Trpv1 (transient receptor potential cation channel, subfamily V, member 1) - Rat Genome Database

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Gene: Trpv1 (transient receptor potential cation channel, subfamily V, member 1) Rattus norvegicus
Analyze
Symbol: Trpv1
Name: transient receptor potential cation channel, subfamily V, member 1
RGD ID: 628841
Description: Enables several functions, including ATP binding activity; calmodulin binding activity; and ligand-gated ion channel activity. Involved in several processes, including calcium ion import across plasma membrane; cellular response to organonitrogen compound; and cellular response to temperature stimulus. Acts upstream of or within response to heat and response to pH. Located in several cellular components, including external side of plasma membrane; neuronal cell body; and postsynaptic membrane. Is integral component of plasma membrane. Used to study myocardial infarction and reflex epilepsy. Human ortholog(s) of this gene implicated in migraine. Orthologous to human TRPV1 (transient receptor potential cation channel subfamily V member 1); INTERACTS WITH (R)-camphor; (S)-nicotine; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: capsaicin receptor; deltaN-TRPV1; osm-9-like TRP channel 1; OTRPC1; transient receptor potential cation channel subfamily V member 1; transient receptor potential vanilloid 1 supraoptic nucleus; TRPV1_SON; vanilloid receptor 1; vanilloid receptor subtype 1; vanilloid receptor type 1 like protein 1; vanilloid receptor type 1-like; vanilloid type 1 receptor; VR.5'sv; Vr1; Vr1l1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Trpv1em1Sage  
Genetic Models: SD-Trpv1em1Sage-/-
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21057,851,428 - 57,876,513 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1057,851,428 - 57,876,513 (+)Ensembl
Rnor_6.01059,799,123 - 59,824,208 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1059,799,123 - 59,824,679 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01059,538,296 - 59,563,441 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41060,109,656 - 60,134,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11060,123,278 - 60,148,562 (+)NCBI
Celera1056,974,294 - 56,999,462 (+)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(R)-camphor  (EXP)
(S)-nicotine  (EXP)
1,2-dimethylhydrazine  (EXP)
1,2-naphthoquinone  (EXP)
17beta-estradiol  (EXP)
1H-benzimidazole  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-arachidonoylglycerol  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (EXP,ISO)
3-phenylprop-2-enal  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-methyl-3-[[1-oxo-2-(propylamino)propyl]amino]-2-thiophenecarboxylic acid methyl ester  (EXP)
6-propyl-2-thiouracil  (EXP)
8-(4-chlorophenylthio)-cAMP  (EXP,ISO)
acrolein  (ISO)
acrylamide  (EXP)
adenosine 5'-[gamma-thio]triphosphate  (EXP)
aflatoxin B1  (ISO)
allicin  (ISO)
allyl isothiocyanate  (ISO)
alpha-linolenic acid  (EXP)
alpha-Zearalanol  (ISO)
anandamide  (EXP,ISO)
antimycin A  (ISO)
arachidonic acid  (EXP)
aristolochic acid  (ISO)
aspartame  (ISO)
ATP  (EXP)
azoxystrobin  (ISO)
Benzamil  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
bupivacaine  (EXP)
calcium atom  (EXP,ISO)
calcium dichloride  (EXP,ISO)
calcium dihydroxide  (ISO)
calcium(0)  (EXP,ISO)
camphor  (EXP)
Cannabichromene  (ISO)
cannabidiol  (ISO)
cannabidiolic acid  (ISO)
Cannabidivarin  (ISO)
cannabigerol  (ISO)
cannabigerolic acid  (ISO)
capsaicin  (EXP,ISO)
capsazepine  (EXP,ISO)
carbon dioxide  (EXP)
chelerythrine  (EXP)
citric acid  (ISO)
citronellol  (ISO)
citronellol acetate  (ISO)
colforsin daropate hydrochloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
cytarabine  (ISO)
decabromodiphenyl ether  (EXP)
deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dodecyl hydrogen sulfate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
ethylenediaminetetraacetic acid  (ISO)
etoposide  (ISO)
fenpyroximate  (ISO)
fenvalerate  (EXP)
formaldehyde  (EXP,ISO)
fulvestrant  (EXP)
gamma-linolenic acid  (EXP)
geldanamycin  (EXP)
genistein  (ISO)
geraniol  (ISO)
Goe 6976  (EXP)
hydrogen chloride  (EXP,ISO)
hydrogen peroxide  (ISO)
indometacin  (EXP,ISO)
ionomycin  (EXP,ISO)
iron(2+) sulfate (anhydrous)  (ISO)
isophorone  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
Lafutidine  (EXP)
leflunomide  (ISO)
lidocaine  (EXP,ISO)
linoleic acid  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
masoprocol  (EXP)
Mecamylamine  (EXP)
melittin  (EXP)
mepivacaine  (EXP)
methamphetamine  (ISO)
methapyrilene  (ISO)
methyllycaconitine  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (EXP,ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-oleoyldopamine  (EXP,ISO)
N-Vanillyloleamide  (EXP)
nicotine  (EXP)
nitroprusside  (ISO)
nonivamide  (ISO)
Nordihydrocapsaicin  (EXP,ISO)
NS-398  (EXP)
olanzapine  (ISO)
oleanolic acid  (EXP)
p-menthan-3-ol  (ISO)
palmitoyl ethanolamide  (ISO)
phenylarsine oxide  (EXP)
phenylephrine  (ISO)
phenylmethanesulfonyl fluoride  (ISO)
phorbol 12,13-dibutanoate  (EXP)
phorbol 13-acetate 12-myristate  (EXP,ISO)
potassium chromate  (ISO)
procaine  (EXP)
pyrimidifen  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resiniferatoxin  (EXP,ISO)
ricinoleic acid  (ISO)
rimonabant  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
ruthenium red  (EXP,ISO)
saccharin  (ISO)
SB 203580  (EXP)
SB 431542  (ISO)
serotonin  (EXP)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium chloride  (EXP,ISO)
tacrolimus hydrate  (EXP,ISO)
tamoxifen  (EXP)
tebufenpyrad  (ISO)
tetracaine  (EXP)
titanium dioxide  (ISO)
topiramate  (EXP)
tributylstannane  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
Triton X-100  (EXP)
tyrphostin AG 1478  (ISO)
U-73122  (EXP)
valproic acid  (ISO)
WIN 55212-2  (EXP)
wortmannin  (ISO)
xenon atom  (ISO)
xenon(0)  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
behavioral response to pain  (ISO)
calcium ion import across plasma membrane  (IBA,IDA,ISO)
calcium ion transmembrane transport  (IDA,IMP)
calcium ion transport  (IDA,ISO)
cellular response to acidic pH  (IDA,ISO)
cellular response to alkaloid  (IMP)
cellular response to ATP  (IDA)
cellular response to cytokine stimulus  (IDA)
cellular response to growth factor stimulus  (IEP)
cellular response to heat  (IDA,ISO)
cellular response to nerve growth factor stimulus  (IEP)
cellular response to temperature stimulus  (IEP)
cellular response to tumor necrosis factor  (IEP)
detection of chemical stimulus involved in sensory perception of pain  (ISO)
detection of temperature stimulus involved in sensory perception of pain  (ISO)
detection of temperature stimulus involved in thermoception  (ISO)
diet induced thermogenesis  (ISO)
excitatory postsynaptic potential  (IEA)
fever generation  (ISO)
glutamate secretion  (IDA)
inflammatory response  (IEP)
ion transmembrane transport  (ISO)
lipid metabolic process  (ISO)
microglial cell activation  (IMP)
negative regulation of establishment of blood-brain barrier  (IMP)
negative regulation of heart rate  (IMP)
negative regulation of mitochondrial membrane potential  (IMP)
negative regulation of systemic arterial blood pressure  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO)
peptide secretion  (ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of cytosolic calcium ion concentration  (IDA)
positive regulation of gastric acid secretion  (IMP)
positive regulation of nitric oxide biosynthetic process  (IMP)
protein homotetramerization  (IDA)
release of sequestered calcium ion into cytosol  (IEA)
response to capsazepine  (IMP,ISO)
response to heat  (IDA,ISO)
response to organonitrogen compound  (ISO)
response to pain  (ISO)
response to peptide hormone  (IEP)
response to pH  (IDA,IEP,ISO)
sensory perception of mechanical stimulus  (ISO)
sensory perception of pain  (ISO)
smooth muscle contraction involved in micturition  (ISO)
temperature homeostasis  (ISO)
thermoception  (ISO)
urinary bladder smooth muscle contraction  (ISO)

References

References - curated
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13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
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24. MGD data from the GO Consortium
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30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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Additional References at PubMed
PMID:10764638   PMID:10931826   PMID:11140687   PMID:11418861   PMID:11466438   PMID:11549313   PMID:11683872   PMID:11884385   PMID:12095983   PMID:12097645   PMID:12161756   PMID:12194871  
PMID:12513687   PMID:12527134   PMID:12560124   PMID:12623992   PMID:12658436   PMID:12687689   PMID:12709508   PMID:12761211   PMID:12764195   PMID:12808128   PMID:12867271   PMID:12872047  
PMID:12906841   PMID:12911749   PMID:14506258   PMID:14523239   PMID:14622148   PMID:14630912   PMID:14960593   PMID:14963041   PMID:14996838   PMID:15033437   PMID:15036590   PMID:15066994  
PMID:15071115   PMID:15078554   PMID:15084474   PMID:15135918   PMID:15135921   PMID:15146042   PMID:15152030   PMID:15173182   PMID:15190102   PMID:15194687   PMID:15220301   PMID:15254097  
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PMID:15738113   PMID:15738186   PMID:15744307   PMID:15763167   PMID:15782105   PMID:15883036   PMID:15885224   PMID:15893596   PMID:15907794   PMID:15931076   PMID:16039054   PMID:16081411  
PMID:16087784   PMID:16091583   PMID:16162831   PMID:16196077   PMID:16283857   PMID:16304633   PMID:16365187   PMID:16399878   PMID:16477145   PMID:16503963   PMID:16510717   PMID:16541240  
PMID:16564619   PMID:16564637   PMID:16566843   PMID:16595689   PMID:16645591   PMID:16709252   PMID:16793902   PMID:16831854   PMID:16887920   PMID:16901936   PMID:16971522   PMID:16996476  
PMID:17004230   PMID:17005903   PMID:17065246   PMID:17169618   PMID:17176640   PMID:17194758   PMID:17239544   PMID:17258716   PMID:17266134   PMID:17287441   PMID:17329430   PMID:17363391  
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PMID:17698068   PMID:17712480   PMID:17714453   PMID:17717412   PMID:17765209   PMID:17767493   PMID:17900568   PMID:17907014   PMID:17932142   PMID:17950047   PMID:17977563   PMID:17991707  
PMID:18029293   PMID:18032552   PMID:18063665   PMID:18089839   PMID:18172555   PMID:18178674   PMID:18182051   PMID:18226965   PMID:18256211   PMID:18272293   PMID:18272658   PMID:18294619  
PMID:18297068   PMID:18331834   PMID:18337316   PMID:18341994   PMID:18364471   PMID:18391945   PMID:18403445   PMID:18455478   PMID:18455988   PMID:18466747   PMID:18482991   PMID:18498707  
PMID:18499628   PMID:18551569   PMID:18617618   PMID:18632800   PMID:18660449   PMID:18706981   PMID:18722504   PMID:18752301   PMID:18755153   PMID:18755744   PMID:18775990   PMID:18777111  
PMID:18797299   PMID:18806620   PMID:18832423   PMID:18973552   PMID:19026992   PMID:19052196   PMID:19055783   PMID:19064314   PMID:19154775   PMID:19158342   PMID:19208258   PMID:19223122  
PMID:19236852   PMID:19236908   PMID:19283865   PMID:19286963   PMID:19298229   PMID:19307060   PMID:19397388   PMID:19406204   PMID:19419422   PMID:19464796   PMID:19523146   PMID:19561608  
PMID:19584302   PMID:19619635   PMID:19683949   PMID:19720962   PMID:19753113   PMID:19767149   PMID:19778904   PMID:19801576   PMID:19806360   PMID:19843694   PMID:19860893   PMID:19889854  
PMID:19958810   PMID:20142275   PMID:20145248   PMID:20182791   PMID:20211611   PMID:20351268   PMID:20407214   PMID:20414199   PMID:20422007   PMID:20424317   PMID:20511124   PMID:20534813  
PMID:20592193   PMID:20638226   PMID:20639627   PMID:20691059   PMID:20858418   PMID:20875131   PMID:20878780   PMID:20924599   PMID:21044346   PMID:21118579   PMID:21182905   PMID:21219650  
PMID:21241462   PMID:21256210   PMID:21316356   PMID:21414401   PMID:21473865   PMID:21474425   PMID:21480900   PMID:21486787   PMID:21514666   PMID:21518266   PMID:21554904   PMID:21555515  
PMID:21569553   PMID:21645329   PMID:21645527   PMID:21674494   PMID:21794120   PMID:21868092   PMID:21903882   PMID:21911503   PMID:21926175   PMID:22108615   PMID:22168801   PMID:22178141  
PMID:22178825   PMID:22215506   PMID:22270459   PMID:22314222   PMID:22358093   PMID:22390080   PMID:22426238   PMID:22427437   PMID:22466126   PMID:22525132   PMID:22528458   PMID:22562048  
PMID:22570472   PMID:22609428   PMID:22634729   PMID:22656960   PMID:22688302   PMID:22789851   PMID:22820913   PMID:22849826   PMID:22865090   PMID:22870919   PMID:22942745   PMID:22998799  
PMID:23018770   PMID:23021218   PMID:23074220   PMID:23077056   PMID:23091405   PMID:23147107   PMID:23201260   PMID:23234417   PMID:23283344   PMID:23301515   PMID:23324998   PMID:23345400  
PMID:23360390   PMID:23376589   PMID:23384628   PMID:23408423   PMID:23443231   PMID:23555720   PMID:23584686   PMID:23638900   PMID:23707800   PMID:23728381   PMID:23811042   PMID:23832015  
PMID:23902373   PMID:23916509   PMID:23919305   PMID:23965996   PMID:24147119   PMID:24152419   PMID:24154957   PMID:24158445   PMID:24185761   PMID:24217926   PMID:24307802   PMID:24312564  
PMID:24339305   PMID:24401144   PMID:24548973   PMID:24567510   PMID:24569998   PMID:24577898   PMID:24746025   PMID:24808184   PMID:24816396   PMID:24838827   PMID:24861565   PMID:24877063  
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PMID:26387947   PMID:26481104   PMID:26516054   PMID:26524655   PMID:26526845   PMID:26574143   PMID:26621124   PMID:26643912   PMID:26796050   PMID:26836139   PMID:26855542   PMID:26880264  
PMID:26880553   PMID:26888187   PMID:26900062   PMID:26902776   PMID:26965218   PMID:26970948   PMID:26987748   PMID:27062913   PMID:27143360   PMID:27180305   PMID:27189587   PMID:27255083  
PMID:27267133   PMID:27338549   PMID:27411353   PMID:27627464   PMID:27662603   PMID:27665186   PMID:27774580   PMID:27822750   PMID:27827430   PMID:27842306   PMID:27872485   PMID:27900462  
PMID:27915078   PMID:27923234   PMID:28062485   PMID:28188777   PMID:28205139   PMID:28337884   PMID:28359919   PMID:28512115   PMID:28542001   PMID:28599085   PMID:28606782   PMID:28627595  
PMID:28710476   PMID:28722259   PMID:28848196   PMID:28983729   PMID:29121795   PMID:29159869   PMID:29196683   PMID:29209900   PMID:29215540   PMID:29235496   PMID:29304162   PMID:29332300  
PMID:29335353   PMID:29351423   PMID:29421435   PMID:29466323   PMID:29479030   PMID:29537196   PMID:29550358   PMID:29740093   PMID:29930087   PMID:30006640   PMID:30046815   PMID:30078015  
PMID:30079821   PMID:30121230   PMID:30159798   PMID:30260820   PMID:30292787   PMID:30335684   PMID:30444177   PMID:30567389   PMID:30627906   PMID:30676422   PMID:30764505   PMID:30804201  
PMID:30898677   PMID:30989631   PMID:31074030   PMID:31186372   PMID:31451732   PMID:31582966   PMID:31724952   PMID:31836538   PMID:32345612   PMID:32345727   PMID:32372526   PMID:32557241  
PMID:32570786   PMID:32574651   PMID:32708653   PMID:32764237   PMID:32867278   PMID:32871764   PMID:32946867   PMID:33060203   PMID:33092809   PMID:33180962   PMID:33327798   PMID:33707202  
PMID:34022223   PMID:34082374   PMID:34215968  


Genomics

Comparative Map Data
Trpv1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21057,851,428 - 57,876,513 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1057,851,428 - 57,876,513 (+)Ensembl
Rnor_6.01059,799,123 - 59,824,208 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1059,799,123 - 59,824,679 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01059,538,296 - 59,563,441 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41060,109,656 - 60,134,939 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11060,123,278 - 60,148,562 (+)NCBI
Celera1056,974,294 - 56,999,462 (+)NCBICelera
Cytogenetic Map10q24NCBI
TRPV1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl173,565,444 - 3,609,411 (-)EnsemblGRCh38hg38GRCh38
GRCh38173,565,446 - 3,609,411 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37173,468,740 - 3,512,705 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36173,415,490 - 3,459,454 (-)NCBINCBI36hg18NCBI36
Build 34173,415,490 - 3,442,920NCBI
Celera173,482,474 - 3,526,423 (-)NCBI
Cytogenetic Map17p13.2NCBI
HuRef173,360,449 - 3,404,458 (-)NCBIHuRef
CHM1_1173,479,568 - 3,523,488 (-)NCBICHM1_1
Trpv1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391173,124,975 - 73,152,148 (+)NCBIGRCm39mm39
GRCm39 Ensembl1173,125,118 - 73,152,068 (+)Ensembl
GRCm381173,234,149 - 73,261,322 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1173,234,292 - 73,261,242 (+)EnsemblGRCm38mm10GRCm38
MGSCv371173,051,761 - 73,074,009 (+)NCBIGRCm37mm9NCBIm37
MGSCv361173,054,454 - 73,076,702 (+)NCBImm8
Celera1180,775,520 - 80,797,773 (+)NCBICelera
Cytogenetic Map11B4NCBI
cM Map1145.25NCBI
Trpv1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546713,221,391 - 13,239,089 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546713,221,391 - 13,239,089 (+)NCBIChiLan1.0ChiLan1.0
TRPV1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1173,609,952 - 3,655,011 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl173,609,952 - 3,637,579 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0173,612,781 - 3,658,608 (-)NCBIMhudiblu_PPA_v0panPan3
TRPV1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1947,404,987 - 47,443,871 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl947,404,972 - 47,431,926 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha946,568,483 - 46,594,656 (-)NCBI
ROS_Cfam_1.0948,249,767 - 48,289,671 (-)NCBI
UMICH_Zoey_3.1947,022,952 - 47,055,374 (-)NCBI
UNSW_CanFamBas_1.0947,316,168 - 47,344,663 (-)NCBI
UU_Cfam_GSD_1.0947,371,882 - 47,400,241 (-)NCBI
Trpv1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560255,578,132 - 55,623,675 (+)NCBI
SpeTri2.0NW_004936677277,304 - 326,907 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRPV1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1249,677,291 - 49,701,325 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11249,676,536 - 49,709,634 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21251,536,224 - 51,560,849 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRPV1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1163,071,158 - 3,091,068 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl163,071,526 - 3,090,330 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605918,732,125 - 18,762,847 (+)NCBIVero_WHO_p1.0
Trpv1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247866,231,494 - 6,249,001 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D10Got236  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21057,863,919 - 57,864,057 (+)MAPPERmRatBN7.2
Rnor_6.01059,811,617 - 59,811,754NCBIRnor6.0
Rnor_5.01059,550,850 - 59,550,987UniSTSRnor5.0
RGSC_v3.41060,122,093 - 60,122,230UniSTSRGSC3.4
Cytogenetic Map10q24UniSTS
PMC126639P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21057,855,410 - 57,855,586 (+)MAPPERmRatBN7.2
Rnor_6.01059,803,106 - 59,803,281NCBIRnor6.0
Rnor_5.01059,542,279 - 59,542,454UniSTSRnor5.0
RGSC_v3.41060,113,639 - 60,113,814UniSTSRGSC3.4
Celera1056,978,277 - 56,978,452UniSTS
Cytogenetic Map10q24UniSTS
RH127973  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21057,876,145 - 57,876,350 (+)MAPPERmRatBN7.2
Rnor_6.01059,823,841 - 59,824,045NCBIRnor6.0
Rnor_5.01059,563,074 - 59,563,278UniSTSRnor5.0
RGSC_v3.41060,134,572 - 60,134,776UniSTSRGSC3.4
Celera1056,999,095 - 56,999,299UniSTS
Cytogenetic Map10q24UniSTS
PMC16295P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21057,876,156 - 57,876,418 (+)MAPPERmRatBN7.2
Rnor_6.01059,823,852 - 59,824,113NCBIRnor6.0
Rnor_5.01059,563,085 - 59,563,346UniSTSRnor5.0
RGSC_v3.41060,134,583 - 60,134,844UniSTSRGSC3.4
Celera1056,999,106 - 56,999,367UniSTS
Cytogenetic Map10q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
1578762Toxo1Toxoplasma gondii resistance QTL 1brain integrity trait (VT:0010579)percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)105220003059378278Rat
1354585Eae18aExperimental allergic encephalomyelitis QTL 18a7.50.0004nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)105379738558445852Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)105527369660677262Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat


Genetic Models
This gene Trpv1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:564
Count of miRNA genes:186
Interacting mature miRNAs:216
Transcripts:ENSRNOT00000026456, ENSRNOT00000026493
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 8
Low 2 39 25 12 25 4 4 64 13 16 11 4
Below cutoff 3 41 16 14 7 14 4 7 8 14 23 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1059,804,916 - 59,824,679 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000026493   ⟹   ENSRNOP00000026493
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1057,851,428 - 57,876,513 (+)Ensembl
Rnor_6.0 Ensembl1059,799,123 - 59,824,208 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1057,851,428 - 57,876,513 (+)Ensembl
Rnor_6.0 Ensembl1059,805,149 - 59,824,208 (+)Ensembl
RefSeq Acc Id: NM_031982   ⟹   NP_114188
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21057,851,428 - 57,876,513 (+)NCBI
Rnor_6.01059,799,123 - 59,824,208 (+)NCBI
Rnor_5.01059,538,296 - 59,563,441 (+)NCBI
RGSC_v3.41060,109,656 - 60,134,939 (+)RGD
Celera1056,974,294 - 56,999,462 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_114188   ⟸   NM_031982
- UniProtKB: O35433 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026493   ⟸   ENSRNOT00000026493

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
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
Sequenced By: MCW
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
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
Sequenced By: MCW
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Sequenced By: MCW
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)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
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
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
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/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
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
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628841 AgrOrtholog
Ensembl Genes ENSRNOG00000019486 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026493 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026493 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.20 UniProtKB/Swiss-Prot
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot
  Ion_trans_dom UniProtKB/Swiss-Prot
  TRPV UniProtKB/Swiss-Prot
  TRPV1 UniProtKB/Swiss-Prot
  TRPV1-4_channel UniProtKB/Swiss-Prot
KEGG Report rno:83810 UniProtKB/Swiss-Prot
NCBI Gene 83810 ENTREZGENE
PANTHER PTHR10582 UniProtKB/Swiss-Prot
  PTHR10582:SF17 UniProtKB/Swiss-Prot
Pfam Ank_2 UniProtKB/Swiss-Prot
  Ion_trans UniProtKB/Swiss-Prot
PharmGKB TRPV1 RGD
PhenoGen Trpv1 PhenoGen
PRINTS TRPVRECEPTOR UniProtKB/Swiss-Prot
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot
  ANK_REPEAT UniProtKB/Swiss-Prot
SMART ANK UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48403 UniProtKB/Swiss-Prot
UniProt O35433 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q920B3 UniProtKB/Swiss-Prot
  Q920B4 UniProtKB/Swiss-Prot
  Q9JLM0 UniProtKB/Swiss-Prot
  Q9JM56 UniProtKB/Swiss-Prot
  Q9JM57 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Trpv1  transient receptor potential cation channel, subfamily V, member 1      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Trpv1  transient receptor potential cation channel, subfamily V, member 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains six transmembrane-spanning domains (S1-S6), a pore-forming region between S5 and S6, and the cytoplasmically oriented C- and N-terminal regions 634416
gene_expression expressed by nociceptive primary afferent neurons and urothelial cells 70582
gene_function ion channel protein 70582
gene_process essential for the thermal hypersensitivity associated with inflammation of the hind paw 70582
gene_process vailloids increase intracellular Ca2+ and evoke NO release in urothelial cells and the effect is Trpv1-dependent 70582
gene_process causes pain sensations induced by capsaicin 70582
gene_process participates in acid and heat detection 70582