Htr3a (5-hydroxytryptamine receptor 3A) - Rat Genome Database

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Gene: Htr3a (5-hydroxytryptamine receptor 3A) Rattus norvegicus
Analyze
Symbol: Htr3a
Name: 5-hydroxytryptamine receptor 3A
RGD ID: 61818
Description: Exhibits serotonin-gated cation-selective channel activity. Involved in several processes, including positive regulation of ion transmembrane transporter activity; response to cocaine; and response to ethanol. Localizes to several cellular components, including glutamatergic synapse; integral component of synaptic membrane; and neuronal cell body. Human ortholog(s) of this gene implicated in irritable bowel syndrome. Orthologous to human HTR3A (5-hydroxytryptamine receptor 3A); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 1-bromopropane; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 5-HT-3; 5-HT3; 5-HT3 receptor; 5-HT3-A; 5-HT3A; 5-HT3R; 5-hydroxytryptamine (serotonin) receptor 3a; 5-hydroxytryptamine (serotonin) receptor 3A, ionotropic; 5-hydroxytryptamine receptor 3; 5HT3; 5HT3 receptor; Htr3; serotonin receptor 3A; serotonin-gated ion channel receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2849,242,018 - 49,254,475 (-)NCBI
Rnor_6.0 Ensembl853,211,438 - 53,223,804 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0853,211,436 - 53,223,878 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0851,803,895 - 51,816,278 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4852,161,147 - 52,173,514 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1852,180,200 - 52,192,425 (-)NCBI
Celera848,799,808 - 48,812,052 (-)NCBICelera
Cytogenetic Map8q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-trichloroethane  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1-bromopropane  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methylserotonin  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
acrylamide  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
alfentanil  (ISO)
ammonium chloride  (EXP)
atrazine  (ISO)
benzamides  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bisphenol F  (EXP)
butan-1-ol  (ISO)
cadmium dichloride  (ISO)
capsaicin  (ISO)
carvacrol  (ISO)
cisplatin  (ISO)
citronellol  (ISO)
clozapine  (ISO)
cocaine  (EXP,ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dieldrin  (EXP)
dopamine  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
fipronil  (ISO)
folic acid  (ISO)
gamma-aminobutyric acid  (EXP)
geraniol  (ISO)
gingerol  (ISO)
GR 65630  (ISO)
hydromorphone  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
m-Chlorophenylbiguanide  (EXP)
methamphetamine  (ISO)
metoclopramide  (EXP,ISO)
morphine  (ISO)
N,N-diethyl-m-toluamide  (ISO)
nickel atom  (EXP)
nitrates  (EXP)
O-methyleugenol  (ISO)
Ondansetron  (EXP,ISO)
Polygodial  (ISO)
potassium dichromate  (ISO)
propan-1-ol  (ISO)
pyridines  (EXP)
raloxifene  (ISO)
Ramosetron hydrochloride  (EXP,ISO)
remifentanil  (ISO)
SB 431542  (ISO)
serotonin  (EXP,ISO)
sodium arsenite  (ISO)
sufentanil  (ISO)
tamoxifen  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
thymol  (ISO)
thymol sulfate(1-)  (ISO)
toluene  (ISO)
trichloroethene  (ISO)
valproic acid  (ISO)
vortioxetine  (EXP,ISO)

References

Additional References at PubMed
PMID:7509203   PMID:7616200   PMID:9950429   PMID:12411518   PMID:12411529   PMID:12611954   PMID:12617944   PMID:12937671   PMID:14499437   PMID:14648680   PMID:15135935   PMID:15905216  
PMID:15975728   PMID:16407231   PMID:17150309   PMID:17161536   PMID:17467903   PMID:18063656   PMID:18313044   PMID:18357529   PMID:18931259   PMID:19026634   PMID:19077442   PMID:19154775  
PMID:19247214   PMID:19556691   PMID:19558425   PMID:19799413   PMID:19944698   PMID:20023641   PMID:20359130   PMID:20682192   PMID:20691988   PMID:20817619   PMID:21186576   PMID:21291881  
PMID:21514668   PMID:22289689   PMID:22358093   PMID:22528232   PMID:22845622   PMID:23035083   PMID:23399761   PMID:24949809   PMID:25119048   PMID:25913635   PMID:26724993   PMID:27904941  
PMID:28115218   PMID:28761086   PMID:28795477  


Genomics

Comparative Map Data
Htr3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2849,242,018 - 49,254,475 (-)NCBI
Rnor_6.0 Ensembl853,211,438 - 53,223,804 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0853,211,436 - 53,223,878 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0851,803,895 - 51,816,278 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4852,161,147 - 52,173,514 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1852,180,200 - 52,192,425 (-)NCBI
Celera848,799,808 - 48,812,052 (-)NCBICelera
Cytogenetic Map8q23NCBI
HTR3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11113,974,881 - 113,990,313 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl11113,975,075 - 113,990,313 (+)EnsemblGRCh38hg38GRCh38
GRCh3811113,975,108 - 113,990,313 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711113,845,830 - 113,861,035 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611113,351,120 - 113,366,245 (+)NCBINCBI36hg18NCBI36
Build 3411113,351,119 - 113,366,242NCBI
Celera11110,998,666 - 111,013,897 (+)NCBI
Cytogenetic Map11q23.2NCBI
HuRef11109,774,553 - 109,789,782 (+)NCBIHuRef
CHM1_111113,729,890 - 113,745,126 (+)NCBICHM1_1
Htr3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39948,810,513 - 48,822,451 (-)NCBIGRCm39mm39
GRCm39 Ensembl948,810,513 - 48,822,399 (-)Ensembl
GRCm38948,899,213 - 48,911,152 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl948,899,213 - 48,911,099 (-)EnsemblGRCm38mm10GRCm38
MGSCv37948,707,318 - 48,719,204 (-)NCBIGRCm37mm9NCBIm37
MGSCv36948,651,146 - 48,662,968 (-)NCBImm8
Celera946,196,535 - 46,208,676 (-)NCBICelera
Cytogenetic Map9A5.3NCBI
Htr3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541215,589,117 - 15,602,211 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541215,589,117 - 15,602,211 (+)NCBIChiLan1.0ChiLan1.0
HTR3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111112,696,271 - 112,711,507 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11112,695,891 - 112,711,695 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011108,851,954 - 108,869,119 (+)NCBIMhudiblu_PPA_v0panPan3
HTR3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1519,324,087 - 19,338,250 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl519,324,444 - 19,338,294 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha519,248,270 - 19,261,807 (-)NCBI
ROS_Cfam_1.0519,345,236 - 19,358,844 (-)NCBI
UMICH_Zoey_3.1519,409,269 - 19,422,833 (-)NCBI
UNSW_CanFamBas_1.0519,311,211 - 19,324,318 (-)NCBI
UU_Cfam_GSD_1.0519,357,640 - 19,371,211 (-)NCBI
HTR3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl941,574,650 - 41,588,582 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1941,575,085 - 41,589,083 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2946,389,414 - 46,403,415 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HTR3A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11105,359,139 - 105,375,217 (+)NCBI
ChlSab1.1 Ensembl1105,359,730 - 105,374,664 (+)Ensembl
Htr3a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247849,470,440 - 9,483,132 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8873867753738677Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)81038843955388439Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)81038843955388439Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81137326757541668Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81144825156448251Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81144825156448251Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81766655562666555Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)82071759265717592Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)82146491991140553Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)821813070100873963Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82784149672841496Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82986798359908353Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)829867983106526740Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)829867983106526740Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)829867983106526740Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)83014480075144800Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)83014480075144800Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)83091811258858224Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)83091811275918112Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)830918112107206309Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)83220198154065241Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)83220198175971421Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)832888352101374135Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866062857995Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83355866065717592Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83355866089058369Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83355866089058369Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83355866089058369Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83355866089058369Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)833558660109028082Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)833558660109028082Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)833558660109028082Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)833558764113580387Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83504141480041414Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83592559480925594Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)839230130106506973Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83992790184927901Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83995802284958022Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84421919789542960Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)844219197100873963Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84571234480003418Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84571234490712344Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84571247575971259Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84658843754065241Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84658843796998640Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)847200750106394378Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)847200750106394378Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)847200750106394378Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)847200750106394378Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)847200750106394378Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)847200750106394378Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)850529563106506973Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:206
Count of miRNA genes:134
Interacting mature miRNAs:154
Transcripts:ENSRNOT00000008965
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 nervous system renal system reproductive system respiratory system
High
Medium
Low 3 12 74 2 17
Below cutoff 15 16 4 6 4 18 18 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008965   ⟹   ENSRNOP00000008965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl853,211,438 - 53,223,804 (-)Ensembl
RefSeq Acc Id: NM_024394   ⟹   NP_077370
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,020 - 49,254,389 (-)NCBI
Rnor_6.0853,211,438 - 53,223,804 (-)NCBI
Rnor_5.0851,803,895 - 51,816,278 (-)NCBI
RGSC_v3.4852,161,147 - 52,173,514 (-)RGD
Celera848,799,808 - 48,812,052 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243021   ⟹   XP_006243083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,018 - 49,254,471 (-)NCBI
Rnor_6.0853,211,436 - 53,223,877 (-)NCBI
Rnor_5.0851,803,895 - 51,816,278 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595928   ⟹   XP_017451417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,018 - 49,254,475 (-)NCBI
Rnor_6.0853,211,436 - 53,223,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082195   ⟹   XP_038938123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,018 - 49,249,675 (-)NCBI
RefSeq Acc Id: XM_039082196   ⟹   XP_038938124
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,018 - 49,251,949 (-)NCBI
RefSeq Acc Id: XM_039082197   ⟹   XP_038938125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2849,242,018 - 49,251,946 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_077370   ⟸   NM_024394
- Peptide Label: precursor
- UniProtKB: P35563 (UniProtKB/Swiss-Prot),   Q62999 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243083   ⟸   XM_006243021
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451417   ⟸   XM_017595928
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000008965   ⟸   ENSRNOT00000008965
RefSeq Acc Id: XP_038938124   ⟸   XM_039082196
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938125   ⟸   XM_039082197
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938123   ⟸   XM_039082195
- Peptide Label: isoform X3
Protein Domains
Neur_chan_LBD   Neur_chan_memb

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 (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)
ACI/EurMcwi (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
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/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 (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)
F344/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
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
FHH/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)
FHH/EurMcwi (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
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)
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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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
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
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 (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
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)
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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
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)
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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/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
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 (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 (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
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 (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 (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 (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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 51809587 51809588 C A snv KFRS3B/Kyo (KyushuU), RCS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61818 AgrOrtholog
Ensembl Genes ENSRNOG00000006595 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000008965 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000008965 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.70.170.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 5HT3_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  5HT3_rcpt_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_lig-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_channel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neuro-gated_channel_TM_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotrans-gated_channel_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotransmitter_ion_chnl_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:79246 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 79246 ENTREZGENE
PANTHER PTHR18945 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Neur_chan_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_memb UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HTR3A RGD
PhenoGen Htr3a PhenoGen
PRINTS 5HT3ARECEPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  5HT3RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NRIONCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NEUROTR_ION_CHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs LIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt 5HT3A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q62999 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Htr3a  5-hydroxytryptamine receptor 3A  Htr3a  5-hydroxytryptamine (serotonin) receptor 3A, ionotropic  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-17 Htr3a  5-hydroxytryptamine (serotonin) receptor 3A, ionotropic  Htr3a  5-hydroxytryptamine (serotonin) receptor 3a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Htr3a  5-hydroxytryptamine (serotonin) receptor 3a      Name updated 70584 APPROVED
2001-05-08 Htr3  5-Hydroxytryptamine (serotonin) receptor 3A      Symbol inconsistent with Human and Mouse 62408 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_drugs HT3R antagonist tropisetron blocks fast membrane potential depolarizations induced by serotonin 625727
gene_expression expressed in central and peripheral neurons 625727
gene_expression expressed in the cerebellum 727384
gene_expression expressed in a subset of GABAergic interneurons 625727
gene_function ligand-gated ion channel receptor for serotonin 625727
gene_function cation-selective ligand-gated ion channel 625614
gene_other dendrites and somata of 5HT3R secreting neurons placed in close apposition of serotonergic fibres indicating possible synaptic contacts 625727
gene_other dendrites and somata of 5HT3R secreting neurons are placed in close apposition of serotonergic fibres indicating possible synaptic contacts 625727
gene_process may play an important role in synaptic activation in neocortical VIP/CCK in GABAergic interneurons by serotonergic afferent fibres from brainstem raphe nuclei 625727
gene_process may be involved in mediating fast synaptic transmission in neocortex region of brain 625614
gene_process mediates visceral afferent information and visceral reflexes, nociception and cognition 625727