Tbx6 (T-box 6) - Rat Genome Database

Name: Tbx6
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Advanced Search (OLGA)

Gene: Tbx6 (T-box 6) Mus musculus

Analyze

Symbol:

Tbx6

Name:

T-box 6

RGD ID:

1317069

MGI Page

MGI

Description:

Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in negative regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including negative regulation of neuron maturation; regulation of gene expression; and somite rostral/caudal axis specification. Located in nucleus. Part of chromatin. Is expressed in several structures, including 4-cell stage embryo; embryo ectoderm; embryo mesenchyme; genitourinary system; and primitive streak. Used to study spondylocostal dysostosis. Human ortholog(s) of this gene implicated in spondylocostal dysostosis 5. Orthologous to human TBX6 (T-box transcription factor 6).

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

rib-vertebrae; rv; T-box protein 6; T-box transcription factor TBX6

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):	TBX6 (T-box transcription factor 6)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Rattus norvegicus (Norway rat):	Tbx6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Tbx6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TBX6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TBX6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tbx6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TBX6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TBX6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tbx6 (T-box transcription factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Tbx6 (T-box transcription factor 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	TBX6 (T-box transcription factor 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tbx6 (T-box 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid\|ZFIN)
Drosophila melanogaster (fruit fly):	Doc1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Doc2	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Doc3	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	tbx16l	Alliance	DIOPT (OrthoFinder\|PANTHER\|ZFIN)
Caenorhabditis elegans (roundworm):	tbx-40	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	sea-1	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	tbx6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCm39 - Mouse Genome Assembly GRCm39

Position:

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	126,380,655 - 126,384,720 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	126,380,655 - 126,384,732 (+)	Ensembl		GRCm39 Ensembl
GRCm38	7	126,781,483 - 126,785,548 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	126,781,483 - 126,785,560 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	133,924,997 - 133,929,062 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	126,572,631 - 126,576,696 (+)	NCBI		MGSCv36	mm8
Celera	7	126,628,828 - 126,632,893 (+)	NCBI		Celera
Cytogenetic Map	7	F3	NCBI
cM Map	7	69.25	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

autistic disorder (ISO)

CAKUT (ISO)

chromosome 16p11.2 deletion syndrome, 593-kb (ISO)

chromosome 16p11.2 duplication syndrome (ISO)

coronin-1A deficiency (ISO)

dilated cardiomyopathy (ISO)

Episodic Kinesigenic Dyskinesia (ISO)

episodic kinesigenic dyskinesia 1 (ISO)

genetic disease (ISO)

Glycogen Storage Disease XII (ISO)

Neurodevelopmental Disorders (ISO)

schizophrenia (ISO)

scoliosis (ISO)

spondylocostal dysostosis (ISO)

spondylocostal dysostosis 2 (ISO)

spondylocostal dysostosis 5 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

2,4-di-tert-butylphenol (ISO)

2-hydroxypropanoic acid (ISO)

6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (EXP)

6-propyl-2-thiouracil (ISO)

all-trans-retinoic acid (ISO)

amitrole (ISO)

aphidicolin (EXP)

arsenous acid (ISO)

benzo[a]pyrene (EXP,ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

butylated hydroxyanisole (EXP)

cadmium dichloride (ISO)

carbon nanotube (EXP)

CHIR 99021 (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

diethylstilbestrol (EXP)

dolutegravir (ISO)

endosulfan (ISO)

fluoxetine (EXP)

folic acid (EXP,ISO)

hydroxyurea (EXP)

lipopolysaccharide (ISO)

methimazole (ISO)

methotrexate (EXP)

methoxyacetic acid (EXP)

methylmercury chloride (EXP)

N-ethyl-N-nitrosourea (EXP)

niclosamide (ISO)

ozone (EXP)

phenobarbital (ISO)

pirinixic acid (ISO)

rac-lactic acid (ISO)

resveratrol (EXP,ISO)

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

SB 431542 (ISO)

sodium arsenite (EXP)

trichloroethene (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell fate specification (IBA)

heart looping (IBA)

mesoderm formation (IMP)

mesodermal cell fate specification (IMP)

negative regulation of DNA-binding transcription factor activity (IDA)

negative regulation of neuron maturation (IGI)

negative regulation of neuron projection development (IGI)

negative regulation of transcription by RNA polymerase II (IDA)

positive regulation of DNA-templated transcription (IEA)

positive regulation of transcription by RNA polymerase II (IDA)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IBA)

signal transduction involved in regulation of gene expression (IDA)

somite rostral/caudal axis specification (IDA)

vasculogenesis (IBA)

Cellular Component

chromatin (IBA,IDA)

nucleoplasm (TAS)

nucleus (IBA,IDA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity (IEA)

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

protein binding (ISO)

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

RNA polymerase II-specific DNA-binding transcription factor binding (IPI)

sequence-specific double-stranded DNA binding (ISO)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal cervical atlas morphology (IAGP)

abnormal cervical vertebrae morphology (IAGP)

abnormal digestive system development (IAGP)

abnormal direction of embryo turning (IAGP)

abnormal direction of heart looping (IAGP)

abnormal embryo development (IAGP)

abnormal intersomitic artery morphology (IAGP)

abnormal intervertebral disk development (IAGP)

abnormal lumbar vertebrae morphology (IAGP)

abnormal mesoderm development (IAGP)

abnormal motile primary cilium morphology (IAGP)

abnormal motile primary cilium physiology (IAGP)

abnormal neural tube morphology (IAGP)

abnormal notochord morphology (IAGP)

abnormal paraxial mesoderm morphology (IAGP)

abnormal somite development (IAGP)

abnormal tail development (IAGP)

abnormal thoracic vertebrae morphology (IAGP)

abnormal vascular development (IAGP)

abnormal vertebrae development (IAGP)

abnormal vertebrae morphology (IAGP)

abnormal vertebral arch development (IAGP)

abnormal vertebral articular process morphology (IAGP)

abnormal vertebral body development (IAGP)

abnormal vertebral column morphology (IAGP)

abnormal vertebral transverse process morphology (IAGP)

cervical vertebral fusion (IAGP)

decreased body length (IAGP)

decreased embryonic cilium length (IAGP)

embryonic lethality during organogenesis, complete penetrance (IAGP)

enlarged tail bud (IAGP)

enlarged vertebral body (IAGP)

fused somites (IAGP)

fusion of vertebral arches (IAGP)

fusion of vertebral bodies (IAGP)

hematoma (IAGP)

impaired somite development (IAGP)

kidney cyst (IAGP)

kinked neural tube (IAGP)

kinked tail (IAGP)

prenatal lethality, complete penetrance (IAGP)

reduced female fertility (IAGP)

rib fusion (IAGP)

short tail (IAGP)

single kidney (IAGP)

small vertebral body (IAGP)

vertebral fusion (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	MGDs mouse GO annotations	MGD data from the GO Consortium
2.	MGD IEA	MGD IEA
3.	Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos.	Neidhardt L, etal., Mech Dev 2000 Nov;98(1-2):77-94.
4.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
5.	HNF3beta and Lim1 interact in the visceral endoderm to regulate primitive streak formation and anterior-posterior polarity in the mouse embryo.	Perea-Gomez A, etal., Development 1999 Oct;126(20):4499-511.
6.	Mouse MP Annotation Import Pipeline	RGD automated import pipeline
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Tbt-1, a new T-box transcription factor induced in activated Th1 and CD8+ T cells.	Shier P, etal., Immunogenetics 2000 Aug;51(10):771-8.
10.	Dll1 is a downstream target of Tbx6 in the paraxial mesoderm.	White PH and Chapman DL, Genesis. 2005 Jul;42(3):193-202.
11.	Regulation of Tbx6 expression by Notch signaling.	White PH, etal., Genesis. 2005 Jun;42(2):61-70.

Additional References at PubMed

PMID:4073528	PMID:8878690	PMID:8889548	PMID:8954725	PMID:9490412	PMID:9770268	PMID:9933572	PMID:10021340	PMID:10090727	PMID:10203826	PMID:10421635	PMID:10617567
PMID:10837126	PMID:10906448	PMID:11002339	PMID:11124811	PMID:11290295	PMID:11703922	PMID:12135932	PMID:12177162	PMID:12431380	PMID:12464437	PMID:12477932	PMID:12588859
PMID:12620991	PMID:12748966	PMID:12915233	PMID:13129926	PMID:14681479	PMID:15057272	PMID:15136723	PMID:15142971	PMID:15170225	PMID:15545628	PMID:15618518	PMID:15755804
PMID:15857914	PMID:16109169	PMID:16127714	PMID:16467359	PMID:16505380	PMID:16602821	PMID:16751104	PMID:16801545	PMID:16943278	PMID:17117439	PMID:17507393	PMID:17507402
PMID:17584735	PMID:17668009	PMID:17681139	PMID:18045842	PMID:18157121	PMID:18171685	PMID:18287559	PMID:18347064	PMID:18356246	PMID:18403408	PMID:18448090	PMID:18462699
PMID:18498097	PMID:18519639	PMID:18575602	PMID:18579680	PMID:18849530	PMID:19539783	PMID:19561075	PMID:19786569	PMID:19853565	PMID:19906845	PMID:19956724	PMID:20335362
PMID:20346937	PMID:20630950	PMID:20637190	PMID:20832395	PMID:21098559	PMID:21267068	PMID:21331042	PMID:21368122	PMID:21445260	PMID:21555575	PMID:21693517	PMID:21731673
PMID:21750544	PMID:21799763	PMID:21873635	PMID:21909376	PMID:22164283	PMID:22484060	PMID:22546692	PMID:22675207	PMID:22721678	PMID:22954964	PMID:23015435	PMID:23326414
PMID:23671110	PMID:23747598	PMID:23830831	PMID:24284205	PMID:24318810	PMID:24633704	PMID:24803591	PMID:25152336	PMID:25371364	PMID:25641698	PMID:25813538	PMID:26305214
PMID:26534985	PMID:26593875	PMID:27760115	PMID:27930333	PMID:28606934	PMID:28619992	PMID:28664156	PMID:29084802	PMID:29141987	PMID:29203676	PMID:29650695	PMID:29761784
PMID:29895619	PMID:29915126	PMID:30100166	PMID:30201686	PMID:30307510	PMID:30548789	PMID:30578417	PMID:30661984	PMID:31010673	PMID:31888956	PMID:32156757	PMID:32439762
PMID:32561646	PMID:32597756	PMID:32855167	PMID:33210601	PMID:34256037	PMID:34446717	PMID:35276131	PMID:35514236	PMID:35876795	PMID:35950911	PMID:36123354	PMID:36197846
PMID:36517595	PMID:37024462	PMID:37414952	PMID:38345319

Genomics

Comparative Map Data

Tbx6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	126,380,655 - 126,384,720 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	126,380,655 - 126,384,732 (+)	Ensembl		GRCm39 Ensembl
GRCm38	7	126,781,483 - 126,785,548 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	126,781,483 - 126,785,560 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	133,924,997 - 133,929,062 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	126,572,631 - 126,576,696 (+)	NCBI		MGSCv36	mm8
Celera	7	126,628,828 - 126,632,893 (+)	NCBI		Celera
Cytogenetic Map	7	F3	NCBI
cM Map	7	69.25	NCBI

TBX6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	16	30,085,793 - 30,091,924 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	30,085,793 - 30,091,924 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	30,097,114 - 30,103,245 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	30,004,583 - 30,010,709 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	16	30,004,582 - 30,010,709	NCBI
Celera	16	72,692,515 - 72,698,605 (+)	NCBI		Celera
Cytogenetic Map	16	p11.2	NCBI
HuRef	16	27,758,384 - 27,764,471 (-)	NCBI		HuRef
CHM1_1	16	31,312,871 - 31,318,962 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	16	30,368,436 - 30,374,583 (-)	NCBI		T2T-CHM13v2.0

Tbx6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	190,818,397 - 190,823,824 (+)	NCBI		GRCr8
mRatBN7.2	1	181,387,851 - 181,392,762 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	181,388,684 - 181,392,593 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	189,739,992 - 189,743,901 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	196,926,065 - 196,929,974 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	189,593,407 - 189,597,316 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	198,214,797 - 198,218,706 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	198,214,797 - 198,218,706 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	205,194,665 - 205,198,574 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	185,957,068 - 185,960,977 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	186,106,948 - 186,110,858 (+)	NCBI
Celera	1	179,044,203 - 179,048,112 (+)	NCBI		Celera
Cytogenetic Map	1	q36	NCBI

Tbx6
(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_004955493	6,888,832 - 6,894,831 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955493	6,888,832 - 6,894,840 (+)	NCBI	ChiLan1.0	ChiLan1.0

TBX6
(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	18	30,835,101 - 30,841,791 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	16	35,384,089 - 35,390,860 (+)	NCBI		NHGRI_mPanPan1
PanPan1.1	16	30,460,305 - 30,467,090 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	16	30,460,305 - 30,467,070 (-)	Ensembl	panpan1.1		panPan2

TBX6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	18,093,201 - 18,098,592 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	18,093,189 - 18,097,636 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	19,671,796 - 19,677,028 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	18,229,138 - 18,233,798 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	18,229,553 - 18,233,575 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	18,028,090 - 18,033,321 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	17,943,488 - 17,948,720 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	18,259,114 - 18,263,768 (-)	NCBI		UU_Cfam_GSD_1.0

Tbx6
(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_024409344	124,304,611 - 124,309,711 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936501	12,402,724 - 12,407,571 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936501	12,402,709 - 12,407,571 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TBX6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	18,271,983 - 18,277,580 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	18,271,983 - 18,277,864 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

TBX6
(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	5	26,566,673 - 26,573,258 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	5	26,567,700 - 26,572,820 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666068	2,965,580 - 2,971,082 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tbx6
(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_004624782	13,169,719 - 13,174,056 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624782	13,169,096 - 13,174,498 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tbx6
153 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	388
Count of miRNA genes:	225
Interacting mature miRNAs:	241
Transcripts:	ENSMUST00000094037, ENSMUST00000172352
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 (GRCm39)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1357460	Vtbt4_m	vertebral trabecular bone trait 4 (mouse)			Not determined		7	101693381	135693530	Mouse
11059561	Lmr21a_m	leishmaniasis resistance 21a (mouse)					7	117750722	127967336	Mouse
25314307	Mlh1fc2_m	MLH1 foci count 2 (mouse)					7	6502999	133501729	Mouse
38501066	Tip2_m	tuberculosis immunophenotype 2, spleen CFU (mouse)					7	124299223	126899172	Mouse
27095903	Scvln10_m	sacral vertebrae length 2, 10 week (mouse)					7	81449748	126499172	Mouse
11059562	Lmr21b_m	leishmaniasis resistance 21b (mouse)					7	110967235	144967336	Mouse
26884440	Sklq4_m	skull length QTL 4, 5 week (mouse)					7	65249748	126499172	Mouse
1302032	Alcp12_m	alcohol preference locus 12 (mouse)			Not determined		7	111166122	144995196	Mouse
27226778	Femd11_m	femur midshaft diameter 11, 16 week (mouse)					7	56949748	134001729	Mouse
4141945	Il4ppq_m	IL-4 producing potential QTL (mouse)			Not determined		7	124513662	128819324	Mouse
11039524	Tbbr3_m	Trypanosoma brucei brucei response 3 (mouse)					7	100750722	134750843	Mouse
27226769	Tibl12_m	tibia length 12, 10 week (mouse)					7	87249208	126499172	Mouse
12792978	Fbmd3_m	femoral bone mineral density 3, females only (mouse)					7	7050288	142367832	Mouse
27226765	Tibl18_m	tibia length 18, 16 week (mouse)					7	81849748	126499172	Mouse
4142444	Femwf5_m	femur work to failure 5 (mouse)			Not determined			112552248	144995196	Mouse
1301447	Fembm3_m	femoral bone morphometry 3 (mouse)			Not determined		7	100993261	134993342	Mouse
1300677	Bmd9_m	bone mineral density 9 (mouse)			Not determined		7	116634089	144995196	Mouse
10412104	Tons2_m	tongue size 2 (mouse)			Not determined		7	99837716	133837716	Mouse
4142312	Nilac4_m	nicotine induced locomotor activity 4 (mouse)			Not determined		7	102485219	136485380	Mouse
1300747	Skts2_m	skin tumor susceptibility 2 (mouse)			Not determined		7	112922733	144995196	Mouse
1301898	Alcp14_m	alcohol preference locus 14 (mouse)			Not determined		7	111166122	144995196	Mouse
1357711	Adbg1_m	adult body growth 1 (mouse)			Not determined		7	118693381	144398314	Mouse
38501072	Stsl7_m	Salmonella typhimurium susceptibility locus 7 (mouse)					7	115699235	128501724	Mouse
1301903	Tlsm1_m	thymic lymphoma susceptible 1 (mouse)			Not determined		7	122250663	135170901	Mouse
10402499	Lmr21_m	leishmaniasis resistance 21 (mouse)			Not determined		7	110967235	144967336	Mouse
1301773	Stheal7_m	soft tissue heal 7 (mouse)			Not determined		7	119132573	144995196	Mouse
27226751	Femd5_m	femur midshaft diameter 5, 10 week (mouse)					7	53249748	143153737	Mouse
27095933	Ulnl3_m	ulna length 3, 5 week (mouse)					7	73149748	143153737	Mouse
1300721	Cfbw3_m	cystic fibrosis body weight 3 (mouse)			Not determined		7	101693381	135693530	Mouse
1301105	Cfld4_m	cystic fibrosis lung disease 4 (mouse)			Not determined		7	101693381	135693530	Mouse
1300528	Ssial3_m	susceptibility to sialadenitis 3 (mouse)			Not determined		7	93391848	127392041	Mouse
27095930	Ulnl10_m	ulna length 10, 16 week (mouse)					7	80849748	126699172	Mouse
5491192	Mobq1_m	multigenic obesity QTL 1 (mouse)			Not determined		7	105250663	139250811	Mouse
14700684	Civq1_m	cerebral infarct volume QTL 1 (mouse)					7	109707335	143707335	Mouse
1300670	Sluc19_m	susceptibility to lung cancer 19 (mouse)			Not determined		7	111166122	144995196	Mouse
14700687	Civq5_m	cerebral infarct volume QTL 5 (mouse)					7	109707335	143707335	Mouse
14700688	Civq6_m	cerebral infarct volume QTL 6 (mouse)					7	109707335	143707335	Mouse
26884398	Humsd6_m	humerus midshaft diameter 6, 16 week (mouse)					7	78649748	136901729	Mouse
1301478	Eae26_m	susceptibility to experimental allergic encephalomyelitis 26 (mouse)			Not determined		7	98164922	132165010	Mouse
1301158	Eae4_m	susceptibility to experimental allergic encephalomyelitis 4 (mouse)			Not determined		7	19147398	141919804	Mouse
1357613	Bsbob2_m	BSB obesity 2 (mouse)			Not determined		7	122250663	128819324	Mouse
27226790	Feml15_m	femur length 15, 10 week (mouse)					7	87249208	126499172	Mouse
13524852	Asrq7a_m	acoustic startle response 7a (mouse)					7	105350008	139350008	Mouse
13524850	Asrq7_m	acoustic startle response 7 (mouse)					7	98394974	132394974	Mouse
15092059	Wogrme1_m	week one growth rate, maternal effect 1 (mouse)					7	117199227	134101729	Mouse

Markers in Region

Tbx6

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	7	F3	UniSTS
cM Map	7	61.0	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.

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_011538	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC124505	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AI152111	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AW047428	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY654733	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC140951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BF607954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH466531	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905856	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905857	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905859	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905860	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905861	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ905862	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM027349	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM027350	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM027351	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	HM027352	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U57331	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSMUST00000094037 ⟹ ENSMUSP00000091579

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39 Ensembl	7	126,380,655 - 126,384,732 (+)	Ensembl
GRCm38.p6 Ensembl	7	126,781,483 - 126,785,560 (+)	Ensembl

Ensembl Acc Id:

ENSMUST00000172352 ⟹ ENSMUSP00000126418

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39 Ensembl	7	126,380,655 - 126,384,531 (+)	Ensembl
GRCm38.p6 Ensembl	7	126,781,483 - 126,785,359 (+)	Ensembl

RefSeq Acc Id:

NM_011538 ⟹ NP_035668

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39	7	126,380,655 - 126,384,720 (+)	NCBI
GRCm38	7	126,781,483 - 126,785,548 (+)	NCBI
MGSCv37	7	133,924,997 - 133,929,062 (+)	RGD
Celera	7	126,628,828 - 126,632,893 (+)	RGD
cM Map	7		ENTREZGENE

Sequence:

show sequence

CACAAGGCCAGAAGAAACTACAACATGTACCATCCACGAGAGTTGTACCCCTCCCTGGGGACTG
GCTACCGTCTGGGACACCCCCAGCCTGGGGCAGACTCCACCTTCCCACCTGCCCTGACAGAGGG
TTACCGCTACCCTGATTTGGATACTTCTAAACTGGATTGCTTCCTCTCTGGGATCGAGGCAGCT
CCCCACACTCTGGCTGCAGCCGCTCCTTTGCCCCTTCTCCCATCTGCTCTGGGCCCCGAGACAG
CACCGCCACCCCCAGAGGCCCTTCACTCGCTTCCTGGGGTCAGCCTGAGCTTGGAGAACCAGGA
ACTGTGGAAGGAATTCAGCGCTGTGGGGACAGAGATGATCATCACCAAGGCTGGCAGGCGCATG
TTCCCTGCTTGCCGAGTATCAGTCACTGGCCTGGACCCAGAGGCCCGCTACTTGTTTCTTCTGG
ATGTGGTTCCAGTGGATGGGGCCCGATACCGCTGGCAGGGCCAGCACTGGGAGCCAAGTGGCAA
GGCTGAACCCCGCCTACCCGACCGTGTCTACATTCACCCTGACTCTCCTGCCACTGGTGCCCAC
TGGATGCGGCAGCCCGTATCCTTCCATCGTGTTAAGCTCACCAACAGCACACTGGACCCCCATG
GCCACCTGATCTTGCACTCGATGCACAAGTACCAGCCTCGCATCCACCTGGTGAGAGCCACCCA
ACTATGCAGCCAACACTGGGGGGGTGTGGCCTCCTTCCGATTTCCTGAGACCACATTCATCTCT
GTGACAGCCTACCAGAACCCTAGGATCACACAGCTGAAGATCGCAGCCAATCCCTTTGCCAAAG
GTTTCCGAGAAAATGGCAGAAACTGTAAGAGGGAGCGGGATGCCCGTGTGAAGAGGAAACTTCG
GGGCCCAGAGCCAGTGGCCACAGAGGCCTGTGGGAGTGGGGATACACCAGGGGGTCCCTGTGAC
TCCACCCTGGGTGGGGACATTCGGGACTCAGATCCAGAGCAGGCCCCAACCCCCCAGGAAGCTG
CTTCTGCCTCAGCTCCTCCATGTGGGGGCCCCAGTGCTGAGGCCTACCTTCTACACCCTGCCGC
TTTTCATGGCGCCCCCAGTCACCTACCAGCCAGGACCCCCAGCTTCGCTGAGGCTCCAGACCCT
GGGCGCCCAGCCCCCTACTCAGCTGCATTTCTGGACCTACAGCCTGGACCAGGGGGCTCTGCCT
ATCAGGCAGCTCCATCTGTACCATCCTTTGCCCCACACTTCATCCAAGGGGGTCCCTTCCCTCT
ACCGTACCCAGGACCTGGAGGTTATCTGGACATGGGATCCAAGCCAATGTACTGAGCCTCGGTG
TAGTAACCCTATGCCATCTTCCCTTGATCCTCCAGCTCCCTTCCCCCAGCCTGGTAGCATCCGC
ATTGAAGTGGTATCCCCCTCCCCCCCACCAAATGGCTGGCTTGGGCCTCTCTTCCACCCTTTAG
TTCACACCTTGATTTCACTCCACCCCCTCTGGCTTCAAAGCTCAGGCAAGGCAGCTCTGAGTCC
AGCTGGGGCCTGCTTCCCCTCAGCTCTCACCTTAGTGCGAATGGAGGGAGCCTCTGCCTGGCCA
AATGGGGCTCCCAGCCCAGTACCCCCACCTCCTGGGGGCCTTGTTACTAGTGCAAGCCATGCCA
ATTTGTTCTCAGGATCAGAGTATTTTTGTTAATAAAACTCCAAAGACATTAAAAAAAAAAAAAA
AAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_035668	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC53110	(Get FASTA)	NCBI Sequence Viewer
	AAI40952	(Get FASTA)	NCBI Sequence Viewer
	AAT72924	(Get FASTA)	NCBI Sequence Viewer
	ADN33270	(Get FASTA)	NCBI Sequence Viewer
	ADN33271	(Get FASTA)	NCBI Sequence Viewer
	ADN33272	(Get FASTA)	NCBI Sequence Viewer
	ADN33273	(Get FASTA)	NCBI Sequence Viewer
	ADN94739	(Get FASTA)	NCBI Sequence Viewer
	ADN94740	(Get FASTA)	NCBI Sequence Viewer
	ADN94742	(Get FASTA)	NCBI Sequence Viewer
	ADN94743	(Get FASTA)	NCBI Sequence Viewer
	ADN94744	(Get FASTA)	NCBI Sequence Viewer
	ADN94745	(Get FASTA)	NCBI Sequence Viewer
	EDL17437	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSMUSP00000091579
	ENSMUSP00000091579.5
	ENSMUSP00000126418.2
GenBank Protein	P70327	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_035668 ⟸ NM_011538

- UniProtKB:

B2RU37 (UniProtKB/Swiss-Prot), Q5SDA2 (UniProtKB/Swiss-Prot), P70327 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MYHPRELYPSLGTGYRLGHPQPGADSTFPPALTEGYRYPDLDTSKLDCFLSGIEAAPHTLAAAA
PLPLLPSALGPETAPPPPEALHSLPGVSLSLENQELWKEFSAVGTEMIITKAGRRMFPACRVSV
TGLDPEARYLFLLDVVPVDGARYRWQGQHWEPSGKAEPRLPDRVYIHPDSPATGAHWMRQPVSF
HRVKLTNSTLDPHGHLILHSMHKYQPRIHLVRATQLCSQHWGGVASFRFPETTFISVTAYQNPR
ITQLKIAANPFAKGFRENGRNCKRERDARVKRKLRGPEPVATEACGSGDTPGGPCDSTLGGDIR
DSDPEQAPTPQEAASASAPPCGGPSAEAYLLHPAAFHGAPSHLPARTPSFAEAPDPGRPAPYSA
AFLDLQPGPGGSAYQAAPSVPSFAPHFIQGGPFPLPYPGPGGYLDMGSKPMY

hide sequence

Ensembl Acc Id:

ENSMUSP00000126418 ⟸ ENSMUST00000172352

Ensembl Acc Id:

ENSMUSP00000091579 ⟸ ENSMUST00000094037

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P70327-F1-model_v2	AlphaFold	P70327	1-436	view protein structure

Promoters

RGD ID:

8665579

Promoter ID:

EPDNEW_M10821

Type:

single initiation site

Name:

Tbx6_1

Description:

Mus musculus T-box 6 , mRNA.

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm38	7	126,781,548 - 126,781,608	EPDNEW

RGD ID:

6842170

Promoter ID:

MM_KWN:52705

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

3T3L1_Day4, BoneMarrow_0Hour, BoneMarrow_4Hour, Brain, ES_Cell, Kidney, Lung, MEF_B4, MEF_B6, Spleen

Transcripts:

ENSMUST00000073564, NM_011538

Position:

Mouse Assembly	Chr	Position (strand)	Source
MGSCv36	7	133,924,141 - 133,925,147 (+)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	MGI:102539	AgrOrtholog
Ensembl Genes	ENSMUSG00000030699	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSMUST00000094037	ENTREZGENE
	ENSMUST00000094037.5	UniProtKB/Swiss-Prot
	ENSMUST00000172352.8	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.820	UniProtKB/Swiss-Prot
InterPro	p53-like_TF_DNA-bd	UniProtKB/Swiss-Prot
	T-box_DNA-bd	UniProtKB/Swiss-Prot
	T-box_sf	UniProtKB/Swiss-Prot
	TF_Brachyury	UniProtKB/Swiss-Prot
	TF_T-box	UniProtKB/Swiss-Prot
	TF_T-box_CS	UniProtKB/Swiss-Prot
KEGG Report	mmu:21389	UniProtKB/Swiss-Prot
MGD	MGI:102539	ENTREZGENE
NCBI Gene	21389	ENTREZGENE
PANTHER	PTHR11267	UniProtKB/Swiss-Prot
	T-BOX TRANSCRIPTION FACTOR TBX6	UniProtKB/Swiss-Prot
Pfam	T-box	UniProtKB/Swiss-Prot
PhenoGen	Tbx6	PhenoGen
PRINTS	BRACHYURY	UniProtKB/Swiss-Prot
	TBOX	UniProtKB/Swiss-Prot
PROSITE	TBOX_1	UniProtKB/Swiss-Prot
	TBOX_2	UniProtKB/Swiss-Prot
	TBOX_3	UniProtKB/Swiss-Prot
SMART	TBOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF49417	UniProtKB/Swiss-Prot
UniProt	B2RU37	ENTREZGENE
	P70327	ENTREZGENE
	Q5SDA2	ENTREZGENE
	TBX6_MOUSE	UniProtKB/Swiss-Prot
UniProt Secondary	B2RU37	UniProtKB/Swiss-Prot
	Q5SDA2	UniProtKB/Swiss-Prot

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Mammalian Phenotype

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