Advanced Search (OLGA)

Gene: Nphp3 (nephrocystin 3) Rattus norvegicus

Analyze

Symbol:

Nphp3

Name:

nephrocystin 3

RGD ID:

1563856

Description:

Predicted to be involved in several processes, including determination of left/right symmetry; photoreceptor cell maintenance; and regulation of Wnt signaling pathway. Predicted to act upstream of or within several processes, including establishment or maintenance of cell polarity; extracellular matrix organization; and non-motile cilium assembly. Predicted to be located in cilium. Predicted to be active in ciliary base and ciliary inversin compartment. Human ortholog(s) of this gene implicated in Meckel syndrome 7; hypertension; nephronophthisis; nephronophthisis 3; and renal-hepatic-pancreatic dysplasia. Orthologous to human NPHP3 (nephrocystin 3); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; cadmium dichloride.

Type:

protein-coding

RefSeq Status:

INFERRED

Previously known as:

LOC363126; nephrocystin-3; nephronophthisis 3 (adolescent); RGD1563856; similar to nephrocystin 3

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):	NPHP3 (nephrocystin 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Nphp3 (nephronophthisis 3 (adolescent))	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Nphp3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NPHP3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NPHP3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nphp3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NPHP3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NPHP3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nphp3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Nphp3 (nephrocystin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CIMAP1A (ciliary microtubule associated protein 1A)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	NPHP3 (nephrocystin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Nphp3 (nephronophthisis 3 (adolescent))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nphp3 (nephronophthisis 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	nphp3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	113,500,708 - 113,541,179 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	8	113,500,509 - 113,541,179 (+)	Ensembl				GRCr8
mRatBN7.2	8	104,621,908 - 104,662,383 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	104,621,864 - 104,662,383 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	8	110,269,003 - 110,309,487 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	108,468,194 - 108,508,680 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	106,310,899 - 106,351,380 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	112,526,553 - 112,575,745 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	112,526,553 - 112,575,745 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	8	111,913,834 - 111,963,488 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	8	109,065,400 - 109,105,882 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	8	103,986,600 - 104,026,761 (+)	NCBI		Celera
Cytogenetic Map	8	q32	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Disease Models (ISO)

autosomal dominant polycystic kidney disease (ISS)

autosomal recessive polycystic kidney disease (ISO)

cystic kidney disease (ISO)

hypertension (ISO)

Joubert syndrome (ISO)

Meckel syndrome 7 (ISO)

Multiple Abnormalities (ISO)

nephronophthisis (ISO)

nephronophthisis 1 (ISO)

nephronophthisis 3 (ISO,ISS)

Renal-Hepatic-Pancreatic Dysplasia 1 (ISO)

retinitis pigmentosa 1 (ISO)

visceral heterotaxy 5 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

3,4-methylenedioxymethamphetamine (ISO)

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

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

aristolochic acid A (ISO)

Benoxacor (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

choline (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dimethyl sulfoxide (ISO)

Enterolactone (ISO)

enzyme inhibitor (ISO)

folic acid (ISO)

formaldehyde (ISO)

L-methionine (ISO)

methyl methanesulfonate (ISO)

ozone (ISO)

paracetamol (EXP)

sodium arsenite (ISO)

temozolomide (ISO)

titanium dioxide (ISO)

Tributyltin oxide (ISO)

trimellitic anhydride (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

atrial septum development (IEA,ISO)

biological_process (ND)

cilium assembly (IEA,ISO)

convergent extension (IBA)

convergent extension involved in gastrulation (IEA,ISO)

determination of intestine left/right asymmetry (IEA,ISO)

determination of left/right symmetry (IBA,IEA,ISO)

determination of liver left/right asymmetry (IEA,ISO)

determination of pancreatic left/right asymmetry (IEA,ISO)

determination of stomach left/right asymmetry (IEA,ISO)

establishment or maintenance of cell polarity (ISO)

extracellular matrix organization (ISO)

heart looping (IEA,ISO)

kidney development (IBA,IEA,ISO)

kidney morphogenesis (IBA,IEA,ISO)

lipid metabolic process (ISO)

lung development (IEA,ISO)

maintenance of animal organ identity (IEA,ISO)

negative regulation of canonical Wnt signaling pathway (IEA,ISO)

non-motile cilium assembly (ISO)

photoreceptor cell maintenance (IEA,ISO)

regulation of Wnt signaling pathway, planar cell polarity pathway (IEA,ISO)

ureter development (IEA,ISO)

Wnt signaling pathway (IEA)

Cellular Component

ciliary base (IBA,IEA,ISO)

ciliary inversin compartment (IBA,IEA,ISO)

ciliary tip (IEA,ISO)

cilium (IEA,ISO)

Molecular Function

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.	Bergmann C, etal., Am J Hum Genet. 2008 Apr;82(4):959-70. doi: 10.1016/j.ajhg.2008.02.017. Epub 2008 Mar 27.
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.	Evidence of oligogenic inheritance in nephronophthisis.	Hoefele J, etal., J Am Soc Nephrol. 2007 Oct;18(10):2789-95. Epub 2007 Sep 12.
4.	Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis.	Olbrich H, etal., Nat Genet. 2003 Aug;34(4):455-9.
5.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
6.	GOA pipeline	RGD automated data 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.	Comprehensive gene review and curation	RGD comprehensive gene curation
10.	Mutations of NPHP2 and NPHP3 in infantile nephronophthisis.	Tory K, etal., Kidney Int. 2009 Apr;75(8):839-47. doi: 10.1038/ki.2008.662. Epub 2009 Jan 28.

Additional References at PubMed

PMID:1385849	PMID:7539536	PMID:20007846	PMID:20169535	PMID:20462968	PMID:22085962	PMID:22328406	PMID:22832925	PMID:24178445	PMID:29395339

Genomics

Comparative Map Data

Nphp3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	113,500,708 - 113,541,179 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	8	113,500,509 - 113,541,179 (+)	Ensembl				GRCr8
mRatBN7.2	8	104,621,908 - 104,662,383 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	104,621,864 - 104,662,383 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	8	110,269,003 - 110,309,487 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	108,468,194 - 108,508,680 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	106,310,899 - 106,351,380 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	112,526,553 - 112,575,745 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	112,526,553 - 112,575,745 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	8	111,913,834 - 111,963,488 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	8	109,065,400 - 109,105,882 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	8	103,986,600 - 104,026,761 (+)	NCBI		Celera
Cytogenetic Map	8	q32	NCBI

NPHP3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	132,680,609 - 132,722,409 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	132,680,609 - 132,722,432 (-)	Ensembl			hg38	GRCh38
GRCh37	3	132,399,453 - 132,441,253 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	133,882,144 - 133,923,966 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	3	133,882,151 - 133,923,974	NCBI
Celera	3	130,824,943 - 130,866,763 (-)	NCBI		Celera
Cytogenetic Map	3	q22.1	NCBI
HuRef	3	129,779,095 - 129,821,371 (-)	NCBI		HuRef
CHM1_1	3	132,362,464 - 132,404,314 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	3	135,425,099 - 135,466,912 (-)	NCBI		T2T-CHM13v2.0

Nphp3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	103,879,743 - 103,921,010 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	103,879,743 - 103,921,017 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	9	104,002,544 - 104,043,811 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	104,002,544 - 104,043,818 (+)	Ensembl			mm10	GRCm38
MGSCv37	9	103,904,874 - 103,946,141 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	9	103,860,949 - 103,901,892 (+)	NCBI		MGSCv36	mm8
Celera	9	103,555,338 - 103,596,843 (+)	NCBI		Celera
Cytogenetic Map	9	F1	NCBI
cM Map	9	56.11	NCBI

Nphp3
(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_004955501	5,799,879 - 5,837,022 (+)	Ensembl
ChiLan1.0	NW_004955501	5,799,879 - 5,837,022 (+)	NCBI	ChiLan1.0	ChiLan1.0

NPHP3
(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	2	130,629,761 - 130,672,759 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	130,636,218 - 130,677,487 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	129,753,399 - 129,795,300 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	137,229,994 - 137,271,458 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2

NPHP3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	23	29,662,486 - 29,703,629 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	23	29,645,641 - 29,703,805 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	23	29,637,421 - 29,678,561 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	23	30,176,434 - 30,217,575 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	23	30,176,684 - 30,217,513 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	23	29,872,412 - 29,913,301 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	23	29,929,544 - 29,970,895 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	23	30,177,261 - 30,218,423 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Nphp3
(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_024405602	69,251,499 - 69,287,758 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936529	6,009,301 - 6,049,447 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936529	6,013,321 - 6,048,249 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NPHP3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	73,858,427 - 73,900,967 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	13	73,843,770 - 73,901,020 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	81,415,846 - 81,445,656 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NPHP3
(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	15	57,550,878 - 57,629,106 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	57,551,189 - 57,592,661 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666041	30,538,900 - 30,580,436 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nphp3
(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_004624730	8,816,643 - 8,874,649 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624730	8,824,370 - 8,874,614 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Nphp3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	8	95,318,236 - 95,359,272 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Nphp3
429 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	64
Count of miRNA genes:	49
Interacting mature miRNAs:	63
Transcripts:	ENSRNOT00000014636
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2303171	Bp331	Blood pressure QTL 331	5.57	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	105462581	132782436	Rat
1549909	Stresp11	Stress response QTL 11	6.83	0.0019	stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	8	82352698	127352698	Rat
631210	Bw3	Body weight QTL3	5.9		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight to body weight ratio (CMO:0000654)	8	61019838	121662124	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	49849908	118871671	Rat
9590292	Uminl3	Urine mineral level QTL 3	3.62	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	8	80768445	125768445	Rat
8694446	Bw170	Body weight QTL 170	12.07	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	8	80768445	125768445	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	70041301	121080908	Rat
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	68690349	119799881	Rat
10450865	Bw175	Body weight QTL 175	4.1		total fat pad mass (VT:0015008)	adipose tissue molecular composition measurement (CMO:0000484)	8	84192326	129192326	Rat
724539	Cm19	Cardiac mass QTL 19	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	8	103375781	129871912	Rat
738011	Anxrr9	Anxiety related response QTL 9	6.1		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	8	102413464	132782436	Rat
8693654	Alc32	Alcohol consumption QTL 32	2	0.755	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	8	97492344	116428905	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	55428333	127966348	Rat
634332	Pia18	Pristane induced arthritis QTL 18	4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	8	84192326	132782436	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	39106363	114525825	Rat
2300181	Bmd55	Bone mineral density QTL 55	5.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	85348065	130348065	Rat
631217	Activ1	Activity QTL 1	15.9		voluntary movement trait (VT:0003491)	number of photobeam interruptions in an experimental apparatus (CMO:0001517)	8	111249511	117802327	Rat
1300171	Bp184	Blood pressure QTL 184	3.66		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	8	79394435	132782436	Rat
2313400	Anxrr25	Anxiety related response QTL 25			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	8	98145073	122898010	Rat
8694200	Abfw4	Abdominal fat weight QTL 4	9.07	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	8	80768445	125768445	Rat
8694392	Bw161	Body weight QTL 161	8.06	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	8	80768445	125768445	Rat
61437	Cia6	Collagen induced arthritis QTL 6			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	8	91340911	131690273	Rat

Expression

RNA-SEQ Expression

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

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	161	91	90	59	86	59	6	349	186	11	140	80	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191882	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000014636 ⟹ ENSRNOP00000014636

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	8	113,500,509 - 113,541,179 (+)	Ensembl
mRatBN7.2 Ensembl	8	104,621,864 - 104,662,383 (+)	Ensembl
Rnor_6.0 Ensembl	8	112,526,553 - 112,575,745 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000122199 ⟹ ENSRNOP00000101255

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	8	113,500,648 - 113,538,863 (+)	Ensembl

RefSeq Acc Id:

NM_001191882 ⟹ NP_001178811

RefSeq Status:

INFERRED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	8	113,500,708 - 113,541,179 (+)	NCBI
mRatBN7.2	8	104,621,908 - 104,662,383 (+)	NCBI
Rnor_6.0	8	112,526,553 - 112,575,745 (+)	NCBI
Rnor_5.0	8	111,913,834 - 111,963,488 (+)	NCBI
Celera	8	103,986,600 - 104,026,761 (+)	NCBI

Sequence:

show sequence

ATGGGCACAGCCTCGTCGTTGGTGAGCCCCGCTGGTGGGGAGGTGATCGAGGACACGTACGGGG
CAGGCGGCGGCGAGGCCTGCGAGATCCCGGTGGAAGTGAAGCCCAAGGCTCGCCTGCTGCGTAG
CTCGTTCCGCAGGGGCGCGGGAGCCGGGCCCGGGTCGCTGCCTCGGGCGGCGGGGGCCGGCGGG
CTGCTGGGCGCCAGCTTCAAGTCCACCGGCTCGTCTGTGCCCGAGCTAGAGTATGCGGCGGCCG
AGTTCGAGCGGCTCAAGAAAGAGTACGAGATCTTCCGGGTCAGCAAGAACCAGGAGTTGCTGTC
CATGGGTCGCCGAGAGGCCAAGCTGGACACGGAGAACAAGCGGCTGCGGGCGGAGCTGCAGGTA
CTTCAGAAAACTTACCAGAAGATACTTCGGGAAAAAGAGGGTGCATTAGAAGCAAAATACCAAG
CCATGGAGAGAGCAGTCACATTTGAACACGATAGAGACAGGGTTAAAAGGCAATTCAAGATTTT
TAGGGAGACCAAAGAAAATGAAATTCAGGACTTGCTGAGGGCCAAGCGAGAGCTGGAGAGCAAA
CTTCAGAGGCTGCAGGCCCAGGGGATCCAGGTGTTTGACCCTGGGGAGTCTGACTCCGATGACA
ACGGCGCCGATGTCACTGCTGCCGGAACCCAATGTGAATACTGGGCCAGCAGAGCCCTGGGCAG
CGAGCATTCCATAGACAGCATGATCCAGCTTCAGCAGCCTTTCAGAGGTCCCGAGTTTGCCCAC
AGTTCCATAGATGTGGAAGGACCCTTCGCAAACATCAACCGAGATGACTGGGACGCTGCTGTGG
CTGGTTTATTACAAGCCACCCCCTTGTTCTCACATTCCCTGTGGTGTCACCCAGTCAGATGTTA
CCTCATCTATTCAGAGGAAACCCAGCCCGAAATGGAACTTTTCCTTAAGGACCATTCACCTAAA
CTTAAAAGAATGTGCGAGACAATGGGATACTTCTTCCATGCTGTTTATTTTCCAATAGATGTTG
AAAATCAGTACCTTACTCTAAGAAAATGGGAGATTGAGAAGAGTTCTTTAGTTATTTTATTCCT
TCACTCGACATTACCAAGTTTTTTACTGGAAGACTGTGAAGAAGCCTTTCTGCAAAACCCAGAA
GGAAAACTACGATTAATCTACCACCGTTTGGAGGACGGGAAAGCCACTTCCGACTCTGTCCAGC
GGTTACTGGATCAGGTTTCTAACCTAAGCGAGACCACTAAAGCCAAGATAATCGAACACTCTGG
AGATCTCTCAGAGGGAGTGTATAAGATTTACATGGGTGTGGAAAAGATTATCAAACAGGACATC
CTTGGCCTCGAGAACACAGACGTGGAGGTGAAGGATGGGGGCAGTGAGGATTCCAGTCCAGAAG
AAGATGATTTTGGGGATGTTCTGTGGGACGTACACGACGAGCAAGAACAGATAGAAGCCTTTCA
GCGGGCTTCTAGCTCCGCCCACGAACTGGGATTTGAGAAGTATTACCAGCGCCTGGATGATCTG
GTGGTGGCGCCAGCCCCGATCCCACCACTCCTGGTTTCTGGAGGACCAGGTTCTGGAAAGTCCC
TTCTTTTATCAAAGTGGATTCAGCTGCAGCAGAAGCATTTCCCTAACACTCTGATCCTGTCTCA
TTTTGTGGGGAGGCCAATGTCATCCAGCTCAGAGTCCTCCTTGATTATCAAGCGTCTGACTCTG
AAGCTGATGCAGCACTTCTGGGCAGTTTCTGCACTGACGCTGGATCCTGCCAAGCTCCTGGAGG
AATTTCCACACTGGCTGGAGAAGCTCTCCGCTCGGCATCAGGGCAGCATCATCATCATCATCGA
CTCCATAGACCAAGTTCAGCAAGTGGAGAAGCACATGAAGTGGCTGATCGACCCCCTGCCGGTG
AATGTCAGAGTCATTGTTTCCGTGAATGTGGAGACCTGCCCTACCGCCTGGAGGTTGTGGCCTA
CTCTGCATCTCGACCCTTTAAGCCCCAAAGACGCCATATCTATGATAACGGCAGAATGCCACTC
CGTGGACGTTCAGTTGAACAGAGAACAGGAGAAGATGCTAGAACAGCACTGCCGTCCAGCCACG
ACCCGCCACGCCCTCTACGTCACCCTTTTCAGCAAGATGCTGGCCTGTGCCGGGAGAGCGGGTG
ACTTAGCTGAAACCCTTCATCGATGCCTGCAGTGTCAGGATACAATGTCGCTGTACAGACTCGT
TCTCCACCACGTCCGGGAGTCCATGCCAAGTGACAAGGAAAAAGAATGGATGACACAGATTCTC
TGCCTCATCAACGTTAGTCACAATGGCGTGAGTGAGTCCGAGCTGATGGAACTGTATCCAGAGA
TGTCCTGGGCCTCTTTGACCTCCATTGTTCACAGTTTACACAAAATGCACCTGCTGACCTACAG
CTGTGGCCTGCTCAGGTTTCAACATCTACAGGCCTGGGAAACAGTGAGGCAGGCGTACATGGAA
GACCCCGCCCTCGTTTCCTCTTATAGGCAAAAGCTGATTGACTATTTTACCTCACAGCTCAGTC
AGGACAGAGTGACCTGGAGAAGCGCAGATGAGCTCCCGTGGCTGTTCCAGCAGCAGGGGAGCAA
ACAGAAGCTGCACAGCTGCCTCCTCAATCTCTTCGTGTCTCAGAACCTCTACAAAAGAGGACAC
TTCGCCGAGTTGCTGAGTTACTGGCAGTTTGTTGGCAAAGACAAAAGCGCCATGGCGACCGAGT
ACTTTGAGTCACTGAAGCAGTATGAGAACTGCGAGGGCGAGGAGAACATGCTGTGCTTAGCCGA
CCTGTACGAAACTCTCGGCCGGTTTCTCAAGGACCTAGGACTTCTCAGCCAGGCCGTGGTGCCT
TTGCAGAGGTCCCTAGAAATTCGGGAGACAGCCTTAGATCCCGATCACCCGAGAGTAGCCCAGT
CCCTCCACCAGCTGGCCGGTGTGTACGTGCAGTGGAAGAAGTTCAGCGATGCCGAGCAGCTGTA
CAAACAGGCCCTGGAGATCTCAGAGAACGCCTACGGTGCGGACCATCCACACGCTGCCCGTGAA
CTTGAGGCGCTTGCGACTTTGTACCACAAACAAAATAAGTATGAACAAGCTGAACGTTTTAGGA
AAAAGTCGGTTATAATCCGTCAGCAAGCGACGAGGCGAAAAGGCAGTCTGTACGGGTTTGCCCT
ACTACGCAGGCGGGCTCTGCAGTTGGAAGAGCTCACCTTAGGCAAGGACAAGCCCGAGAATGCC
CGCACCCTCAACGAACTGGGTGTCCTCTACTACCTTCAAAACAATCTTGAGACAGCAGAGCAGT
TTCTGAAGCGCTCCCTGGAAATGAGGGAGCGGGTCCTGGGACCAGATCATCCAGACTGCGCGCA
GTCCCTGAATAACCTGGCCGCGCTGTGCAATGAAAGGAAGCAGTACGCTAGAGCAGAGGAGCTG
TATGAGCGAGCCCTGGACATCCGGAGGCGAGCGCTGGCTCCTGACCACCCTTCCCTGGCCTACA
CAGTGAAGCACCTTGCAATCTTGTATAAGAAAACGGGAAGAGTTGACAAAGCTGTACCTCTGTA
TGAATTGGCTGTTGAAATTCGGCAGAAATCCTTTGGCCCAAAGCACCCCAGTGTAGCCACTGCC
TTGGTAAACTTGGCAGTCCTTCATAGCCAAATGAAAAAGCACAGCGAAGCCCTGCCGCTCTATG
AAAGAGCCTTAAAGATTTACGAAGATAGCTTGGGACGGATGCATCCTAGAGTTGGAGAAACATT
AAAAAACTTAGCTGTGCTCAGCTATGAAGAAGGGAATTTTGAAAAGGCTGCTGAACTGTACAAA
AGGGCGATGGAAATTAAAGAAGCAGAGACATCACTTTTGGGTGGAAAAGCTCCTTCAAGGCAGT
CATCAAGTGGAGACACGCTTCTCTTTAAAACAACTCATTCTCCTAACGTTTTCCTTCCCCAAGG
ACAAAGCTAACTGTCAATTCTTTGCAAGAATACTTCCGGCTCAAACAACTAAACATCTGGAACA
CTCTAACTCAAAACTTAATGTTTTTATAGAAAAATCATTTTTGCAACATCAGCAGTGTTGTTTA
ACTGGCGTTTGTATGATGTATTGAATTGTTGTGCCAAGTGTAAATTGATTAAAGAACCTGGTTC
CTATGGGATGAGATCCAGGATGAAGACATCAGCATTCAGTGGCATGAGGAGTGGCTTGGTCTCT
GAAACAAGAGCTGGCAGGATCCCATGGTTTAAGAATTCCACGGTTCTTTTCCTCCCTCAAGAGC
CTTAGTTAGCCCTGTTGTTTATTGTCTGTTCCTAGCAGGGCTCTGAGCCAGCTCTCTACCTCAA
AGAACTTTCAAGGGCTACATGTGAGGGTCAGAGGTCAGCCTTGGATATCATTCCTCAGGTG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001178811	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000014636
	ENSRNOP00000014636.7
	ENSRNOP00000101255.1

RefSeq Acc Id:

NP_001178811 ⟸ NM_001191882

- UniProtKB:

D4A1W7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MGTASSLVSPAGGEVIEDTYGAGGGEACEIPVEVKPKARLLRSSFRRGAGAGPGSLPRAAGAGG
LLGASFKSTGSSVPELEYAAAEFERLKKEYEIFRVSKNQELLSMGRREAKLDTENKRLRAELQV
LQKTYQKILREKEGALEAKYQAMERAVTFEHDRDRVKRQFKIFRETKENEIQDLLRAKRELESK
LQRLQAQGIQVFDPGESDSDDNGADVTAAGTQCEYWASRALGSEHSIDSMIQLQQPFRGPEFAH
SSIDVEGPFANINRDDWDAAVAGLLQATPLFSHSLWCHPVRCYLIYSEETQPEMELFLKDHSPK
LKRMCETMGYFFHAVYFPIDVENQYLTLRKWEIEKSSLVILFLHSTLPSFLLEDCEEAFLQNPE
GKLRLIYHRLEDGKATSDSVQRLLDQVSNLSETTKAKIIEHSGDLSEGVYKIYMGVEKIIKQDI
LGLENTDVEVKDGGSEDSSPEEDDFGDVLWDVHDEQEQIEAFQRASSSAHELGFEKYYQRLDDL
VVAPAPIPPLLVSGGPGSGKSLLLSKWIQLQQKHFPNTLILSHFVGRPMSSSSESSLIIKRLTL
KLMQHFWAVSALTLDPAKLLEEFPHWLEKLSARHQGSIIIIIDSIDQVQQVEKHMKWLIDPLPV
NVRVIVSVNVETCPTAWRLWPTLHLDPLSPKDAISMITAECHSVDVQLNREQEKMLEQHCRPAT
TRHALYVTLFSKMLACAGRAGDLAETLHRCLQCQDTMSLYRLVLHHVRESMPSDKEKEWMTQIL
CLINVSHNGVSESELMELYPEMSWASLTSIVHSLHKMHLLTYSCGLLRFQHLQAWETVRQAYME
DPALVSSYRQKLIDYFTSQLSQDRVTWRSADELPWLFQQQGSKQKLHSCLLNLFVSQNLYKRGH
FAELLSYWQFVGKDKSAMATEYFESLKQYENCEGEENMLCLADLYETLGRFLKDLGLLSQAVVP
LQRSLEIRETALDPDHPRVAQSLHQLAGVYVQWKKFSDAEQLYKQALEISENAYGADHPHAARE
LEALATLYHKQNKYEQAERFRKKSVIIRQQATRRKGSLYGFALLRRRALQLEELTLGKDKPENA
RTLNELGVLYYLQNNLETAEQFLKRSLEMRERVLGPDHPDCAQSLNNLAALCNERKQYARAEEL
YERALDIRRRALAPDHPSLAYTVKHLAILYKKTGRVDKAVPLYELAVEIRQKSFGPKHPSVATA
LVNLAVLHSQMKKHSEALPLYERALKIYEDSLGRMHPRVGETLKNLAVLSYEEGNFEKAAELYK
RAMEIKEAETSLLGGKAPSRQSSSGDTLLFKTTHSPNVFLPQGQS

hide sequence

Ensembl Acc Id:

ENSRNOP00000014636 ⟸ ENSRNOT00000014636

Ensembl Acc Id:

ENSRNOP00000101255 ⟸ ENSRNOT00000122199

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A1W7-F1-model_v2	AlphaFold	D4A1W7	1-1325	view protein structure

Transcriptome

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

Promoters

RGD ID:

13696233

Promoter ID:

EPDNEW_R6758

Type:

multiple initiation site

Name:

Nphp3_1

Description:

nephrocystin 3

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	8	112,526,536 - 112,526,596	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1563856	AgrOrtholog
BioCyc Gene	G2FUF-29298	BioCyc
Ensembl Genes	ENSRNOG00000048978	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000014636	ENTREZGENE
	ENSRNOT00000014636.8	UniProtKB/TrEMBL
	ENSRNOT00000122199.1	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.10	UniProtKB/TrEMBL
	3.40.50.300	UniProtKB/TrEMBL
InterPro	NPHP3-like_N	UniProtKB/TrEMBL
	NPHP3_ab_dom	UniProtKB/TrEMBL
	NPHP3_hel	UniProtKB/TrEMBL
	P-loop_NTPase	UniProtKB/TrEMBL
	TPR-like_helical	UniProtKB/TrEMBL
	TPR_NPHP3	UniProtKB/TrEMBL
	TPR_repeat	UniProtKB/TrEMBL
NCBI Gene	363126	ENTREZGENE
PANTHER	NEPHROCYSTIN-3	UniProtKB/TrEMBL
	TETRATRICOPEPTIDE REPEAT PROTEIN (AFU_ORTHOLOGUE AFUA_6G03870)	UniProtKB/TrEMBL
Pfam	NPHP3	UniProtKB/TrEMBL
	NPHP3_hel	UniProtKB/TrEMBL
	NPHP3_N	UniProtKB/TrEMBL
	TPR_12	UniProtKB/TrEMBL
	TPR_7	UniProtKB/TrEMBL
	TPR_NPHP3	UniProtKB/TrEMBL
PhenoGen	Nphp3	PhenoGen
PROSITE	TPR	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000048978	RatGTEx
SMART	TPR	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48452	UniProtKB/TrEMBL
	SSF52540	UniProtKB/TrEMBL
UniProt	A0ABK0L045_RAT	UniProtKB/TrEMBL
	D4A1W7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-29	Nphp3	nephrocystin 3	Nphp3	nephronophthisis 3 (adolescent)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-06	Nphp3	nephronophthisis 3 (adolescent)	RGD1563856_predicted	similar to nephrocystin 3 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1563856_predicted	similar to nephrocystin 3 (predicted)	LOC363126	similar to nephrocystin 3	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC363126	similar to nephrocystin 3			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM