Slc6a3 (solute carrier family 6 member 3) - Rat Genome Database

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Gene: Slc6a3 (solute carrier family 6 member 3) Rattus norvegicus
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Symbol: Slc6a3
Name: solute carrier family 6 member 3
RGD ID: 3715
Description: Enables dopamine:sodium symporter activity; enzyme binding activity; and signaling receptor binding activity. Involved in several processes, including dopamine transport; response to cAMP; and response to ethanol. Located in dopaminergic synapse; neuron projection; and plasma membrane. Is integral component of postsynaptic membrane and integral component of presynaptic membrane. Biomarker of Parkinsonism; heroin dependence; high grade glioma; hyperprolactinemia; and hypertension. Human ortholog(s) of this gene implicated in attention deficit hyperactivity disorder; nicotine dependence; and obesity. Orthologous to human SLC6A3 (solute carrier family 6 member 3); PARTICIPATES IN alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; buprenorphine pharmacodynamics pathway; INTERACTS WITH (S)-amphetamine; (S)-nicotine; 1-[2-(benzhydryloxy)ethyl]-4-(3-phenylpropyl)piperazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DA transporter; DAT; Dat1; sodium-dependent dopamine transporter; Solute carrier family 6 (neurotransmitter transporter dopamine) member 3; solute carrier family 6 (neurotransmitter transporter), member 3; Solute carrier family 6 (neurotransmitter transporter, dopamine), member 3; solute carrier family 6, member 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc6a3m1Span  
Genetic Models: F344-Slc6a3m1Span
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,709,443 - 29,750,413 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl132,321,580 - 32,363,983 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0132,323,011 - 32,363,983 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0133,745,060 - 33,788,878 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,516,568 - 30,557,540 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1130,518,078 - 30,558,861 (-)NCBI
Celera128,357,426 - 28,397,883 (-)NCBICelera
Cytogenetic Map1p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20S)-ginsenoside Rg3  (ISO)
(R)-noradrenaline  (ISO)
(R)-octopamine  (ISO)
(S)-amphetamine  (EXP,ISO)
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-[2-(benzhydryloxy)ethyl]-4-(3-phenylpropyl)piperazine  (EXP,ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,5-dimethoxy-4-bromophenethylamine  (ISO)
2-aminopropiophenone  (ISO)
2-phenylethylamine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nitrotoluene  (EXP)
7-NITROINDAZOLE  (ISO)
acrylamide  (EXP)
albiflorin  (EXP)
alcohol  (ISO)
all-trans-retinoic acid  (ISO)
alpha,alpha-trehalose  (ISO)
AM-251  (EXP)
aminorex  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP,ISO)
Aroclor 1254  (EXP,ISO)
arsenite(3-)  (EXP,ISO)
atrazine  (EXP)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bupropion  (ISO)
butyric acid  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
chlorpyrifos  (EXP,ISO)
citalopram  (ISO)
clozapine  (ISO)
cocaine  (EXP,ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyhalothrin  (EXP)
DDD  (ISO)
DDE  (EXP,ISO)
DDT  (ISO)
dextran sulfate  (ISO)
diazinon  (EXP)
dieldrin  (EXP,ISO)
diethyldithiocarbamic acid  (EXP)
diethylstilbestrol  (EXP)
dihydro-beta-erythroidine  (EXP)
dopamine  (EXP,ISO)
elemental selenium  (EXP)
endosulfan  (EXP)
estrone  (ISO)
ethanol  (ISO)
fluoxetine  (EXP,ISO)
ganglioside GM1  (EXP)
geraniol  (ISO)
glyburide  (ISO)
haloperidol  (EXP,ISO)
heptachlor  (EXP,ISO)
herbicide  (EXP)
ibogaine  (ISO)
ibuprofen  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
isoliquiritigenin  (ISO)
ketamine  (ISO)
linalool  (EXP)
lipopolysaccharide  (ISO)
maneb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
Mazindol  (EXP,ISO)
Mecamylamine  (EXP)
melatonin  (EXP,ISO)
melittin  (ISO)
mephedrone  (EXP,ISO)
mepyramine  (ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (ISO)
methcathinone  (ISO)
methoxychlor  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
minocycline  (ISO)
modafinil  (EXP,ISO)
monensin A  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (EXP,ISO)
naltrexone  (ISO)
nicotine  (EXP,ISO)
nomifensine  (EXP,ISO)
Nonylphenol  (EXP)
octopamine  (ISO)
oleic acid  (ISO)
oxidopamine  (EXP)
paraquat  (EXP,ISO)
permethrin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
piperazines  (ISO)
piperidines  (ISO)
pirinixic acid  (EXP,ISO)
probenecid  (ISO)
propofol  (ISO)
quinolinic acid  (EXP)
quinpirole  (EXP,ISO)
raloxifene  (EXP)
reboxetine  (ISO)
reserpine  (ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
SCH 23390  (ISO)
selenium atom  (EXP)
serotonin  (ISO)
simazine  (EXP,ISO)
staurosporine  (ISO)
sulpiride  (ISO)
tamoxifen  (EXP)
telmisartan  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
trichostatin A  (EXP)
triphenyl phosphate  (EXP)
tryptamine  (ISO)
tyramine  (ISO)
valproic acid  (EXP,ISO)
vanoxerine dihydrochloride  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
WIN 55212-2  (EXP)
wortmannin  (ISO)
zinc atom  (ISO)
zinc sulfate  (EXP)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
Parkinson's disease pathway  (IEA)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)

References

References - curated
1. Baucum AJ 2nd, etal., J Neurosci. 2004 Mar 31;24(13):3436-43.
2. Beard J, etal., J Nutr. 2003 Apr;133(4):1174-9.
3. Cremona ML, etal., Nat Neurosci. 2011 Apr;14(4):469-77. doi: 10.1038/nn.2781. Epub 2011 Mar 13.
4. du Bois TM, etal., Neurochem Res. 2008 Jul;33(7):1224-31. Epub 2008 Feb 8.
5. Epstein LH, etal., Obes Res. 2002 Dec;10(12):1232-40.
6. Foster JD, etal., Brain Res Mol Brain Res 2003 Jan 31;110(1):100-8.
7. Gainetdinov RR, etal., Science 1999 Jan 15;283(5400):397-401.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Giros B, etal., FEBS Lett 1991 Dec 16;295(1-3):149-54.
10. GOA data from the GO Consortium
11. Kahn RS, etal., J Pediatr 2003 Jul;143(1):104-10.
12. Kilty JE, etal., Science 1991 Oct 25;254(5031):578-9.
13. Kuge H, etal., J Lipid Res. 2020 Dec;61(12):1747-1763. doi: 10.1194/jlr.RA120001087. Epub 2020 Sep 22.
14. Li S, etal., Neurosci Lett. 2004 Jun 3;363(1):29-32.
15. Li Y, etal., Med Sci Monit. 2017 Jun 9;23:2805-2815.
16. Loder MK and Melikian HE, J Biol Chem 2003 Jun 13;278(24):22168-74. Epub 2003 Apr 7.
17. Lonjon M, etal., Neurosci Lett. 2004 Jan 9;354(2):131-4.
18. Mengual E and Pickel VM, J Comp Neurol. 2004 Jan 12;468(3):395-409.
19. MGD data from the GO Consortium
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Need AC, etal., Ann Hum Genet. 2006 May;70(Pt 3):293-303.
22. Nirenberg MJ, etal., J Neurosci. 1996 Jan 15;16(2):436-47.
23. OMIM Disease Annotation Pipeline
24. Owens WA, etal., J Neurochem. 2005 Sep;94(5):1402-10. Epub 2005 Jun 30.
25. Page G, etal., Neurochem Int. 2004 Oct;45(5):627-32.
26. Perry ML, etal., J Neurochem. 2010 Aug;114(3):666-74. Epub 2010 Apr 20.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. Pipeline to import SMPDB annotations from SMPDB into RGD
29. Ramamoorthy S, etal., Biochem Biophys Res Commun. 2010 Jan 15;391(3):1517-21. doi: 10.1016/j.bbrc.2009.12.110. Epub 2009 Dec 24.
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Richardson RM, etal., Brain Res. 2005 Jan 25;1032(1-2):11-22.
34. Robinson DL, etal., Alcohol Clin Exp Res. 2005 May;29(5):746-55.
35. Salkovic-Petrisic M and Lackovic Z, J Neural Transm. 2003 Jan;110(1):15-29.
36. Salvatore MF, etal., Neurobiol Aging. 2003 Dec;24(8):1147-54.
37. Shimada S, etal., Science 1991 Oct 25;254(5031):576-8.
38. Simoni D, etal., J Med Chem. 2005 May 5;48(9):3337-43.
39. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
40. Vaughan RA, etal., J Neurosci Methods. 2005 Apr 15;143(1):33-40. Epub 2004 Dec 2.
41. Wang D, etal., Neurosci Lett. 2015 Oct 8;606:60-5. doi: 10.1016/j.neulet.2015.08.024. Epub 2015 Aug 18.
42. Watanabe Y, etal., J Nucl Med. 1997 Mar;38(3):470-4.
43. Zhang H, etal., Mol Brain. 2009 May 6;2:10.
Additional References at PubMed
PMID:1502198   PMID:8628395   PMID:9247269   PMID:9520487   PMID:11150348   PMID:11343649   PMID:12480180   PMID:12521926   PMID:12958153   PMID:14499307   PMID:15128747   PMID:15505207  
PMID:15935059   PMID:16024787   PMID:16708013   PMID:16765459   PMID:16885233   PMID:17255098   PMID:17363452   PMID:17439486   PMID:17561841   PMID:17651428   PMID:17761882   PMID:17873367  
PMID:17978168   PMID:18198344   PMID:18216182   PMID:18588534   PMID:18671743   PMID:18845198   PMID:19046383   PMID:19135135   PMID:19357284   PMID:19766189   PMID:20170186   PMID:20688912  
PMID:20816972   PMID:21118819   PMID:21396352   PMID:21698001   PMID:21957239   PMID:22133315   PMID:22570010   PMID:22722938   PMID:22778840   PMID:23161550   PMID:23300642   PMID:23567316  
PMID:23612789   PMID:25179220   PMID:25943760   PMID:26048990   PMID:26056032   PMID:26658810   PMID:26707058   PMID:26911894   PMID:27789384   PMID:28116523   PMID:28167616   PMID:28495886  
PMID:28894302   PMID:30472113   PMID:30745563   PMID:31599465   PMID:31728018  


Genomics

Comparative Map Data
Slc6a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,709,443 - 29,750,413 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl132,321,580 - 32,363,983 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0132,323,011 - 32,363,983 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0133,745,060 - 33,788,878 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,516,568 - 30,557,540 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1130,518,078 - 30,558,861 (-)NCBI
Celera128,357,426 - 28,397,883 (-)NCBICelera
Cytogenetic Map1p11NCBI
SLC6A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl51,392,794 - 1,445,440 (-)EnsemblGRCh38hg38GRCh38
GRCh3851,392,794 - 1,445,440 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3751,392,909 - 1,445,555 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3651,445,909 - 1,498,538 (-)NCBINCBI36hg18NCBI36
Build 3451,445,908 - 1,498,543NCBI
Celera51,429,610 - 1,484,220 (-)NCBI
Cytogenetic Map5p15.33NCBI
HuRef51,373,680 - 1,426,892 (-)NCBIHuRef
CHM1_151,392,820 - 1,445,528 (-)NCBICHM1_1
Slc6a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391373,684,270 - 73,726,791 (+)NCBIGRCm39mm39
GRCm39 Ensembl1373,684,866 - 73,726,791 (+)Ensembl
GRCm381373,536,128 - 73,578,672 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1373,536,747 - 73,578,672 (+)EnsemblGRCm38mm10GRCm38
MGSCv371373,674,195 - 73,716,120 (+)NCBIGRCm37mm9NCBIm37
MGSCv361374,002,749 - 74,044,674 (+)NCBImm8
Celera1375,865,546 - 75,907,463 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.1NCBI
Slc6a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955504721,429 - 747,630 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955504721,470 - 747,553 (-)NCBIChiLan1.0ChiLan1.0
SLC6A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.151,437,567 - 1,488,829 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl51,437,567 - 1,488,829 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v051,687,079 - 1,739,729 (-)NCBIMhudiblu_PPA_v0panPan3
SLC6A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13411,209,118 - 11,245,456 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3411,210,939 - 11,246,742 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3415,719,083 - 15,755,282 (+)NCBI
ROS_Cfam_1.03411,109,747 - 11,147,167 (+)NCBI
UMICH_Zoey_3.13411,160,852 - 11,196,981 (+)NCBI
UNSW_CanFamBas_1.03411,139,913 - 11,176,047 (+)NCBI
UU_Cfam_GSD_1.03411,350,821 - 11,387,021 (+)NCBI
Slc6a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213244,198,128 - 244,239,922 (+)NCBI
SpeTri2.0NW_004936815359,775 - 400,690 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1679,186,108 - 79,220,297 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11679,186,114 - 79,220,302 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21685,853,611 - 85,887,787 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.141,209,013 - 1,258,797 (-)NCBI
ChlSab1.1 Ensembl41,209,019 - 1,258,866 (-)Ensembl
Vero_WHO_p1.0NW_02366605435,775,947 - 35,824,591 (-)NCBI
Slc6a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624751694,165 - 720,287 (-)NCBI

Position Markers
D1Rat377  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,743,235 - 29,743,400 (+)MAPPERmRatBN7.2
Rnor_6.0132,356,806 - 32,356,970NCBIRnor6.0
Rnor_5.0133,780,289 - 33,780,453UniSTSRnor5.0
RGSC_v3.4130,550,363 - 30,550,527UniSTSRGSC3.4
RGSC_v3.4130,550,362 - 30,550,527RGDRGSC3.4
RGSC_v3.1130,553,307 - 30,553,472RGD
FHH x ACI Map121.7699UniSTS
FHH x ACI Map121.7699RGD
Cytogenetic Map1p11UniSTS
D1Wox51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,708,849 - 29,708,992 (+)MAPPERmRatBN7.2
Rnor_6.0132,322,418 - 32,322,560NCBIRnor6.0
Rnor_5.0133,745,901 - 33,746,043UniSTSRnor5.0
RGSC_v3.4130,515,975 - 30,516,117UniSTSRGSC3.4
Celera128,356,833 - 28,356,975UniSTS
Cytogenetic Map1p11UniSTS
RH94715  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,708,645 - 29,708,778 (+)MAPPERmRatBN7.2
Rnor_6.0132,322,214 - 32,322,346NCBIRnor6.0
Rnor_5.0133,745,697 - 33,745,829UniSTSRnor5.0
RGSC_v3.4130,515,771 - 30,515,903UniSTSRGSC3.4
Celera128,356,629 - 28,356,761UniSTS
Cytogenetic Map1p11UniSTS
RH94400  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,708,037 - 29,708,210 (+)MAPPERmRatBN7.2
Rnor_6.0132,321,606 - 32,321,778NCBIRnor6.0
Rnor_5.0133,745,089 - 33,745,261UniSTSRnor5.0
RGSC_v3.4130,515,163 - 30,515,335UniSTSRGSC3.4
Celera128,356,021 - 28,356,193UniSTS
Cytogenetic Map1p11UniSTS
PMC304098P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,724,402 - 29,724,503 (+)MAPPERmRatBN7.2
Rnor_6.0132,337,973 - 32,338,073NCBIRnor6.0
Rnor_5.0133,761,456 - 33,761,556UniSTSRnor5.0
RGSC_v3.4130,531,530 - 30,531,630UniSTSRGSC3.4
Celera128,372,004 - 28,372,104UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11131465834993348Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11249343957493439Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11362925158629251Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11614314349547474Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11614314349547474Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12034156058000154Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12107930566079305Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12130082249454378Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12181262344409802Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12340642868406428Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)12429779978748000Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat


Genetic Models
This gene Slc6a3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:59
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000040291
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 4
Low 6 8 32 1 6 1
Below cutoff 3 14 38 28 11 28 6 6 24 26 27 10 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040291   ⟹   ENSRNOP00000047272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl132,323,011 - 32,363,983 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079987   ⟹   ENSRNOP00000070728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl132,321,580 - 32,362,359 (-)Ensembl
RefSeq Acc Id: NM_012694   ⟹   NP_036826
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,709,443 - 29,750,413 (-)NCBI
Rnor_6.0132,323,011 - 32,363,983 (-)NCBI
Rnor_5.0133,745,060 - 33,788,878 (-)NCBI
RGSC_v3.4130,516,568 - 30,557,540 (-)RGD
Celera128,357,426 - 28,397,883 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036826 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41100 (Get FASTA)   NCBI Sequence Viewer  
  AAA73143 (Get FASTA)   NCBI Sequence Viewer  
  AAB21099 (Get FASTA)   NCBI Sequence Viewer  
  EDL87653 (Get FASTA)   NCBI Sequence Viewer  
  P23977 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036826   ⟸   NM_012694
- UniProtKB: P23977 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070728   ⟸   ENSRNOT00000079987
RefSeq Acc Id: ENSRNOP00000047272   ⟸   ENSRNOT00000040291

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)
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 (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)
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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)
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 (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)
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
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/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
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 (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
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
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
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
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
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 (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
SBH/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: 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
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 (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 (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
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 (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 (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/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3715 AgrOrtholog
Ensembl Genes ENSRNOG00000017302 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000047272 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070728 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000040291 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000079987 UniProtKB/Swiss-Prot
InterPro Na/ntran_symport UniProtKB/Swiss-Prot
  Na/ntran_symport_dopamine UniProtKB/Swiss-Prot
  SNS_sf UniProtKB/Swiss-Prot
KEGG Report rno:24898 UniProtKB/Swiss-Prot
NCBI Gene 24898 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot
Pfam SNF UniProtKB/Swiss-Prot
PharmGKB SLC6A3 RGD
PhenoGen Slc6a3 PhenoGen
PRINTS DOPTRANSPORT UniProtKB/Swiss-Prot
  NANEUSMPORT UniProtKB/Swiss-Prot
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot
TIGR TC234653
UniProt P23977 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc6a3  solute carrier family 6 member 3  Slc6a3  solute carrier family 6 (neurotransmitter transporter), member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc6a3  solute carrier family 6 (neurotransmitter transporter, dopamine), member 3    solute carrier family 6, member 3  Name updated 1299863 APPROVED
2003-04-09 Slc6a3  solute carrier family 6, member 3    Solute carrier family 6 (neurotransmitter transporter, dopamine), member 3  Name updated 629478 APPROVED
2002-06-10 Slc6a3  Solute carrier family 6 (neurotransmitter transporter, dopamine), member 3      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization putative integral plasma membrane protein 730166
gene_expression expressed in substantia nigra and ventral tegmental area 730166
gene_function sodium-dependent dopamine transporter 730166
gene_function sodium-dependent dopamine transporter 730214
gene_function sodium-dependent dopamine transporter 730247
gene_protein 620 amino acid protein 730166
gene_regulation constitutively internalized and recycled to plasma membrane; protein kinase C activation accelerates endocytosis of protein and attenuates recycling to cell surface 1299034