Pkd1 (polycystin 1, transient receptor potential channel interacting) - Rat Genome Database

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Gene: Pkd1 (polycystin 1, transient receptor potential channel interacting) Rattus norvegicus
Analyze
Symbol: Pkd1
Name: polycystin 1, transient receptor potential channel interacting
RGD ID: 3333
Description: Predicted to enable several functions, including Wnt receptor activity; transcription regulator inhibitor activity; and transmembrane transporter binding activity. Predicted to contribute to calcium channel activity. Involved in positive regulation of cytosolic calcium ion concentration. Located in lateral plasma membrane. Used to study polycystic kidney disease. Human ortholog(s) of this gene implicated in autosomal dominant polycystic kidney disease; intracranial aneurysm; and polycystic kidney disease 1. Orthologous to human PKD1 (polycystin 1, transient receptor potential channel interacting); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-acetamidofluorene; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: polycystic kidney disease 1; polycystic kidney disease 1 homolog; polycystic kidney disease 1 homolog (human); polycystin 1; polycystin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Pkd1em2Mcwi ; Pkd1em3Mcwi ; Pkd1em1Mcwi ; Pkd1em6Mcwi
Genetic Models: LEW-Pkd1em2Mcwi ; LEW-Pkd1em6Mcwi ; LEW-Pkd1em1Mcwi ; LEW-Pkd1em3Mcwi
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,077,733 - 14,125,682 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,078,679 - 14,125,681 (+)EnsemblGRCr8
mRatBN7.21013,573,779 - 13,621,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,573,021 - 13,621,128 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,320,767 - 18,367,923 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,809,613 - 17,856,769 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,308,806 - 13,355,967 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01013,914,057 - 13,962,008 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,915,214 - 13,962,008 (+)Ensemblrn6Rnor6.0
Rnor_5.01013,731,035 - 13,778,993 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41013,801,445 - 13,848,212 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,254,601 - 13,301,131 (+)NCBICelera
RGSC_v3.11013,801,471 - 13,848,236 (+)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2-acetamidofluorene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acetylcholine  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
FR900359  (ISO)
gentamycin  (EXP)
indometacin  (ISO)
ketamine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nitrofen  (EXP)
okadaic acid  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylephrine  (ISO)
pirinixic acid  (ISO)
potassium chloride  (ISO)
progesterone  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sulindac  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
vitamin E  (ISO)
xylitol  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (IEA)
blood vessel development  (IEA,ISO)
branching morphogenesis of an epithelial tube  (IEA,ISO)
calcium ion transmembrane transport  (IEA,ISO)
calcium ion transport  (IBA,IEA,ISO)
cartilage condensation  (IEA,ISO)
cartilage development  (IEA,ISO)
cell surface receptor signaling pathway  (IEA,ISO)
cell surface receptor signaling pathway via JAK-STAT  (IEA,ISO)
cell-cell adhesion  (IEA,ISO)
chordate embryonic development  (IEA)
detection of mechanical stimulus  (IEA,ISO)
digestive tract development  (IEA,ISO)
embryonic placenta development  (IEA,ISO)
establishment of cell polarity  (IEA,ISO)
genitalia development  (IEA,ISO)
heart development  (IEA,ISO)
in utero embryonic development  (IEA,ISO)
kidney development  (IEA,ISO)
liver development  (IEA,ISO)
lung epithelium development  (IEA,ISO)
lymph vessel morphogenesis  (IEA,ISO)
mesonephric duct development  (IEA,ISO)
mesonephric tubule development  (IEA,ISO)
metanephric ascending thin limb development  (IEA,ISO)
metanephric collecting duct development  (IEA,ISO)
metanephric distal tubule morphogenesis  (IEA,ISO)
metanephric proximal tubule development  (IEA,ISO)
mitocytosis  (IEA,ISO)
neural tube development  (IEA,ISO)
nitrogen cycle metabolic process  (IEA,ISO)
peptidyl-serine phosphorylation  (ISO)
placenta blood vessel development  (IEA,ISO)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
protein export from nucleus  (IEA,ISO)
protein heterotetramerization  (IEA,ISO)
regulation of cell adhesion  (IEA,ISO)
regulation of cell cycle  (IEA,ISO)
regulation of cell cycle process  (IEA)
regulation of G1/S transition of mitotic cell cycle  (IEA,ISO)
regulation of gene expression  (IEA)
regulation of mitotic spindle organization  (IEA,ISO)
regulation of proteasomal protein catabolic process  (IEA,ISO)
response to fluid shear stress  (IEA,ISO)
skin development  (IEA,ISO)
spinal cord development  (IEA,ISO)
Wnt signaling pathway  (IEA,ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. A genetic interaction network of five genes for human polycystic kidney and liver diseases defines polycystin-1 as the central determinant of cyst formation. Fedeles SV, etal., Nat Genet. 2011 Jun 19;43(7):639-47. doi: 10.1038/ng.860.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Novel PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease (ADPKD). Hoefele J, etal., Nephrol Dial Transplant. 2011 Jul;26(7):2181-8. Epub 2010 Nov 29.
5. Functional polycystin-1 dosage governs autosomal dominant polycystic kidney disease severity. Hopp K, etal., J Clin Invest. 2012 Nov 1;122(11):4257-73. doi: 10.1172/JCI64313. Epub 2012 Oct 15.
6. Tuberin-dependent membrane localization of polycystin-1: a functional link between polycystic kidney disease and the TSC2 tumor suppressor gene. Kleymenova E, etal., Mol Cell 2001 Apr;7(4):823-32.
7. Late onset of renal and hepatic cysts in Pkd1-targeted heterozygotes. Lu W, etal., Nat Genet. 1999 Feb;21(2):160-1. doi: 10.1038/5944.
8. Cholangiocyte cilia detect changes in luminal fluid flow and transmit them into intracellular Ca2+ and cAMP signaling. Masyuk AI, etal., Gastroenterology. 2006 Sep;131(3):911-20.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
12. Screening the 3' region of the polycystic kidney disease 1 (PKD1) gene reveals six novel mutations. Peral B, etal., Am J Hum Genet. 1996 Jan;58(1):86-96.
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Comprehensive gene review and curation RGD comprehensive gene curation
17. Association of mutation position in polycystic kidney disease 1 (PKD1) gene and development of a vascular phenotype. Rossetti S, etal., Lancet. 2003 Jun 28;361(9376):2196-201.
18. Tissue-specific expression and splicing of the rat polycystic kidney disease 1 gene. Xu H, etal., DNA Seq 2001 Dec;12(5-6):361-6.
Additional References at PubMed
PMID:9171830   PMID:9192675   PMID:10677526   PMID:10770959   PMID:11593033   PMID:11891195   PMID:11901144   PMID:12007403   PMID:12482949   PMID:12514735   PMID:15326289   PMID:15545994  
PMID:15548533   PMID:15632090   PMID:15858826   PMID:16282979   PMID:16311606   PMID:17980165   PMID:18285569   PMID:19056867   PMID:19135240   PMID:19158352   PMID:19897428   PMID:20181743  
PMID:20862291   PMID:21518438   PMID:23001567   PMID:24039875   PMID:24740233   PMID:24767999   PMID:24939912   PMID:25367197   PMID:25405894   PMID:25807483   PMID:25888683   PMID:25889640  
PMID:26739494   PMID:27214281   PMID:28154160   PMID:28408623   PMID:29126879   PMID:29133434   PMID:29949809   PMID:30093605   PMID:33065236   PMID:34407229  


Genomics

Comparative Map Data
Pkd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,077,733 - 14,125,682 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,078,679 - 14,125,681 (+)EnsemblGRCr8
mRatBN7.21013,573,779 - 13,621,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,573,021 - 13,621,128 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1018,320,767 - 18,367,923 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,809,613 - 17,856,769 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01013,308,806 - 13,355,967 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01013,914,057 - 13,962,008 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,915,214 - 13,962,008 (+)Ensemblrn6Rnor6.0
Rnor_5.01013,731,035 - 13,778,993 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41013,801,445 - 13,848,212 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,254,601 - 13,301,131 (+)NCBICelera
RGSC_v3.11013,801,471 - 13,848,236 (+)NCBI
Cytogenetic Map10q12NCBI
PKD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38162,088,708 - 2,135,898 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl162,088,708 - 2,135,898 (-)Ensemblhg38GRCh38
GRCh37162,138,709 - 2,185,899 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36162,078,712 - 2,125,900 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34162,078,711 - 2,125,900NCBI
Celera162,350,824 - 2,400,282 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef162,063,439 - 2,112,133 (-)NCBIHuRef
CHM1_1162,138,626 - 2,185,837 (-)NCBICHM1_1
T2T-CHM13v2.0162,108,809 - 2,158,372 (-)NCBIT2T-CHM13v2.0
Pkd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391724,767,657 - 24,815,457 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1724,768,808 - 24,815,482 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381724,548,689 - 24,596,514 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1724,549,834 - 24,596,508 (+)Ensemblmm10GRCm38
MGSCv371724,686,895 - 24,733,459 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361724,277,550 - 24,324,083 (+)NCBIMGSCv36mm8
Celera1725,067,435 - 25,114,509 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.4NCBI
Pkd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544215,145,640 - 15,178,377 (+)Ensembl
ChiLan1.0NW_00495544215,132,555 - 15,178,377 (+)NCBIChiLan1.0ChiLan1.0
LOC100972297
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21832,327,012 - 32,348,526 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11637,144,981 - 37,166,519 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v016604,927 - 1,697,831 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1162,176,778 - 2,185,337 (-)NCBIPanPan1.1PanPan1.1panPan2
PKD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,811,051 - 38,865,503 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl638,837,964 - 38,865,503 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha640,062,677 - 40,104,408 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0639,132,038 - 39,173,761 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl639,132,038 - 39,173,760 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1638,816,853 - 38,858,566 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0638,789,176 - 38,830,884 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,267,946 - 39,309,679 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pkd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344104,751,303 - 104,783,237 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366941,930,621 - 1,957,179 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366941,923,383 - 1,958,160 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl339,849,609 - 39,899,455 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1339,849,579 - 39,899,455 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2342,282,099 - 42,331,966 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PKD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.151,985,165 - 2,031,518 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl51,983,632 - 2,015,551 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606829,031,552 - 29,079,001 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624913118,733 - 165,859 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624913118,520 - 166,939 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkd1
77 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:566
Count of miRNA genes:240
Interacting mature miRNAs:288
Transcripts:ENSRNOT00000015092
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat

Markers in Region
RH143904  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,620,574 - 13,620,692 (+)MAPPERmRatBN7.2
Rnor_6.01013,961,445 - 13,961,562NCBIRnor6.0
Rnor_5.01013,778,430 - 13,778,547UniSTSRnor5.0
RGSC_v3.41013,847,649 - 13,847,766UniSTSRGSC3.4
Celera1013,300,568 - 13,300,685UniSTS
RH 3.4 Map10191.5UniSTS
Cytogenetic Map10q12UniSTS
RH94522  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,621,172 - 13,621,274 (+)MAPPERmRatBN7.2
Rnor_6.01013,962,043 - 13,962,144NCBIRnor6.0
Rnor_5.01013,779,028 - 13,779,129UniSTSRnor5.0
RGSC_v3.41013,848,247 - 13,848,348UniSTSRGSC3.4
Celera1013,301,166 - 13,301,267UniSTS
Cytogenetic Map10q12UniSTS
RH138827  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,621,139 - 13,621,352 (+)MAPPERmRatBN7.2
Rnor_6.01013,962,010 - 13,962,222NCBIRnor6.0
Rnor_5.01013,778,995 - 13,779,207UniSTSRnor5.0
RGSC_v3.41013,848,214 - 13,848,426UniSTSRGSC3.4
Celera1013,301,133 - 13,301,345UniSTS
Cytogenetic Map10q12UniSTS
Pkd1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,617,394 - 13,617,955 (+)MAPPERmRatBN7.2
Rnor_6.01013,958,265 - 13,958,825NCBIRnor6.0
Rnor_5.01013,775,250 - 13,775,810UniSTSRnor5.0
RGSC_v3.41013,844,496 - 13,845,056UniSTSRGSC3.4
Celera1013,297,465 - 13,298,025UniSTS
Cytogenetic Map10q12UniSTS


Genetic Models
This gene Pkd1 is modified in the following models/strains:
LEW-Pkd1em2Mcwi     LEW-Pkd1em6Mcwi     LEW-Pkd1em1Mcwi     LEW-Pkd1em3Mcwi    


Expression

RNA-SEQ Expression

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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015092   ⟹   ENSRNOP00000015092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,078,679 - 14,125,681 (+)Ensembl
mRatBN7.2 Ensembl1013,573,021 - 13,621,128 (+)Ensembl
Rnor_6.0 Ensembl1013,915,214 - 13,962,008 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000116450   ⟹   ENSRNOP00000089569
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,078,679 - 14,125,681 (+)Ensembl
mRatBN7.2 Ensembl1013,573,021 - 13,621,128 (+)Ensembl
RefSeq Acc Id: NM_001414013   ⟹   NP_001400942
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,078,679 - 14,125,682 (+)NCBI
mRatBN7.21013,574,133 - 13,621,138 (+)NCBI
RefSeq Acc Id: XM_008767539   ⟹   XP_008765761
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,077,744 - 14,125,681 (+)NCBI
mRatBN7.21013,573,783 - 13,621,137 (+)NCBI
Rnor_6.01013,914,057 - 13,962,004 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767540   ⟹   XP_008765762
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,077,744 - 14,125,681 (+)NCBI
mRatBN7.21013,573,783 - 13,621,137 (+)NCBI
Rnor_6.01013,914,057 - 13,962,004 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767541   ⟹   XP_008765763
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,077,738 - 14,120,353 (+)NCBI
mRatBN7.21013,573,779 - 13,615,811 (+)NCBI
Rnor_6.01013,914,057 - 13,956,650 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085207   ⟹   XP_038941135
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,101,996 - 14,125,681 (+)NCBI
mRatBN7.21013,597,450 - 13,621,138 (+)NCBI
RefSeq Acc Id: XM_063268414   ⟹   XP_063124484
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,077,733 - 14,125,681 (+)NCBI
RefSeq Acc Id: XM_063268415   ⟹   XP_063124485
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,077,744 - 14,125,681 (+)NCBI
RefSeq Acc Id: XM_063268416   ⟹   XP_063124486
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,097,841 - 14,125,681 (+)NCBI
RefSeq Acc Id: XP_008765761   ⟸   XM_008767539
- Peptide Label: isoform X2
- UniProtKB: Q9ERV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765762   ⟸   XM_008767540
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AC84 (UniProtKB/TrEMBL),   Q9ERV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765763   ⟸   XM_008767541
- Peptide Label: isoform X6
- UniProtKB: A6HCU0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015092   ⟸   ENSRNOT00000015092
RefSeq Acc Id: XP_038941135   ⟸   XM_039085207
- Peptide Label: isoform X7
Ensembl Acc Id: ENSRNOP00000089569   ⟸   ENSRNOT00000116450
RefSeq Acc Id: NP_001400942   ⟸   NM_001414013
- Peptide Label: precursor
- UniProtKB: F1MAD3 (UniProtKB/TrEMBL),   Q9ERV0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124484   ⟸   XM_063268414
- Peptide Label: isoform X1
- UniProtKB: F1MAD3 (UniProtKB/TrEMBL),   Q9ERV0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124485   ⟸   XM_063268415
- Peptide Label: isoform X4
- UniProtKB: Q9ERV0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124486   ⟸   XM_063268416
- Peptide Label: isoform X5
- UniProtKB: Q9ERV0 (UniProtKB/TrEMBL)
Protein Domains
C-type lectin   GAIN-B   PKD   PLAT   REJ   WSC

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3333 AgrOrtholog
BioCyc Gene G2FUF-25846 BioCyc
Ensembl Genes ENSRNOG00000010771 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015092 ENTREZGENE
  ENSRNOT00000015092.8 UniProtKB/TrEMBL
  ENSRNOT00000116450 ENTREZGENE
  ENSRNOT00000116450.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/TrEMBL
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  Cys-rich_flank_reg_C UniProtKB/TrEMBL
  GAIN_B UniProtKB/TrEMBL
  GPS_dom UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LipOase_LH2 UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
  PKD/Chitinase_dom UniProtKB/TrEMBL
  PKD/REJ-like UniProtKB/TrEMBL
  PKD1_2_channel UniProtKB/TrEMBL
  PKD_1 UniProtKB/TrEMBL
  PKD_dom UniProtKB/TrEMBL
  PKD_dom_sf UniProtKB/TrEMBL
  PLAT/LH2_dom_sf UniProtKB/TrEMBL
  PLAT_polycystin1 UniProtKB/TrEMBL
  Polycystin_cat UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ-like UniProtKB/TrEMBL
  WSC_carb-bd UniProtKB/TrEMBL
NCBI Gene 24650 ENTREZGENE
PANTHER POLYCYSTIN-1 UniProtKB/TrEMBL
  POLYCYSTIN-1 UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  PKD UniProtKB/TrEMBL
  PKD_channel UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
  WSC UniProtKB/TrEMBL
PhenoGen Pkd1 PhenoGen
PRINTS POLYCYSTIN1 UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  LRR UniProtKB/TrEMBL
  PKD UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
  WSC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010771 RatGTEx
SMART CLECT UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  LH2 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
  PKD UniProtKB/TrEMBL
  WSC UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  L domain-like UniProtKB/TrEMBL
  Lipase_LipOase UniProtKB/TrEMBL
  PKD UniProtKB/TrEMBL
UniProt A0A8I6AC84 ENTREZGENE, UniProtKB/TrEMBL
  A6HCU0 ENTREZGENE, UniProtKB/TrEMBL
  F1MAD3 ENTREZGENE, UniProtKB/TrEMBL
  Q9ERV0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Pkd1  polycystic kidney disease 1  Pkd1  polycystic kidney disease 1 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Pkd1  polycystic kidney disease 1 homolog (human)  Pkd1  polycystic kidney disease 1 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Pkd1  polycystic kidney disease 1 homolog    Polycystic kidney disease 1  Name updated 625702 APPROVED
2002-06-10 Pkd1  Polycystic kidney disease 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization found localized to the Golgi and lateral cell membrane 633539
gene_expression displays ubiquitous expression 633540
gene_regulation requires the Tsc2 tumor suprressor gene for correct transport from the Golgi to the lateral cell membrane 633539