Nphp3 (nephrocystin 3) - Rat Genome Database

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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 extracellular matrix organization; kidney morphogenesis; 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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28104,621,908 - 104,662,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8104,621,864 - 104,662,383 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8110,269,003 - 110,309,487 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08108,468,194 - 108,508,680 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08106,310,899 - 106,351,380 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08112,526,553 - 112,575,745 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8112,526,553 - 112,575,745 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08111,913,834 - 111,963,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48109,065,400 - 109,105,882 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8103,986,600 - 104,026,761 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28104,621,908 - 104,662,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8104,621,864 - 104,662,383 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8110,269,003 - 110,309,487 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08108,468,194 - 108,508,680 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08106,310,899 - 106,351,380 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08112,526,553 - 112,575,745 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8112,526,553 - 112,575,745 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08111,913,834 - 111,963,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48109,065,400 - 109,105,882 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8103,986,600 - 104,026,761 (+)NCBICelera
Cytogenetic Map8q32NCBI
NPHP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383132,680,609 - 132,722,409 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3132,680,609 - 132,722,432 (-)EnsemblGRCh38hg38GRCh38
GRCh373132,399,453 - 132,441,253 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363133,882,144 - 133,923,966 (-)NCBINCBI36Build 36hg18NCBI36
Build 343133,882,151 - 133,923,974NCBI
Celera3130,824,943 - 130,866,763 (-)NCBICelera
Cytogenetic Map3q22.1NCBI
HuRef3129,779,095 - 129,821,371 (-)NCBIHuRef
CHM1_13132,362,464 - 132,404,314 (-)NCBICHM1_1
T2T-CHM13v2.03135,425,099 - 135,466,912 (-)NCBIT2T-CHM13v2.0
Nphp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399103,879,743 - 103,921,010 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9103,879,743 - 103,921,017 (+)EnsemblGRCm39 Ensembl
GRCm389104,002,544 - 104,043,811 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9104,002,544 - 104,043,818 (+)EnsemblGRCm38mm10GRCm38
MGSCv379103,904,874 - 103,946,141 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369103,860,949 - 103,901,892 (+)NCBIMGSCv36mm8
Celera9103,555,338 - 103,596,843 (+)NCBICelera
Cytogenetic Map9F1NCBI
cM Map956.11NCBI
Nphp3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555015,799,879 - 5,837,022 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555015,799,879 - 5,837,022 (+)NCBIChiLan1.0ChiLan1.0
NPHP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan13130,636,218 - 130,677,487 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03129,753,399 - 129,795,300 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13137,229,994 - 137,271,458 (-)NCBIpanpan1.1PanPan1.1panPan2
NPHP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12329,662,486 - 29,703,629 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2329,645,641 - 29,703,805 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2329,637,421 - 29,678,561 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02330,176,434 - 30,217,575 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2330,176,684 - 30,217,513 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12329,872,412 - 29,913,301 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02329,929,544 - 29,970,895 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02330,177,261 - 30,218,423 (-)NCBIUU_Cfam_GSD_1.0
Nphp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560269,251,499 - 69,287,758 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365296,009,301 - 6,049,447 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365296,013,321 - 6,048,249 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPHP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1373,858,427 - 73,900,967 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11373,843,770 - 73,901,020 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21381,415,846 - 81,445,656 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPHP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11557,550,878 - 57,629,106 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1557,551,189 - 57,592,661 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604130,538,900 - 30,580,436 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nphp3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247308,816,643 - 8,874,649 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247308,824,370 - 8,874,614 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nphp3
143 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8102370617108923645Rat


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 4
Low 3 41 57 41 19 41 8 11 74 35 37 11 8
Below cutoff 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000014636   ⟹   ENSRNOP00000014636
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8104,621,864 - 104,662,383 (+)Ensembl
Rnor_6.0 Ensembl8112,526,553 - 112,575,745 (+)Ensembl
RefSeq Acc Id: NM_001191882   ⟹   NP_001178811
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28104,621,908 - 104,662,383 (+)NCBI
Rnor_6.08112,526,553 - 112,575,745 (+)NCBI
Rnor_5.08111,913,834 - 111,963,488 (+)NCBI
Celera8103,986,600 - 104,026,761 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178811 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014636
  ENSRNOP00000014636.6
RefSeq Acc Id: NP_001178811   ⟸   NM_001191882
- UniProtKB: D4A1W7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014636   ⟸   ENSRNOT00000014636

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 AssemblyChrPosition (strand)Source
Rnor_6.08112,526,536 - 112,526,596EPDNEW

Additional Information

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
  ENSRNOT00000014636.7 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  TPR-like_helical 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 TPR_12 UniProtKB/TrEMBL
  TPR_7 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 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