Hif3a (hypoxia inducible factor 3 subunit alpha)

Gene: Hif3a (hypoxia inducible factor 3 subunit alpha) Rattus norvegicus

Analyze

Symbol:

Hif3a

Name:

hypoxia inducible factor 3 subunit alpha

RGD ID:

70332

Description:

Enables DNA-binding transcription factor activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including cytosol; mitochondrion; and nuclear speck. Predicted to be part of chromatin. Biomarker of pulmonary hypertension. Orthologous to human HIF3A (hypoxia inducible factor 3 subunit alpha); PARTICIPATES IN hypoxia inducible factor pathway; INTERACTS WITH 17beta-estradiol; 6-propyl-2-thiouracil; allethrin.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

HIF-3 alpha; HIF-3-alpha; HIF3 alpha 1; HIF3-alpha; HIF3-alpha-1; hypoxia inducible factor 3 alpha; hypoxia inducible factor 3 alpha subunit; hypoxia inducible factor 3, alpha subunit; hypoxia inducible factor 3a; hypoxia-inducible factor 3 alpha; hypoxia-inducible factor 3-alpha; Inhibitory PAS (Per/Arnt/Sim) domain protein; Ipas; MOP7

RGD Orthologs

Alliance Genes

More Info

more info ...

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	86,846,196 - 86,878,527 (-)	NCBI		GRCr8
mRatBN7.2	1	77,718,110 - 77,750,448 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	77,722,471 - 77,749,758 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	83,102,824 - 83,130,220 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	91,666,890 - 91,694,278 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	84,857,927 - 84,885,322 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	78,976,318 - 78,997,869 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	78,976,318 - 78,997,869 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	80,223,828 - 80,245,130 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	77,377,465 - 77,408,704 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	77,455,581 - 77,486,815 (-)	NCBI
Celera	1	72,207,606 - 72,229,353 (-)	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

Chronic Intermittent Hypoxia (IEP)

genetic disease (ISO)

pulmonary hypertension (IEP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,10-phenanthroline (ISO)

17beta-estradiol (EXP,ISO)

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

2-palmitoylglycerol (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4-hydroxyphenyl retinamide (ISO)

4-nitrophenol (ISO)

5-chloro-7-iodoquinolin-8-ol (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (ISO)

aflatoxin B1 (ISO)

allethrin (EXP)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bromobenzene (EXP)

buta-1,3-diene (ISO)

C60 fullerene (EXP)

carbon nanotube (ISO)

chloroprene (ISO)

chlorpyrifos (ISO)

choline (ISO)

clofibrate (ISO)

cobalt dichloride (EXP,ISO)

cobalt(2+) sulfate (ISO)

copper atom (EXP)

copper(0) (EXP)

cyhalothrin (EXP)

cypermethrin (EXP)

delphinidin (ISO)

desferrioxamine B (ISO)

dexamethasone (ISO)

dichloroacetic acid (ISO)

dicrotophos (ISO)

dinophysistoxin 1 (ISO)

dioxygen (ISO)

diquat (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

ethanol (ISO)

fenvalerate (EXP)

folic acid (ISO)

graphite (EXP)

GW 4064 (ISO)

hydrogen peroxide (ISO)

indometacin (ISO)

isoprenaline (EXP,ISO)

L-methionine (ISO)

lead diacetate (EXP,ISO)

menadione (ISO)

mercury atom (ISO)

mercury dibromide (ISO)

mercury(0) (ISO)

methotrexate (ISO)

metyrapone (EXP)

nickel atom (ISO)

ochratoxin A (EXP)

ozone (EXP,ISO)

p-chloromercuribenzoic acid (ISO)

paraquat (ISO)

phenylmercury acetate (ISO)

pioglitazone (EXP)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

pyrethrins (EXP)

resveratrol (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sunitinib (ISO)

thimerosal (ISO)

trichostatin A (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

angiogenesis (IEA)

apoptotic process (IEA)

cellular response to hypoxia (IBA,IEA,ISO)

positive regulation of transcription by RNA polymerase II (IDA)

regulation of DNA-templated transcription (IEA)

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

response to hypoxia (ISO)

transcription by RNA polymerase II (IEA,ISO)

Cellular Component

chromatin (IEA,ISO)

cytoplasm (ISO)

cytosol (IEA,ISO)

mitochondrion (ISO)

nuclear speck (IEA,ISO)

nucleoplasm (ISO)

nucleus (ISO)

plasma membrane (IEA,ISO)

Molecular Function

DNA binding (ISO)

DNA-binding transcription factor activity (IDA,ISO)

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

protein binding (IPI,ISO)

protein dimerization activity (IEA)

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

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

Molecular Pathway Annotations Click to see Annotation Detail View

hypoxia inducible factor pathway (ISO,TAS)

References

References - curated

#	Reference Title	Reference Citation
1.	First evidence of aryl hydrocarbon receptor as a druggable target in hypertension induced by chronic intermittent hypoxia.	Coelho NR, etal., Pharmacol Res. 2020 Sep;159:104869. doi: 10.1016/j.phrs.2020.104869. Epub 2020 May 19.
2.	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.
3.	HIF1alpha and HIF2alpha: sibling rivalry in hypoxic tumour growth and progression.	Keith B, etal., Nat Rev Cancer. 2011 Dec 15;12(1):9-22. doi: 10.1038/nrc3183.
4.	Perivenous expression of the mRNA of the three hypoxia-inducible factor alpha-subunits, HIF1alpha, HIF2alpha and HIF3alpha, in rat liver.	Kietzmann T, etal., Biochem J 2001 Mar 15;354(Pt 3):531-7.
5.	Differential expression of three hypoxia-inducible factor-alpha subunits in pulmonary arteries of rat with hypoxia-induced hypertension.	Li QF and Dai AG, Acta Biochim Biophys Sin (Shanghai). 2005 Oct;37(10):665-72.
6.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
7.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	GOA pipeline	RGD automated data pipeline
9.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
11.	Pro-apoptotic activity of inhibitory PAS domain protein (IPAS), a negative regulator of HIF-1, through binding to pro-survival Bcl-2 family proteins.	Torii S, etal., Cell Death Differ. 2011 Nov;18(11):1711-25. doi: 10.1038/cdd.2011.47. Epub 2011 May 6.

Additional References at PubMed

PMID:9840812	PMID:11573933	PMID:12824304	PMID:16677454	PMID:16683694	PMID:16761101	PMID:18072084	PMID:21558328	PMID:28686686	PMID:29643458	PMID:29660430	PMID:33937412
PMID:35132534

Genomics

Comparative Map Data

Hif3a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	86,846,196 - 86,878,527 (-)	NCBI		GRCr8
mRatBN7.2	1	77,718,110 - 77,750,448 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	77,722,471 - 77,749,758 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	83,102,824 - 83,130,220 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	91,666,890 - 91,694,278 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	84,857,927 - 84,885,322 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	78,976,318 - 78,997,869 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	78,976,318 - 78,997,869 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	80,223,828 - 80,245,130 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	77,377,465 - 77,408,704 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	77,455,581 - 77,486,815 (-)	NCBI
Celera	1	72,207,606 - 72,229,353 (-)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

HIF3A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	46,297,042 - 46,343,433 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	46,297,042 - 46,343,433 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	46,800,299 - 46,846,690 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	51,492,145 - 51,538,530 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	19	43,605,284 - 43,651,680 (+)	NCBI		Celera
Cytogenetic Map	19	q13.32	NCBI
HuRef	19	43,228,311 - 43,274,715 (+)	NCBI		HuRef
CHM1_1	19	46,802,171 - 46,848,539 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	49,124,507 - 49,170,893 (+)	NCBI		T2T-CHM13v2.0

Hif3a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	16,764,918 - 16,796,352 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	16,765,432 - 16,796,352 (-)	Ensembl		GRCm39 Ensembl
GRCm38	7	17,030,993 - 17,062,427 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	17,031,507 - 17,062,427 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	17,616,342 - 17,647,776 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	16,194,256 - 16,215,201 (-)	NCBI		MGSCv36	mm8
Celera	7	14,238,445 - 14,270,033 (-)	NCBI		Celera
Cytogenetic Map	7	A2	NCBI
cM Map	7	9.15	NCBI

Hif3a
(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	495,953 - 518,397 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955574	490,702 - 520,867 (+)	NCBI	ChiLan1.0	ChiLan1.0

HIF3A
(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	52,400,319 - 52,483,212 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	54,307,702 - 54,354,329 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	43,243,290 - 43,326,146 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	51,815,809 - 51,862,039 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	51,815,809 - 51,862,039 (+)	Ensembl	panpan1.1		panPan2

HIF3A
(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	109,479,456 - 109,504,271 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	109,479,128 - 109,504,274 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	108,954,428 - 108,983,166 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	110,001,737 - 110,030,481 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	110,001,055 - 110,030,504 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	109,677,813 - 109,706,546 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	109,312,160 - 109,341,081 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	110,181,254 - 110,209,992 (-)	NCBI		UU_Cfam_GSD_1.0

Hif3a
(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	18,676,862 - 18,705,014 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936664	294,975 - 323,149 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936664	296,288 - 323,143 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HIF3A
(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	52,342,885 - 52,373,058 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	52,342,893 - 52,376,339 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	47,766,624 - 47,782,160 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HIF3A
(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	39,672,580 - 39,718,944 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	39,679,627 - 39,713,227 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666073	19,350,237 - 19,397,181 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hif3a
(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	7,128,285 - 7,157,494 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624832	7,128,285 - 7,157,506 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Hif3a
191 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	46
Count of miRNA genes:	44
Interacting mature miRNAs:	45
Transcripts:	ENSRNOT00000023490
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	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
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
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
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	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
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
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
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	28879780	78430678	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
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	32737273	90665040	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
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	33449848	78449848	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	33449848	78449848	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
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
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
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	35239598	78430678	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	35239598	78430678	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
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
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43284731	118944897	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
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
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
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
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
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	45803140	78430678	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	48963584	144267916	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
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
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
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	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
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
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
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
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
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
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
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	72197680	90508767	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

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		18	14	14		14			5	12	18
Low	3	10	16	8	2	8	1	1	65	19	17	8	1
Below cutoff		12	14	7	14	7	4	7	4	4	6	3	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001388512	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_022528	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089538	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC118918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ277827	(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

RefSeq Acc Id:

ENSRNOT00000023490 ⟹ ENSRNOP00000023490

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	77,722,471 - 77,744,023 (-)	Ensembl
Rnor_6.0 Ensembl	1	78,976,318 - 78,997,869 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000099745 ⟹ ENSRNOP00000097060

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	77,722,471 - 77,749,758 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000101762 ⟹ ENSRNOP00000087469

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	77,722,471 - 77,749,758 (-)	Ensembl

RefSeq Acc Id:

NM_001388512 ⟹ NP_001375441

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	86,850,554 - 86,877,838 (-)	NCBI
mRatBN7.2	1	77,722,471 - 77,749,758 (-)	NCBI

RefSeq Acc Id:

NM_022528 ⟹ NP_071973

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	86,850,554 - 86,872,105 (-)	NCBI
mRatBN7.2	1	77,722,471 - 77,744,023 (-)	NCBI
Rnor_6.0	1	78,976,318 - 78,997,869 (-)	NCBI
Rnor_5.0	1	80,223,828 - 80,245,130 (-)	NCBI
RGSC_v3.4	1	77,377,465 - 77,408,704 (-)	RGD
Celera	1	72,207,606 - 72,229,353 (-)	RGD

Sequence:

show sequence

CACATGGACTGGGACCAAGACAGGTCGAGCACCGAGCTGCGGAAGGAGAAGTCGCGGGATGCGG
CCCGCAGCAGGCGCAGCCAGGAGACGGAGGTGCTGTACCAACTGGCGCACACCCTGCCCTTTGC
GCGCGGCGTCAGCGCGCACCTGGACAAGGCCTCCATCATGCGCCTCACAATCAGCTACTTGCGC
ATGCACCGCCTCTGCGCTGCAGGGGAGTGGAACCAGGTGAGAAAAGAGGGAGAACCACTGGACG
CCTGCTACCTGAAGGCCCTGGAGGGTTTCGTCATGGTGCTCACCGCTGAGGGAGACATGGCTTA
CCTGTCGGAAAATGTCAGCAAGCACCTGGGCCTCAGTCAGCTGGAGCTCATTGGACACAGTATC
TTTGATTTTATCCATCCCTGTGACCAAGAGGAACTCCAGGATGCCCTGACCCCGAGACCAAGCC
TGTCAAAGAAGAAGTCAGAAGCAGCAACAGGACGCCACTTTTCCCTGCGAATGAAGAGCACACT
CACCAGCAGGGGGCGCGCGCTGAACCTCAAAGCGGCCACCTGGAAGGTGCTGCACTGCTCAGGA
CATATGAGGGCCTACAAGCCCCCTGCACAGACTTCCCCCGCCGGGAGCCCTCGCTCCGAGCCTC
CCCTGCAATGCCTGGTGCTTATCTGTGAAGCCATCCCCCACCCAGCCAGTCTGGAGCCCCCACT
GGGCCGAGGGGCCTTTCTCAGTCGCCACAGCCTGGACATGAAGTTCACATACTGCGACGAGAGG
ATTGCAGAAGTTGCTGGCTACAGCCCCGATGACCTGATTGGCTGTTCTGCCTATGAATACATCC
ACGCTTTGGACTCTGATGCAGTCAGCAGGAGCATCCACACTTTGCTGAGCAAGGGCCAGGCAGT
AACAGGGCAGTATCGCTTCCTGGCCCGGACTGGAGGCTATCTGTGGACTCAGACTCAGGCTACA
GTGGTGTCAGGGGGGCGGGGCCCCCAGTCGGAAAGTATCATCTGCGTCCACTTCCTGATCAGCC
GTGTAGAAGAGAACGGAGTGGTGCTGTCCCTGGAACAAACGGAGCAACATACTCGCAGACCCCC
TCAGCTGGGTACCTCCTCGAAGAAGGGTATCCCAGGCAACAGTCTAGACCCTCCCGCTCCACGG
ATCCTGGCCTTCCTGCACCCTCCAGCCCTGAGTGAGGCCTCCCTGGCTGCTGACCCTCGCCGTT
TTTGTAGCCCAGACCTGCGCCGCCTCATGGCACCCATCCTGGATGGACCTCCCACAGCCGCTAC
CCCCAGCACCCCGCAAGCTGCCAGGAGACCCCAAAGTCCTCTTCCGGCTGATCTCCCAGATCAG
TTGGCTGTGGGCTTGGAGAATGCACACAGACTCTCCACTGCCCGGAAAAACAAGACCATGGAGA
CAGATCTAGATATAGCTCAGGACCCTGACACTCCGGACTTGGAGATGTTGGCTCCGTACATCTC
CATGGATGATGACTTCCAGCTCAACTCCAGCGAGCAATTGCCCAAAGTCCACCGCAGACCTCCC
AGGACGGCCCGCAGGCCTCGTGCTCGGAGCTTCCATGGCCTGTCGCCTCCCATCCCTGAGGCCA
CCCTGCTGCCCCGCTGGGGGAGTGATCCACGACTGAACTGTTCCAGCCCCTCCAAGGGGGATCC
CCCCACAGCCCCCCTGACGCCTAGAACTCGGAAGAGGGCCTTGGCCCAGAGCTCAGAGGACAAA
GGGTTGGAGCTGCTGGAAACGAAGCCCCCCAAGCGGTCCCCAAGACTAGAACCTGGAAGTGTCC
TGCTGCCTCCGCTCAGCCTGAGTTTCCTTCTGCAAGGTCGACAACTTCCAGGGAACCAGCCGGA
TCCCAGAGCCCCACTCGTGGATTCGCATGAGCCCTTGGGCCTAGCTCCCTCGCTGCTCTCTCTC
TACCAGCATGAGGAAACTATCCAGTCCAGGAACCACTTCCTCCCAGCAGCAGGCTTGGCCCAGA
CACACTGAGTCAGCCTTCCTCTCAGCCCTCTTCTTCTACCCCAGAAAGGACTCAGCCACACTCC
ACACCAGCAGCAAACACAAGCCGAATTC

hide sequence

RefSeq Acc Id:

XM_039089538 ⟹ XP_038945466

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	86,846,196 - 86,878,527 (-)	NCBI
mRatBN7.2	1	77,718,110 - 77,750,448 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001375441	(Get FASTA)	NCBI Sequence Viewer
	NP_071973	(Get FASTA)	NCBI Sequence Viewer
	XP_038945466	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAB96611	(Get FASTA)	NCBI Sequence Viewer
	EDM08279	(Get FASTA)	NCBI Sequence Viewer
	EDM08280	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000023490
	ENSRNOP00000023490.2
	ENSRNOP00000087469.1
	ENSRNOP00000097060
	ENSRNOP00000097060.1
GenBank Protein	Q9JHS2	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_071973 ⟸ NM_022528
- Peptide Label:	isoform 1
- UniProtKB:	Q9JHS2 (UniProtKB/Swiss-Prot), F1LRL5 (UniProtKB/TrEMBL)
- Sequence:	show sequence MDWDQDRSSTELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRM HRLCAAGEWNQVRKEGEPLDACYLKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIF DFIHPCDQEELQDALTPRPSLSKKKSEAATGRHFSLRMKSTLTSRGRALNLKAATWKVLHCSGH MRAYKPPAQTSPAGSPRSEPPLQCLVLICEAIPHPASLEPPLGRGAFLSRHSLDMKFTYCDERI AEVAGYSPDDLIGCSAYEYIHALDSDAVSRSIHTLLSKGQAVTGQYRFLARTGGYLWTQTQATV VSGGRGPQSESIICVHFLISRVEENGVVLSLEQTEQHTRRPPQLGTSSKKGIPGNSLDPPAPRI LAFLHPPALSEASLAADPRRFCSPDLRRLMAPILDGPPTAATPSTPQAARRPQSPLPADLPDQL AVGLENAHRLSTARKNKTMETDLDIAQDPDTPDLEMLAPYISMDDDFQLNSSEQLPKVHRRPPR TARRPRARSFHGLSPPIPEATLLPRWGSDPRLNCSSPSKGDPPTAPLTPRTRKRALAQSSEDKG LELLETKPPKRSPRLEPGSVLLPPLSLSFLLQGRQLPGNQPDPRAPLVDSHEPLGLAPSLLSLY QHEETIQSRNHFLPAAGLAQTH hide sequence

RefSeq Acc Id:

ENSRNOP00000023490 ⟸ ENSRNOT00000023490

RefSeq Acc Id:	XP_038945466 ⟸ XM_039089538
- Peptide Label:	isoform X1
- UniProtKB:	Q9JHS2 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	NP_001375441 ⟸ NM_001388512
- Peptide Label:	isoform 2
- UniProtKB:	Q9JHS2 (UniProtKB/Swiss-Prot), A0A8I6GMD1 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000087469 ⟸ ENSRNOT00000101762

RefSeq Acc Id:

ENSRNOP00000097060 ⟸ ENSRNOT00000099745

Protein Domains

bHLH PAS

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9JHS2-F1-model_v2	AlphaFold	Q9JHS2	1-662	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:70332	AgrOrtholog
BioCyc Gene	G2FUF-60577	BioCyc
Ensembl Genes	ENSRNOG00000017198	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000023490	ENTREZGENE
	ENSRNOT00000023490.4	UniProtKB/TrEMBL
	ENSRNOT00000099745	ENTREZGENE
	ENSRNOT00000099745.1	UniProtKB/TrEMBL
	ENSRNOT00000101762.1	UniProtKB/TrEMBL
Gene3D-CATH	4.10.280.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	bHLH_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HIF_alpha_subunit	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HLH_DNA-bd_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS_fold	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS_fold_3	UniProtKB/TrEMBL
KEGG Report	rno:64345	UniProtKB/Swiss-Prot
NCBI Gene	64345	ENTREZGENE
PANTHER	HYPOXIA-INDUCIBLE FACTOR 1 ALPHA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HYPOXIA-INDUCIBLE FACTOR 3-ALPHA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	HIF-1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS_11	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS_3	UniProtKB/TrEMBL
PhenoGen	Hif3a	PhenoGen
PROSITE	BHLH	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000017198	RatGTEx
SMART	HLH	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PAS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF47459	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF55785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6A5W6_RAT	UniProtKB/TrEMBL
	A0A8I6GMD1	ENTREZGENE, UniProtKB/TrEMBL
	A6J8F4_RAT	UniProtKB/TrEMBL
	A6J8F5_RAT	UniProtKB/TrEMBL
	F1LRL5	ENTREZGENE, UniProtKB/TrEMBL
	HIF3A_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2018-05-25	Hif3a	hypoxia inducible factor 3 subunit alpha	Hif3a	hypoxia inducible factor 3, alpha subunit	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Hif3a	hypoxia inducible factor 3, alpha subunit		hypoxia inducible factor 3a	Name updated	1299863	APPROVED
2002-06-10	Hif3a	hypoxia inducible factor 3a			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in hepatocytes	68201

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

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Imported Disease Annotations - ClinVar

RGD Manual Annotations