEx
SMART	TBOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49417	UniProtKB/TrEMBL
UniProt	D4A6N8	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-08-05	Tbr1	T-box brain transcription factor 1	Tbr1	T-box, brain, 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-05-24	Tbr1	T-box, brain, 1	LOC100365364	T-box, brain, 1-like	Data merged from RGD:2319214	1643240	APPROVED
2010-05-05	LOC100365364	T-box, brain, 1-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-11-14	Tbr1	T-box, brain, 1	Tbr1	T-box brain gene 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-05	Tbr1	T-box brain gene 1	LOC680427	similar to T-box brain gene 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-01-09	LOC680427	similar to T-box brain gene 1	LOC679107	similar to T-box brain gene 1	Data merged from RGD:1591885	1643240	APPROVED
2006-11-20	LOC680427	similar to T-box brain gene 1			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC679107	similar to T-box brain gene 1			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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