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Gene: Foxa3 (forkhead box A3) Rattus norvegicus

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Symbol:

Foxa3

Name:

forkhead box A3

RGD ID:

2809

Description:

Enables DNA binding activity and DNA-binding transcription factor activity. Involved in several processes, including negative regulation of cell population proliferation; positive regulation of hepatocyte differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to be located in actin cytoskeleton and nucleoplasm. Orthologous to human FOXA3 (forkhead box A3); PARTICIPATES IN forkhead class A signaling pathway; maturity-onset diabetes of the young pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

forkhead box protein A3; Hepatocyte nuclear factor 3 gamma; hepatocyte nuclear factor 3, gamma; hepatocyte nuclear factor 3-gamma; HNF-3-gamma; HNF-3G; Hnf3g

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):	FOXA3 (forkhead box A3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Foxa3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Foxa3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	FOXA3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	FOXA3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Foxa3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	FOXA3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	FOXA3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Foxa3 (forkhead box A3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	TLCD1 (TLC domain containing 1)	HGNC	OMA
Alliance orthologs ³
Mus musculus (house mouse):	Foxa3 (forkhead box A3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	FOXA3 (forkhead box A3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	foxa3 (forkhead box A3)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pha-4	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	fkh	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	foxa4	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	87,790,111 - 87,800,259 (-)	NCBI		GRCr8
mRatBN7.2	1	78,662,067 - 78,672,321 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	78,662,431 - 78,672,155 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	84,051,578 - 84,060,504 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	92,609,178 - 92,618,101 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	85,806,680 - 85,815,606 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	79,921,292 - 79,930,219 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	79,920,752 - 79,930,263 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	81,181,104 - 81,190,030 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	78,368,026 - 78,376,953 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	78,446,136 - 78,455,064 (-)	NCBI
Celera	1	73,128,615 - 73,137,542 (-)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Diabetes Mellitus (IEP)

Prostatic Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

2,4-dinitrotoluene (EXP)

3,3',4,4',5-pentachlorobiphenyl (ISO)

3,3',4,4'-tetrachlorobiphenyl (ISO)

3-chloropropane-1,2-diol (EXP)

3H-1,2-dithiole-3-thione (EXP)

acetamide (EXP)

aflatoxin B1 (EXP,ISO)

aldehydo-D-glucose (ISO)

amiodarone (EXP,ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

Azoxymethane (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

buspirone (EXP)

carbon nanotube (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (EXP)

copper atom (ISO)

copper(0) (ISO)

cyclosporin A (ISO)

D-glucose (ISO)

dextran sulfate (ISO)

diclofenac (ISO)

disulfiram (ISO)

epoxiconazole (ISO)

flutamide (EXP)

fructose (ISO)

furan (EXP)

genistein (EXP)

glafenine (EXP)

glucose (ISO)

herbicide (ISO)

inulin (ISO)

Licochalcone B (ISO)

menadione (ISO)

N-Nitrosopyrrolidine (ISO)

O-methyleugenol (ISO)

ortho-Aminoazotoluene (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP)

phenobarbital (EXP,ISO)

pirinixic acid (ISO)

quercetin (ISO)

reactive oxygen species (ISO)

resveratrol (ISO)

ritodrine (ISO)

sevoflurane (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP)

sulforaphane (EXP)

tamoxifen (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trichloroethene (EXP,ISO)

triclosan (ISO)

triphenyl phosphate (EXP)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure morphogenesis (IBA)

cell differentiation (IBA)

cellular response to starvation (IEA,ISO)

chromatin organization (IEA)

hematopoietic stem cell homeostasis (IEA,ISO)

intracellular glucose homeostasis (IEA,ISO,TAS)

negative regulation of cell population proliferation (IMP)

positive regulation of hepatocyte differentiation (IMP)

positive regulation of transcription by RNA polymerase II (IDA,IEA,ISO)

regulation of DNA-templated transcription (IDA,ISO)

regulation of transcription by RNA polymerase II (IBA,ISO)

response to nutrient levels (IEP)

spermatogenesis (IEA,ISO)

transcription by RNA polymerase II (IEA,ISO)

Cellular Component

actin cytoskeleton (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IEA,ISO)

Molecular Function

DNA binding (IDA,ISO,TAS)

DNA-binding transcription factor activity (IDA,IEA,ISO,TAS)

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

protein binding (ISO)

protein domain specific binding (IEA)

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

sequence-specific DNA binding (IEA,ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

forkhead class A signaling pathway (ISO)

maturity-onset diabetes of the young pathway (IEA)

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.	Gene expression of the three members of hepatocyte nuclear factor-3 is differentially regulated by nutritional and hormonal factors.	Imae M, etal., J Endocrinol. 2000 Oct;167(1):R1-5.
3.	The role of HNF1alpha, HNF3gamma, and cyclic AMP in glucose-6-phosphatase gene activation.	Lin B, etal., Biochemistry. 1997 Nov 18;36(46):14096-106.
4.	Foxa3 (HNF-3gamma) binds to and activates the rat proglucagon gene promoter but is not essential for proglucagon gene expression.	Liu Y, etal., Biochem J 2002 Sep 1;366(Pt 2):633-41.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Adenovirus-transferred HNF-3 gamma conserves some liver functions in primary cultured hepatocytes of adult rats.	Nakamura T, etal., Biochem Biophys Res Commun. 1998 Dec 18;253(2):352-7.
7.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
9.	PID Annotation Import Pipeline	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
10.	GOA pipeline	RGD automated data pipeline
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:1672118	PMID:7683413	PMID:8306889	PMID:8332212	PMID:11546810	PMID:12695546	PMID:17488644	PMID:18239190	PMID:19759516	PMID:25896100	PMID:28358366	PMID:37528786

Genomics

Comparative Map Data

Foxa3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	87,790,111 - 87,800,259 (-)	NCBI		GRCr8
mRatBN7.2	1	78,662,067 - 78,672,321 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	78,662,431 - 78,672,155 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	84,051,578 - 84,060,504 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	92,609,178 - 92,618,101 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	85,806,680 - 85,815,606 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	79,921,292 - 79,930,219 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	79,920,752 - 79,930,263 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	81,181,104 - 81,190,030 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	78,368,026 - 78,376,953 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	78,446,136 - 78,455,064 (-)	NCBI
Celera	1	73,128,615 - 73,137,542 (-)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

FOXA3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	45,864,326 - 45,873,797 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	45,863,989 - 45,873,797 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	46,367,584 - 46,377,055 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	51,059,358 - 51,068,895 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	19	43,172,554 - 43,182,091 (+)	NCBI		Celera
Cytogenetic Map	19	q13.32	NCBI
HuRef	19	42,796,032 - 42,805,584 (+)	NCBI		HuRef
CHM1_1	19	46,369,977 - 46,379,501 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	48,691,764 - 48,701,238 (+)	NCBI		T2T-CHM13v2.0

Foxa3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	18,747,208 - 18,757,464 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	18,747,209 - 18,757,463 (-)	Ensembl		GRCm39 Ensembl
GRCm38	7	19,013,283 - 19,023,539 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	19,013,284 - 19,023,538 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	19,598,632 - 19,608,888 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	18,171,805 - 18,182,061 (-)	NCBI		MGSCv36	mm8
Celera	7	16,424,993 - 16,435,230 (-)	NCBI		Celera
Cytogenetic Map	7	A3	NCBI
cM Map	7	9.46	NCBI

Foxa3
(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_004955574	293,344 - 302,002 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955574	293,344 - 301,955 (+)	NCBI	ChiLan1.0	ChiLan1.0

FOXA3
(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	20	52,029,299 - 52,039,689 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	53,900,693 - 53,911,081 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	42,873,933 - 42,883,479 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	51,410,294 - 51,419,483 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	51,410,473 - 51,418,744 (+)	Ensembl	panpan1.1		panPan2

FOXA3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	109,749,142 - 109,757,149 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	109,748,926 - 109,757,006 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	109,234,450 - 109,242,454 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	110,281,914 - 110,289,921 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	110,281,781 - 110,290,035 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	109,957,939 - 109,965,942 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	109,592,626 - 109,600,628 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	110,461,391 - 110,469,396 (-)	NCBI		UU_Cfam_GSD_1.0

Foxa3
(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_024409349	17,849,096 - 17,856,150 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936706	2,196,468 - 2,203,113 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936706	2,196,530 - 2,202,924 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

FOXA3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	52,181,114 - 52,188,774 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	52,181,095 - 52,188,777 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	47,444,473 - 47,452,404 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

FOXA3
(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	6	39,309,439 - 39,320,102 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	39,310,108 - 39,320,095 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666073	18,951,536 - 18,962,292 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Foxa3
(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_004624832	7,338,478 - 7,350,658 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624832	7,339,612 - 7,350,651 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Foxa3
51 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	308
Count of miRNA genes:	203
Interacting mature miRNAs:	227
Transcripts:	ENSRNOT00000019219
Prediction methods:	Microtar, 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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49393172	94393172	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	78479925	123479925	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	30882023	123479925	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53895117	82174945	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49393172	159356837	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	43333002	88333002	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
1300121	Hrtrt1	Heart rate QTL 1	3.7		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	65789093	115540829	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	66023617	118608521	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	72197680	90508767	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	57336763	151090257	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43284731	118944897	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
1549903	Bp267	Blood pressure QTL 267			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	77876254	106047988	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	48963584	144267916	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	56732668	98773277	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	32737273	90665040	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49361465	82174945	Rat
61344	Bp29	Blood pressure QTL 29	7.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	78350581	123350581	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	77494165	122494165	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43284731	118944897	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	53863041	90532583	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	56949932	101949932	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43284731	118944897	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	43284731	118944897	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	34836858	79836858	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	50343510	99980958	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	77857876	122857876	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	78430536	123430536	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53895117	82174945	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43284731	118944897	Rat
61433	Cia2	Collagen induced arthritis QTL 2	5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	78430754	91209302	Rat

Markers in Region

UniSTS:235614

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	78,662,489 - 78,662,609 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	79,921,268 - 79,921,387	NCBI	Rnor6.0
Rnor_5.0	1	81,181,080 - 81,181,199	UniSTS	Rnor5.0
RGSC_v3.4	1	78,368,002 - 78,368,121	UniSTS	RGSC3.4
Celera	1	73,128,591 - 73,128,710	UniSTS
Cytogenetic Map	1	q21-q22	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	nervous system	renal system	reproductive system	respiratory system
9	10	24	75	90	89	59	24	59	6	191	70	55	45	60	30

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001433737	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_017077	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039101386	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB017043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB017044	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC120692	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L09648	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000019219 ⟹ ENSRNOP00000019219

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	78,662,514 - 78,671,441 (-)	Ensembl
Rnor_6.0 Ensembl	1	79,920,752 - 79,930,263 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000108885 ⟹ ENSRNOP00000091555

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	78,662,431 - 78,672,155 (-)	Ensembl

RefSeq Acc Id:

NM_017077 ⟹ NP_058773

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	87,790,558 - 87,799,485 (-)	NCBI
mRatBN7.2	1	78,662,514 - 78,671,441 (-)	NCBI
Rnor_6.0	1	79,921,292 - 79,930,219 (-)	NCBI
Rnor_5.0	1	81,181,104 - 81,190,030 (-)	NCBI
RGSC_v3.4	1	78,368,026 - 78,376,953 (-)	RGD
Celera	1	73,128,615 - 73,137,542 (-)	RGD

Sequence:

show sequence

GCCCGTAGAGAGACCGAAGCGCTCGGTTCCCCCGGGGGGACCGCAGCCTGGGCGTGTGGGGGCA
CAGGCCCGGGGGATGCTGGGCTCAGTGAAGATGGAGGCCCATGACCTGGCCGAGTGGAGCTACT
ACCCGGAGGCGGGCGAGGTGTATTCTCCAGTGAATCCTGTGCCCACCATGGCCCCTCTCAACTC
CTACATGTCCTTGAACCCTCTTAGCTCTCCCTACCCTCCCGGAGGGCTTCAGGCCTCCCCTCTG
CCTACAGGACCCCTGGCACCCCCAGCCCCCACCGCTCCCCTGGGGCCCACCTTCCCAGGCCTGG
GCGCAGGCAGCGGCACCGGAGGCAGTGCTTCCGGGTATGGCGCCCCAGGGCCCGGGCTTGTACA
CGGAAAGGAAATGGCCAAGGGGTACCGGCGGCCACTGACTCATGCCAAACCACCTTATTCCTAC
ATCTCTCTCATCACCATGGCTATCCAGCAGGCACCAGGCAAGATGCTGACCCTGAGTGAAATCT
ACCAATGGATCATGGACCTCTTCCCGTACTACCGGGAGAACCAGCAACGTTGGCAGAACTCCAT
CCGGCACTCGCTGTCCTTCAATGACTGCTTCGTCAAGGTGGCACGCTCCCCAGACAAACCGGGC
AAAGGCTCCTACTGGGCCTTGCATCCCAGCTCTGGGAACATGTTTGAGAACGGCTGCTATCTCC
GCCGTCAGAAGCGCTTCAAGCTGGAGGAGAAGGCAAAGAAAGGAAACAGTGCCACATCCGCCAC
CAGGAATGGAACAGTGGGGTCAGCCACCTCTGCCACCACTACAGCTGCCACTGCAGTCACTTCC
CCGGCTCAGCCCCAGCCTACGCCGCCGTCTGAGCCCGAGGCCCAGAGTGGGGAAGATGTGGGGG
GTCTGGACTGCGCCTCGCCTCCTTCATCCGCACCCTATTTCACTGGCCTGGAGCTCCCAGGGGA
ACTGAAGTTGGATGCGCCCTACAACTTCAACCACCCTTTCTCTATCAACAACCTGATGTCAGAA
CAGACATCAACACCTTCCAAACTAGATGTGGGGTTTGGGGGCTACGGTGCTGAGAGTGGGGAAC
CTGGGGTCTACTACCAGAGCCTCTATTCCCGCTCTCTGCTCAATGCATCCTAGCGGCGCAACTG
GGAGAAATGCGGTGATGGGGGTTTGCTGTGACAGATGACCGGTTCTTCGGCCCTGATCTTTCTG
GTTACACTCTGCTTATCCAGTTAATTAACATCGTATTTGGTCTATTACTGTGATATGACCCATT
GGCTACTGTGGTAACTGCATGGACTCTTCGGTGGGCCTAGGGTTGGGGTATTGTGAAGGCAGAT
GCATTTGGGAGTGTTACGAAGGTGGCCATGTCGGACATACCGTGAAGGCAATTAGACTGGTGTA
CTATAAAAGCTGCATGTTAAGTGAGTGATCCACTGGGTGCCTGATGGCCGCGATGTCGGAGGAC
ATATTGTTTGGCCCTTTGGATGCT

hide sequence

RefSeq Acc Id:

XM_039101386 ⟹ XP_038957314

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	87,790,111 - 87,800,259 (-)	NCBI
mRatBN7.2	1	78,662,067 - 78,672,321 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001420666	(Get FASTA)	NCBI Sequence Viewer
	NP_058773	(Get FASTA)	NCBI Sequence Viewer
	XP_038957314	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41339	(Get FASTA)	NCBI Sequence Viewer
	BAA32534	(Get FASTA)	NCBI Sequence Viewer
	BAA32535	(Get FASTA)	NCBI Sequence Viewer
	EDM08244	(Get FASTA)	NCBI Sequence Viewer
	EDM08245	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000019219.1
	ENSRNOP00000091555.1
GenBank Protein	P32183	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_058773 ⟸ NM_017077

- UniProtKB:

P32183 (UniProtKB/Swiss-Prot), A6J8I9 (UniProtKB/TrEMBL), G3V7T9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLGSVKMEAHDLAEWSYYPEAGEVYSPVNPVPTMAPLNSYMSLNPLSSPYPPGGLQASPLPTGP
LAPPAPTAPLGPTFPGLGAGSGTGGSASGYGAPGPGLVHGKEMAKGYRRPLTHAKPPYSYISLI
TMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSY
WALHPSSGNMFENGCYLRRQKRFKLEEKAKKGNSATSATRNGTVGSATSATTTAATAVTSPAQP
QPTPPSEPEAQSGEDVGGLDCASPPSSAPYFTGLELPGELKLDAPYNFNHPFSINNLMSEQTST
PSKLDVGFGGYGAESGEPGVYYQSLYSRSLLNAS

hide sequence

Ensembl Acc Id:

ENSRNOP00000019219 ⟸ ENSRNOT00000019219

RefSeq Acc Id:	XP_038957314 ⟸ XM_039101386
- Peptide Label:	isoform X1

Ensembl Acc Id:

ENSRNOP00000091555 ⟸ ENSRNOT00000108885

Protein Domains

Fork-head

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P32183-F1-model_v2	AlphaFold	P32183	1-354	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689755

Promoter ID:

EPDNEW_R279

Type:

single initiation site

Name:

Foxa3_1

Description:

forkhead box A3

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	79,930,271 - 79,930,331	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2809	AgrOrtholog
BioCyc Gene	G2FUF-60543	BioCyc
Ensembl Genes	ENSRNOG00000014256	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000019219.4	UniProtKB/TrEMBL
	ENSRNOT00000108885.1	UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	FH_FOXA3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Fork-head_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Fork_head_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FOX_domain-containing	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TF_fork_head_CS_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TF_fork_head_CS_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	WH-like_DNA-bd_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	WH_DNA-bd_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25100	UniProtKB/Swiss-Prot
NCBI Gene	25100	ENTREZGENE
PANTHER	FORKHEAD BOX PROTEIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HEPATOCYTE NUCLEAR FACTOR 3-GAMMA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Forkhead	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Forkhead_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Foxa3	PhenoGen
PRINTS	FORKHEAD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	FORK_HEAD_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FORK_HEAD_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FORK_HEAD_3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000014256	RatGTEx
SMART	SM00339	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6AFN0_RAT	UniProtKB/TrEMBL
	A6J8I9	ENTREZGENE, UniProtKB/TrEMBL
	A6J8J0_RAT	UniProtKB/TrEMBL
	FOXA3_RAT	UniProtKB/Swiss-Prot
	G3V7T9	ENTREZGENE, UniProtKB/TrEMBL
	P32183	ENTREZGENE
	Q76N13	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Foxa3	forkhead box A3	Hnf3g	hepatocyte nuclear factor 3, gamma	Symbol and Name updated	1299863	APPROVED
2002-11-06	Hnf3g	hepatocyte nuclear factor 3, gamma		Hepatocyte nuclear factor 3 gamma	Name updated	625702	APPROVED
2002-06-10	Hnf3g	Hepatocyte nuclear factor 3 gamma			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in liver, pancreatic islets and intestine during embryonic development	625455
gene_function	D binding protein	625455
gene_function	binds to the rat proglucagon gene G2 promoter element	625455
gene_process	binds to the proglucagon gene G2 element but does not control the expression of islet or intestine proglucagon gene	625455

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 - CTD

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)