Htr2a (5-hydroxytryptamine receptor 2A) - Rat Genome Database

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Gene: Htr2a (5-hydroxytryptamine receptor 2A) Rattus norvegicus
Analyze
Symbol: Htr2a
Name: 5-hydroxytryptamine receptor 2A
RGD ID: 61800
Description: Predicted to enable several functions, including 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding activity; Gq/11-coupled serotonin receptor activity; and serotonin binding activity. Involved in several processes, including blood vessel diameter maintenance; detection of stimulus involved in sensory perception of pain; and modulation of chemical synaptic transmission. Located in several cellular components, including cell body fiber; dendritic shaft; and neuronal cell body. Is integral component of postsynaptic membrane and integral component of presynaptic membrane. Is active in glutamatergic synapse. Used to study congestive heart failure; hyperglycemia; and pancreatitis. Biomarker of bladder neck obstruction and schizophrenia. Human ortholog(s) of this gene implicated in several diseases, including alcohol use disorder; anorexia nervosa; major depressive disorder; obesity; and obsessive-compulsive disorder. Orthologous to human HTR2A (5-hydroxytryptamine receptor 2A); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (R,R)-tramadol; (S)-nicotine; 1-bromopropane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 5-HT-2; 5-HT-2A; 5-HT2A; 5-hydroxytryptamine (serotonin) receptor 2A; 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled; 5Ht-2; serotonin 5HT-2 receptor; serotonin 5HT-2 receptor gene; serotonin receptor 2A
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
mRatBN7.21549,950,035 - 50,022,188 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1549,950,804 - 50,020,928 (+)Ensembl
Rnor_6.01556,666,152 - 56,732,469 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1556,666,012 - 56,735,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,388,557 - 60,454,874 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,463,743 - 55,532,293 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11555,479,522 - 55,548,073NCBI
Celera1549,584,210 - 49,652,169 (+)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R,R)-tramadol  (EXP)
(S)-nicotine  (EXP)
1,2-dichloroethane  (ISO)
1-(3-chlorophenyl)piperazine  (ISO)
1-bromopropane  (EXP)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-(4-iodo-2,5-dimethoxyphenyl)-1-methylethylamine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-phenoxybenzoic acid  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
adinazolam  (EXP)
albiflorin  (EXP)
alprenolol  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
Bardoxolone methyl  (ISO)
benzimidazoles  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bupropion  (EXP)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbon nanotube  (ISO)
chlorpyrifos  (EXP,ISO)
cinchocaine  (EXP)
clozapine  (EXP,ISO)
Clozapine N-oxide  (EXP)
cocaine  (EXP,ISO)
colforsin daropate hydrochloride  (EXP)
corticosterone  (EXP)
corticotropin  (EXP)
cyclosporin A  (EXP)
cyhalothrin  (EXP)
cypermethrin  (EXP)
cyproheptadine  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (EXP)
desipramine  (EXP)
dexamethasone  (EXP)
diazinon  (EXP)
dibenziodolium  (EXP)
dibutyl phthalate  (ISO)
diethyl phthalate  (ISO)
Diisodecyl phthalate  (ISO)
dopamine  (EXP)
fenfluramine  (ISO)
fluoxetine  (EXP,ISO)
fluphenazine  (ISO)
fluvoxamine  (ISO)
gamma-hexachlorocyclohexane  (EXP)
genistein  (ISO)
Goe 6976  (EXP)
GR 127935  (EXP)
haloperidol  (EXP,ISO)
hexadecanoic acid  (ISO)
imipramine  (EXP)
ketanserin  (EXP,ISO)
lithium chloride  (ISO)
loxapine  (EXP)
metergoline  (ISO)
methamidophos  (ISO)
methamphetamine  (EXP)
methiothepin  (ISO)
mianserin  (ISO)
monocrotaline  (EXP)
N,N-dimethyltryptamine  (ISO)
N-desmethylclozapine  (EXP,ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (EXP)
nicotine  (EXP)
nitrates  (EXP)
nitrofen  (EXP)
olanzapine  (EXP,ISO)
paliperidone palmitate  (EXP,ISO)
paracetamol  (EXP)
paraquat  (EXP)
parathion  (EXP)
paroxetine  (ISO)
PCB138  (EXP)
phencyclidine  (EXP)
Phenoxybenzamine  (EXP)
phorbol 12,13-dibutanoate  (EXP)
piperazines  (EXP)
poly(I:C)  (ISO)
progesterone  (EXP,ISO)
quercetin  (EXP)
quetiapine fumarate  (ISO)
raloxifene  (EXP,ISO)
risperidone  (EXP,ISO)
ritanserin  (EXP,ISO)
rotenone  (EXP)
sarpogrelate  (EXP,ISO)
SB 203580  (EXP)
SB 206553  (EXP)
serotonin  (EXP,ISO)
sertraline  (EXP)
sodium arsenite  (EXP)
spiperone  (ISO)
streptozocin  (EXP)
tamoxifen  (ISO)
tebuconazole  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
tramadol  (EXP)
tributylstannane  (ISO)
tryptamine  (ISO)
valproic acid  (ISO)
vincristine  (EXP)
yohimbine  (ISO)
zalcitabine  (EXP,ISO)
ziprasidone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of phospholipase C activity  (ISO)
aging  (IEP)
artery smooth muscle contraction  (IMP)
behavioral response to cocaine  (IDA)
cell death  (IMP)
cellular calcium ion homeostasis  (ISO)
chemical synaptic transmission  (IBA)
detection of mechanical stimulus involved in sensory perception of pain  (IMP)
detection of temperature stimulus involved in sensory perception of pain  (IMP)
G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger  (IBA)
G protein-coupled serotonin receptor signaling pathway  (ISO)
memory  (IMP)
negative regulation of potassium ion transport  (IMP)
negative regulation of synaptic transmission, glutamatergic  (IMP)
phosphatidylinositol 3-kinase signaling  (ISO)
phospholipase C-activating G protein-coupled receptor signaling pathway  (IBA)
phospholipase C-activating serotonin receptor signaling pathway  (IDA)
positive regulation of cell population proliferation  (IMP)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of fat cell differentiation  (ISO)
positive regulation of glycolytic process  (ISO)
positive regulation of kinase activity  (ISO)
positive regulation of MAP kinase activity  (IMP)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of phosphatidylinositol biosynthetic process  (ISO)
positive regulation of vasoconstriction  (IMP)
protein localization to cytoskeleton  (ISO)
regulation of dopamine secretion  (IMP)
regulation of synaptic vesicle exocytosis  (EXP,IDA)
release of sequestered calcium ion into cytosol  (IBA,ISO)
response to xenobiotic stimulus  (IBA,IMP,ISO)
sensory perception of pain  (IMP)
sleep  (IMP)
temperature homeostasis  (IMP)
urinary bladder smooth muscle contraction  (IMP)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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28. MGD data from the GO Consortium
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39. Pipeline to import KEGG annotations from KEGG into RGD
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42. RGD automated data pipeline
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Additional References at PubMed
PMID:7582481   PMID:12058363   PMID:12237191   PMID:12388782   PMID:12670306   PMID:12682061   PMID:12732339   PMID:12753068   PMID:12842309   PMID:14499437   PMID:14499940   PMID:14643760  
PMID:14689478   PMID:15019576   PMID:15065122   PMID:15115744   PMID:15126129   PMID:15129779   PMID:15190056   PMID:15378508   PMID:15664703   PMID:15695159   PMID:15831837   PMID:15862800  
PMID:15882780   PMID:15970592   PMID:16051396   PMID:16203096   PMID:16360124   PMID:16517693   PMID:16707714   PMID:16737974   PMID:16763082   PMID:16871540   PMID:16901936   PMID:17098333  
PMID:17331657   PMID:17395633   PMID:17398000   PMID:17408640   PMID:17412795   PMID:17562393   PMID:17588622   PMID:17600544   PMID:17617403   PMID:17711618   PMID:17720578   PMID:17726509  
PMID:17888573   PMID:17936780   PMID:18046307   PMID:18155835   PMID:18183075   PMID:18187923   PMID:18403899   PMID:18417104   PMID:18420721   PMID:18425575   PMID:18439999   PMID:18442977  
PMID:18604238   PMID:18703043   PMID:18718516   PMID:18772320   PMID:18801389   PMID:18930597   PMID:19057895   PMID:19167402   PMID:19212317   PMID:19269287   PMID:19279328   PMID:19362128  
PMID:19368306   PMID:19500571   PMID:19556691   PMID:19615378   PMID:19772899   PMID:19879056   PMID:19889983   PMID:19937319   PMID:20085755   PMID:20147548   PMID:20471502   PMID:20662937  
PMID:20719859   PMID:20811878   PMID:20857344   PMID:20861436   PMID:20868513   PMID:21126512   PMID:21186576   PMID:21211552   PMID:21245988   PMID:21276431   PMID:21420940   PMID:21598629  
PMID:21600121   PMID:21683764   PMID:21789169   PMID:22056918   PMID:22106156   PMID:22659115   PMID:22791651   PMID:22871113   PMID:22952915   PMID:23201361   PMID:23248270   PMID:23301505  
PMID:23362947   PMID:23399761   PMID:23592773   PMID:23684573   PMID:23721787   PMID:23787365   PMID:23864045   PMID:24058620   PMID:24287377   PMID:24823545   PMID:24888825   PMID:24949809  
PMID:24997405   PMID:25155310   PMID:25185755   PMID:25584948   PMID:25818050   PMID:26031442   PMID:26051401   PMID:26106048   PMID:26120876   PMID:26371055   PMID:26670377   PMID:26769798  
PMID:27109474   PMID:28258217   PMID:28711602   PMID:28750135   PMID:28795477   PMID:30355630   PMID:30523733   PMID:30645940   PMID:31706992   PMID:32425760   PMID:32504811   PMID:32519137  
PMID:34199392  


Genomics

Comparative Map Data
Htr2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21549,950,035 - 50,022,188 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1549,950,804 - 50,020,928 (+)Ensembl
Rnor_6.01556,666,152 - 56,732,469 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1556,666,012 - 56,735,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01560,388,557 - 60,454,874 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41555,463,743 - 55,532,293 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11555,479,522 - 55,548,073NCBI
Celera1549,584,210 - 49,652,169 (+)NCBICelera
Cytogenetic Map15q11NCBI
HTR2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1346,831,546 - 46,897,076 (-)EnsemblGRCh38hg38GRCh38
GRCh381346,831,546 - 46,898,082 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371347,405,681 - 47,472,217 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361346,305,514 - 46,368,176 (-)NCBINCBI36hg18NCBI36
Build 341346,305,513 - 46,368,176NCBI
Celera1328,463,441 - 28,527,123 (-)NCBI
Cytogenetic Map13q14.2NCBI
HuRef1328,199,237 - 28,264,796 (-)NCBIHuRef
CHM1_11347,373,460 - 47,438,997 (-)NCBICHM1_1
Htr2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391474,878,314 - 74,944,299 (+)NCBIGRCm39mm39
GRCm39 Ensembl1474,878,280 - 74,946,934 (+)Ensembl
GRCm381474,640,874 - 74,706,859 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1474,640,840 - 74,709,494 (+)EnsemblGRCm38mm10GRCm38
MGSCv371475,040,647 - 75,106,666 (+)NCBIGRCm37mm9NCBIm37
MGSCv361473,374,995 - 73,441,014 (+)NCBImm8
Celera1472,148,249 - 72,214,245 (+)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1439.37NCBI
Htr2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955431580,713 - 647,345 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955431583,165 - 646,991 (-)NCBIChiLan1.0ChiLan1.0
HTR2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11346,694,273 - 46,759,826 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1346,694,273 - 46,759,826 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01327,976,415 - 28,042,941 (-)NCBIMhudiblu_PPA_v0panPan3
HTR2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1224,453,715 - 4,510,934 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl224,453,715 - 4,511,037 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha224,498,607 - 4,555,448 (+)NCBI
ROS_Cfam_1.0224,566,315 - 4,626,240 (+)NCBI
UMICH_Zoey_3.1224,348,779 - 4,405,847 (+)NCBI
UNSW_CanFamBas_1.0224,412,667 - 4,469,478 (+)NCBI
UU_Cfam_GSD_1.0224,417,008 - 4,474,072 (+)NCBI
Htr2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945156,850,452 - 156,910,669 (-)NCBI
SpeTri2.0NW_004936565335,238 - 394,683 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HTR2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1120,555,961 - 20,619,629 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11120,555,939 - 20,620,225 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21120,895,106 - 20,956,369 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HTR2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1324,820,029 - 24,884,472 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl324,820,035 - 24,883,432 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605719,114,044 - 19,177,668 (+)NCBIVero_WHO_p1.0
Htr2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247488,154,288 - 8,223,226 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Htr2a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21550,018,770 - 50,018,969 (+)MAPPERmRatBN7.2
Rnor_6.01556,731,983 - 56,732,181NCBIRnor6.0
Rnor_5.01560,454,388 - 60,454,586UniSTSRnor5.0
RGSC_v3.41555,531,807 - 55,532,005UniSTSRGSC3.4
Celera1549,651,683 - 49,651,881UniSTS
Cytogenetic Map15q11UniSTS
G45129  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21549,958,428 - 49,958,664 (+)MAPPERmRatBN7.2
Rnor_6.01556,673,382 - 56,673,617NCBIRnor6.0
Rnor_5.01560,395,787 - 60,396,022UniSTSRnor5.0
RGSC_v3.41555,470,973 - 55,471,208UniSTSRGSC3.4
Celera1549,591,440 - 49,591,675UniSTS
Cytogenetic Map15q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:183
Count of miRNA genes:121
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000013408
Prediction methods:Miranda, 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 19
Low 26 22 14 14 14 45 29 27 7
Below cutoff 2 17 25 17 5 17 8 10 10 5 10 4 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013408   ⟹   ENSRNOP00000013408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1549,950,804 - 50,020,928 (+)Ensembl
Rnor_6.0 Ensembl1556,666,012 - 56,735,382 (+)Ensembl
RefSeq Acc Id: NM_017254   ⟹   NP_058950
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21549,951,196 - 50,019,257 (+)NCBI
Rnor_6.01556,666,152 - 56,732,469 (+)NCBI
Rnor_5.01560,388,557 - 60,454,874 (+)NCBI
RGSC_v3.41555,463,743 - 55,532,293 (+)RGD
Celera1549,584,210 - 49,652,169 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093220   ⟹   XP_038949148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21549,950,055 - 50,022,188 (+)NCBI
RefSeq Acc Id: XM_039093221   ⟹   XP_038949149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21549,950,035 - 50,022,188 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058950   ⟸   NM_017254
- UniProtKB: P14842 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013408   ⟸   ENSRNOT00000013408
RefSeq Acc Id: XP_038949149   ⟸   XM_039093221
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949148   ⟸   XM_039093220
- Peptide Label: isoform X1

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)
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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/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
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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
F344/DuCrl (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/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)
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
F344/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
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)
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)
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)
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
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)
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
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)
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
HXB2/IpcvMcwi (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
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)
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
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)
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
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)
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
LEXF11/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
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)
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
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)
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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
M520/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
M520/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
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)
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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
MNS/Gib (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
MR/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
MR/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
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)
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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: 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)
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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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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/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
WKY/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
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:61800 AgrOrtholog
Ensembl Genes ENSRNOG00000010063 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013408 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013408 UniProtKB/Swiss-Prot
InterPro 5HT2A_rcpt UniProtKB/Swiss-Prot
  5HT_rcpt UniProtKB/Swiss-Prot
  GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
KEGG Report rno:29595 UniProtKB/Swiss-Prot
NCBI Gene 29595 ENTREZGENE
PANTHER PTHR24247:SF30 UniProtKB/Swiss-Prot
Pfam 7tm_1 UniProtKB/Swiss-Prot
PharmGKB HTR2A RGD
PhenoGen Htr2a PhenoGen
PRINTS 5HT2ARECEPTR UniProtKB/Swiss-Prot
  5HTRECEPTOR UniProtKB/Swiss-Prot
  GPCRRHODOPSN UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
SMART 7TM_GPCR_Srsx UniProtKB/Swiss-Prot
UniProt 5HT2A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Htr2a  5-hydroxytryptamine receptor 2A  Htr2a  5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-17 Htr2a  5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled  Htr2a  5-hydroxytryptamine (serotonin) receptor 2A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-10 Htr2a  5-hydroxytryptamine (serotonin) receptor 2A  5Ht-2  serotonin 5HT-2 receptor gene  Data Merged 625702 APPROVED
2002-08-07 5Ht-2  serotonin 5HT-2 receptor gene      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Htr2a  5-hydroxytryptamine (serotonin) receptor 2A      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in brain and myometrial smooth muscle cells 632275
gene_expression expressed in brain and myometrial smooth muscle cells 632276
gene_pathway activates phospholipase C signaling pathway 728941
gene_process involved in promoting cellular transformation 728941
gene_protein showed high-affinity binding of the serotonin antagonists 632275
gene_regulation transcription induced by 5-HT (serotonin) 632276
gene_transcript upstream of the start site has neither classical TATA boxes nor CCAAT sequences, but contains an initiator consensus sequence, two GC boxes (SP-1 binding sites), and several AP-2 binding sites 632276