Prnp (prion protein) - Rat Genome Database

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Gene: Prnp (prion protein) Rattus norvegicus
Analyze
Symbol: Prnp
Name: prion protein
RGD ID: 3410
Description: Enables several functions, including ATP-dependent protein binding activity; chaperone binding activity; and lamin binding activity. Involved in several processes, including negative regulation of long-term synaptic potentiation; positive regulation of protein localization to plasma membrane; and response to copper ion. Located in cytoplasm; plasma membrane; and postsynaptic density. Used to study hyperglycemia and scrapie. Human ortholog(s) of this gene implicated in Creutzfeldt-Jakob disease; Gerstmann-Straussler-Scheinker syndrome; Huntington's disease-like 1; fatal familial insomnia; and kuru. Orthologous to human PRNP (prion protein); PARTICIPATES IN glypican signaling pathway; iron uptake pathway; prion disease pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: major prion protein; Prion protein structural; prion protein, PrP; Prion protein, structural; Prn; PrP
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
mRatBN7.23119,186,073 - 119,201,513 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3119,177,485 - 119,203,937 (+)Ensembl
Rnor_6.03124,515,917 - 124,531,320 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3124,515,978 - 124,531,316 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03131,009,974 - 131,025,370 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43119,676,137 - 119,691,507 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13119,581,709 - 119,597,080 (+)NCBI
Celera3117,986,209 - 118,001,394 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(E)-thiamethoxam  (ISO)
1,2-dichloroethane  (ISO)
1,2-dihexadecanoyl-sn-glycero-3-phosphocholine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2,2-tetramine  (EXP)
2,2,2-trifluoroethanol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
bathocuproine disulfonic acid  (EXP)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzoates  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butyric acid  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
Congo Red  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
diarsenic trioxide  (ISO)
dichloromethane  (ISO)
diethyldithiocarbamic acid  (EXP)
dioxygen  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
edaravone  (EXP)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
ethylbenzene  (ISO)
ethylenediaminetetraacetic acid  (ISO)
etoposide  (ISO)
filipin III  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (EXP,ISO)
gentamycin  (EXP)
glucose  (ISO)
glutathione  (ISO)
glyphosate  (EXP)
GW 1929  (ISO)
heparan sulfate  (ISO)
hydrogen peroxide  (ISO)
indoxyl sulfate  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
lead diacetate  (ISO)
lead tetraacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
luzindole  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
melatonin  (ISO)
mercury dibromide  (ISO)
metam  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitroprusside  (ISO)
nystatin  (ISO)
o-xylene  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
Pyridostigmine bromide  (EXP)
reactive oxygen species  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
tamibarotene  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
tetracycline  (ISO)
thiamethoxam  (ISO)
thioacetamide  (EXP)
toluene  (ISO)
topotecan  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase activity  (ISO)
amyloid precursor protein metabolic process  (ISO)
calcium-mediated signaling using intracellular calcium source  (ISO)
cellular response to amyloid-beta  (ISO)
cellular response to copper ion  (ISO)
cellular response to xenobiotic stimulus  (ISO)
learning or memory  (IMP,ISO)
negative regulation of activated T cell proliferation  (ISO)
negative regulation of amyloid precursor protein catabolic process  (ISO)
negative regulation of amyloid-beta formation  (ISO)
negative regulation of apoptotic process  (IMP,ISO)
negative regulation of calcineurin-NFAT signaling cascade  (ISO)
negative regulation of catalytic activity  (IDA)
negative regulation of dendritic spine maintenance  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of endopeptidase activity  (IEA)
negative regulation of interferon-gamma production  (ISO)
negative regulation of interleukin-17 production  (ISO)
negative regulation of interleukin-2 production  (ISO)
negative regulation of long-term synaptic potentiation  (IDA)
negative regulation of protein phosphorylation  (ISO)
negative regulation of T cell receptor signaling pathway  (ISO)
neuron projection maintenance  (ISO)
obsolete modulation of age-related behavioral decline  (ISO)
positive regulation of cell death  (ISO)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of neuron death  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of protein localization to plasma membrane  (IMP,ISO)
positive regulation of protein targeting to membrane  (ISO)
positive regulation of protein tyrosine kinase activity  (ISO)
protein destabilization  (ISO)
protein homooligomerization  (IEA)
regulation of calcium ion import across plasma membrane  (ISO)
regulation of glutamate receptor signaling pathway  (ISO)
regulation of intracellular calcium activated chloride channel activity  (ISO)
regulation of peptidyl-tyrosine phosphorylation  (ISO)
regulation of potassium ion transmembrane transport  (ISO)
regulation of protein localization  (ISO)
response to amyloid-beta  (ISO)
response to cadmium ion  (IDA)
response to copper ion  (IDA)
response to oxidative stress  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Azzalin A, etal., Biochem Biophys Res Commun. 2006 Jul 21;346(1):108-15. Epub 2006 May 24.
2. Barry AE, etal., J Neurosci. 2011 May 18;31(20):7259-63. doi: 10.1523/JNEUROSCI.6500-10.2011.
3. Beck KE, etal., Biochem Biophys Res Commun. 2006 Aug 4;346(3):866-71. Epub 2006 Jun 6.
4. Bogdan AR, etal., Trends Biochem Sci. 2016 Mar;41(3):274-86. doi: 10.1016/j.tibs.2015.11.012. Epub 2015 Dec 23.
5. Coitinho AS, etal., Eur J Neurosci. 2006 Dec;24(11):3255-64.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Goldfarb LG, etal., Eur J Epidemiol. 1991 Sep;7(5):477-86.
9. Liao YC, etal., Lab Invest 1987 Oct;57(4):370-4.
10. Loberto N, etal., J Neurochem. 2005 Nov;95(3):771-83.
11. Lopez TP, etal., Acta Neuropathol Commun. 2017 Nov 21;5(1):84. doi: 10.1186/s40478-017-0484-y.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. Qin K, etal., Neuroscience. 2006 Sep 1;141(3):1375-88. Epub 2006 Jun 12.
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Rushworth JV, etal., J Biol Chem. 2013 Mar 29;288(13):8935-51. doi: 10.1074/jbc.M112.400358. Epub 2013 Feb 5.
22. Saeki K, etal., Biochem Biophys Res Commun 1996 Feb 6;219(1):47-52.
23. Saeki K, etal., Virus Genes 1996;12(1):15-20.
24. Shyu WC, etal., Mol Neurobiol 2002 Aug;26(1):1-12.
25. Strom A, etal., Eur J Cell Biol. 2011 May;90(5):414-9. doi: 10.1016/j.ejcb.2010.11.015. Epub 2011 Jan 28.
26. Strom A, etal., Lab Invest. 2006 Dec 4;.
27. Um JW, etal., Nat Neurosci. 2012 Sep;15(9):1227-35. doi: 10.1038/nn.3178. Epub 2012 Jul 22.
28. Um JW, etal., Neuron. 2013 Sep 4;79(5):887-902. doi: 10.1016/j.neuron.2013.06.036.
29. Varela-Nallar L, etal., Am J Physiol Cell Physiol. 2006 Jan;290(1):C271-81. Epub 2005 Sep 7.
30. Wopfner F, etal., J Mol Biol 1999 Jun 25;289(5):1163-78.
Additional References at PubMed
PMID:7909925   PMID:9837873   PMID:10037495   PMID:11739375   PMID:11756421   PMID:11900542   PMID:12093733   PMID:12212939   PMID:12477932   PMID:12500977   PMID:12663673   PMID:12911750  
PMID:12927782   PMID:12970341   PMID:14660659   PMID:14741357   PMID:15208260   PMID:15229281   PMID:15262264   PMID:15489334   PMID:15670783   PMID:15753097   PMID:15891070   PMID:15911347  
PMID:16004966   PMID:16139509   PMID:16254249   PMID:16286452   PMID:17405933   PMID:17556367   PMID:17573534   PMID:17854776   PMID:18025469   PMID:18419754   PMID:18436646   PMID:19056867  
PMID:19204296   PMID:19242475   PMID:19278656   PMID:19327369   PMID:19381258   PMID:19457127   PMID:19493159   PMID:19503793   PMID:19581412   PMID:19805070   PMID:19850936   PMID:19927125  
PMID:20145049   PMID:20345906   PMID:20445063   PMID:20564047   PMID:21041683   PMID:21441913   PMID:21478263   PMID:21559407   PMID:21920025   PMID:22102467   PMID:22116041   PMID:22362149  
PMID:22449963   PMID:22854022   PMID:23376485   PMID:23892077   PMID:24225951   PMID:24386462   PMID:24554723   PMID:24780399   PMID:24859148   PMID:25058115   PMID:25931508   PMID:26149502  
PMID:26946358   PMID:28081197   PMID:32788217  


Genomics

Comparative Map Data
Prnp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23119,186,073 - 119,201,513 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3119,177,485 - 119,203,937 (+)Ensembl
Rnor_6.03124,515,917 - 124,531,320 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3124,515,978 - 124,531,316 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03131,009,974 - 131,025,370 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43119,676,137 - 119,691,507 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13119,581,709 - 119,597,080 (+)NCBI
Celera3117,986,209 - 118,001,394 (+)NCBICelera
Cytogenetic Map3q36NCBI
PRNP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38204,686,456 - 4,701,588 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl204,686,350 - 4,701,590 (+)EnsemblGRCh38hg38GRCh38
GRCh37204,667,102 - 4,682,234 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36204,614,797 - 4,630,234 (+)NCBINCBI36hg18NCBI36
Build 34204,615,068 - 4,630,233NCBI
Celera204,736,512 - 4,751,948 (+)NCBI
Cytogenetic Map20p13NCBI
HuRef204,620,194 - 4,635,632 (+)NCBIHuRef
CHM1_1204,667,528 - 4,682,967 (+)NCBICHM1_1
Prnp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392131,751,848 - 131,780,356 (+)NCBIGRCm39mm39
GRCm39 Ensembl2131,751,848 - 131,780,349 (+)Ensembl
GRCm382131,909,928 - 131,938,436 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2131,909,928 - 131,938,429 (+)EnsemblGRCm38mm10GRCm38
MGSCv372131,735,664 - 131,764,167 (+)NCBIGRCm37mm9NCBIm37
MGSCv362131,601,398 - 131,629,868 (+)NCBImm8
Celera2133,143,177 - 133,164,079 (+)NCBICelera
Cytogenetic Map2F2NCBI
cM Map264.07NCBI
Prnp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541515,442,313 - 15,454,644 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541515,442,313 - 15,454,644 (+)NCBIChiLan1.0ChiLan1.0
PRNP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1204,523,141 - 4,525,522 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl204,523,155 - 4,523,916 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0204,713,616 - 4,728,847 (+)NCBIMhudiblu_PPA_v0panPan3
PRNP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12416,845,224 - 16,862,319 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2416,846,207 - 16,859,815 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2416,670,727 - 16,671,500 (-)NCBI
ROS_Cfam_1.02417,263,379 - 17,280,460 (-)NCBI
ROS_Cfam_1.0 Ensembl2417,263,381 - 17,280,378 (-)Ensembl
UMICH_Zoey_3.12416,859,351 - 16,860,124 (-)NCBI
UNSW_CanFamBas_1.02416,965,836 - 16,966,609 (-)NCBI
UU_Cfam_GSD_1.02417,299,279 - 17,300,052 (-)NCBI
LOC101959784
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640165,673,463 - 165,687,259 (-)NCBI
SpeTri2.0NW_00493648514,104,829 - 14,118,614 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRNP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1713,693,628 - 13,705,318 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11713,694,195 - 13,705,126 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21714,656,638 - 14,667,625 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103247014
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1233,368,020 - 33,384,556 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl233,369,629 - 33,370,366 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607111,150,240 - 11,165,879 (+)NCBIVero_WHO_p1.0
Prnp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247415,785,139 - 5,802,162 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC125625P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,199,522 - 119,200,287 (+)MAPPERmRatBN7.2
Rnor_6.03124,529,330 - 124,530,094NCBIRnor6.0
Rnor_5.03131,023,380 - 131,024,144UniSTSRnor5.0
RGSC_v3.43119,689,521 - 119,690,285UniSTSRGSC3.4
Celera3117,999,408 - 118,000,172UniSTS
Cytogenetic Map3q36UniSTS
PMC136859P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,199,810 - 119,200,285 (+)MAPPERmRatBN7.2
Rnor_6.03124,529,618 - 124,530,092NCBIRnor6.0
Rnor_5.03131,023,668 - 131,024,142UniSTSRnor5.0
RGSC_v3.43119,689,809 - 119,690,283UniSTSRGSC3.4
Celera3117,999,696 - 118,000,170UniSTS
Cytogenetic Map3q36UniSTS
RH129872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,201,126 - 119,201,327 (+)MAPPERmRatBN7.2
Rnor_6.03124,530,934 - 124,531,134NCBIRnor6.0
Rnor_5.03131,024,984 - 131,025,184UniSTSRnor5.0
RGSC_v3.43119,691,125 - 119,691,325UniSTSRGSC3.4
Celera3118,001,012 - 118,001,212UniSTS
RH 3.4 Map31003.9UniSTS
Cytogenetic Map3q36UniSTS
RH140731  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,200,591 - 119,200,729 (+)MAPPERmRatBN7.2
Rnor_6.03124,530,399 - 124,530,536NCBIRnor6.0
Rnor_5.03131,024,449 - 131,024,586UniSTSRnor5.0
RGSC_v3.43119,690,590 - 119,690,727UniSTSRGSC3.4
Celera3118,000,477 - 118,000,614UniSTS
RH 3.4 Map31003.8UniSTS
Cytogenetic Map3q36UniSTS
Prnp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,200,553 - 119,200,783 (+)MAPPERmRatBN7.2
Rnor_6.03124,530,361 - 124,530,590NCBIRnor6.0
Rnor_5.03131,024,411 - 131,024,640UniSTSRnor5.0
RGSC_v3.43119,690,552 - 119,690,781UniSTSRGSC3.4
Celera3118,000,439 - 118,000,668UniSTS
Cytogenetic Map3q36UniSTS
Prnp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,199,522 - 119,199,814 (+)MAPPERmRatBN7.2
Rnor_6.03124,529,330 - 124,529,621NCBIRnor6.0
Rnor_5.03131,023,380 - 131,023,671UniSTSRnor5.0
Celera3117,999,408 - 117,999,699UniSTS
Cytogenetic Map3q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:391
Count of miRNA genes:233
Interacting mature miRNAs:278
Transcripts:ENSRNOT00000028881
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.


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 3 43 38 22 19 22 8 11 74 35 41 11 8
Low 19 19 19
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028881   ⟹   ENSRNOP00000028881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3124,515,978 - 124,531,316 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104185   ⟹   ENSRNOP00000093351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3119,186,177 - 119,201,327 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106614   ⟹   ENSRNOP00000093957
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3119,186,081 - 119,203,937 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113525   ⟹   ENSRNOP00000085462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3119,177,485 - 119,201,510 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117610   ⟹   ENSRNOP00000096232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3119,186,081 - 119,203,937 (+)Ensembl
RefSeq Acc Id: NM_012631   ⟹   NP_036763
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23119,186,168 - 119,201,509 (+)NCBI
Rnor_6.03124,515,978 - 124,531,316 (+)NCBI
Rnor_5.03131,009,974 - 131,025,370 (+)NCBI
RGSC_v3.43119,676,137 - 119,691,507 (+)RGD
Celera3117,986,209 - 118,001,394 (+)RGD
Sequence:
RefSeq Acc Id: XM_006235062   ⟹   XP_006235124
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23119,186,073 - 119,201,513 (+)NCBI
Rnor_6.03124,515,917 - 124,531,320 (+)NCBI
Rnor_5.03131,009,974 - 131,025,370 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104280   ⟹   XP_038960208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23119,186,073 - 119,201,513 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036763   ⟸   NM_012631
- Peptide Label: precursor
- UniProtKB: P13852 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235124   ⟸   XM_006235062
- Peptide Label: isoform X1
- UniProtKB: P13852 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028881   ⟸   ENSRNOT00000028881
RefSeq Acc Id: XP_038960208   ⟸   XM_039104280
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000093957   ⟸   ENSRNOT00000106614
RefSeq Acc Id: ENSRNOP00000096232   ⟸   ENSRNOT00000117610
RefSeq Acc Id: ENSRNOP00000085462   ⟸   ENSRNOT00000113525
RefSeq Acc Id: ENSRNOP00000093351   ⟸   ENSRNOT00000104185

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P13852-F1-model_v2 AlphaFold P13852 1-254 view protein structure

Transcriptome

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

Promoters
RGD ID:13692451
Promoter ID:EPDNEW_R2976
Type:multiple initiation site
Name:Prnp_1
Description:prion protein
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_6.03124,515,986 - 124,516,046EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 131023728 131023729 G A snv LEC/Tj (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3410 AgrOrtholog
BioCyc Gene G2FUF-47793 BioCyc
Ensembl Genes ENSRNOG00000021259 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000028881 UniProtKB/Swiss-Prot
  ENSRNOP00000093957 ENTREZGENE
  ENSRNOP00000096232 ENTREZGENE
Ensembl Transcript ENSRNOT00000028881 UniProtKB/Swiss-Prot
  ENSRNOT00000106614 ENTREZGENE
  ENSRNOT00000117610 ENTREZGENE
Gene3D-CATH 1.10.790.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7099864 IMAGE-MGC_LOAD
InterPro Prion UniProtKB/Swiss-Prot
  Prion/Doppel_b-ribbon_dom_sf UniProtKB/Swiss-Prot
  Prion/Doppel_prot_b-ribbon_dom UniProtKB/Swiss-Prot
  Prion_N_dom UniProtKB/Swiss-Prot
KEGG Report rno:24686 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91417 IMAGE-MGC_LOAD
NCBI Gene 24686 ENTREZGENE
Pfam Prion UniProtKB/Swiss-Prot
  Prion_bPrPp UniProtKB/Swiss-Prot
PhenoGen Prnp PhenoGen
PRINTS PRION UniProtKB/Swiss-Prot
PROSITE PRION_1 UniProtKB/Swiss-Prot
  PRION_2 UniProtKB/Swiss-Prot
SMART PRP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54098 UniProtKB/Swiss-Prot
UniProt P13852 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q549H6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Prnp  prion protein    Prion protein, structural  Name updated 629478 APPROVED
2002-06-10 Prnp  Prion protein, structural      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization attached to plasma membrane by glycoinositol phospholipid (GPI) anchor 729621
gene_homology flexible region of structured segment (121-231 aa) conserved within 27 mammalian and 9 avian species 729621