Slc18a2 (solute carrier family 18 member A2) - Rat Genome Database

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Gene: Slc18a2 (solute carrier family 18 member A2) Rattus norvegicus
Analyze
Symbol: Slc18a2
Name: solute carrier family 18 member A2
RGD ID: 3694
Description: Enables amine transmembrane transporter activity; enzyme binding activity; and heat shock protein binding activity. Involved in several processes, including aminergic neurotransmitter loading into synaptic vesicle; response to herbicide; and serotonin uptake. Located in several cellular components, including dopaminergic synapse; neuronal cell body; and secretory vesicle. Is integral component of synaptic vesicle membrane. Is active in postsynapse. Is integral component of neuronal dense core vesicle membrane. Used to study Parkinson's disease and type 1 diabetes mellitus. Biomarker of Machado-Joseph disease; Parkinson's disease; substance-related disorder; and toxic encephalopathy. Human ortholog(s) of this gene implicated in Parkinson's disease. Orthologous to human SLC18A2 (solute carrier family 18 member A2); PARTICIPATES IN dopamine biosynthetic pathway; epinephrine biosynthetic pathway; norepinephrine biosynthetic pathway; INTERACTS WITH (R)-noradrenaline; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MNAT; monoamine transporter; solute carrier family 18 (vesicular monoamine transporter), member 2; solute carrier family 18 (vesicular monoamine), member 2; Solute carrier family 18 A2 (vesicular monoamine transporter 2); solute carrier family 18 member 2; solute carrier family 18, member 2; synaptic vesicular amine transporter; VAT2; vesicular amine transporter 2; VMAT-2; VMAT2
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
mRatBN7.21258,413,748 - 258,449,143 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1258,413,959 - 258,448,325 (+)Ensembl
Rnor_6.01280,397,831 - 280,457,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1280,423,079 - 280,457,148 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01287,782,713 - 287,818,452 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41265,789,917 - 265,824,551 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11266,000,961 - 266,035,596 (+)NCBI
Celera1254,067,617 - 254,102,150 (+)NCBICelera
RH 3.4 Map11709.1RGD
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(R)-noradrenaline  (EXP,ISO)
(S)-amphetamine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
9,10-dimethoxy-3-isobutyl-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-one  (EXP,ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
ammonium chloride  (EXP)
amphetamine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
arsenite(3-)  (ISO)
Asiaticoside  (EXP)
atrazine  (EXP)
b-Dihydrotetrabenazine  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bisphenol F  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (EXP)
chlordecone  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
clozapine  (EXP)
cocaine  (EXP,ISO)
curcumin  (EXP)
cyhalothrin  (EXP)
cypermethrin  (EXP)
D-glucose  (ISO)
dabigatran  (EXP)
DDD  (ISO)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diazinon  (EXP)
dieldrin  (ISO)
dopamine  (EXP,ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
estrone  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
fucoxanthin  (ISO)
ganglioside GM1  (EXP)
genistein  (ISO)
geraniol  (ISO)
glucose  (ISO)
haloperidol  (ISO)
heptachlor  (ISO)
Heptachlor epoxide  (ISO)
herbicide  (EXP)
histamine  (EXP,ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
ketoconazole  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
maneb  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
Mazindol  (ISO)
melatonin  (ISO)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury(0)  (ISO)
methamphetamine  (EXP,ISO)
methoxychlor  (ISO)
methylphenidate  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
nomifensine  (ISO)
oxaliplatin  (EXP)
oxidopamine  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
probenecid  (ISO)
pyrroloquinoline quinone  (EXP)
quinpirole  (ISO)
rabeprazole  (EXP)
raloxifene  (EXP)
reserpine  (EXP,ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
S-methyl-L-thiocitrulline  (EXP)
SB 431542  (ISO)
SCH 23390  (ISO)
serotonin  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simazine  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sulpiride  (ISO)
telmisartan  (ISO)
tetrabenazine  (EXP,ISO)
topotecan  (EXP)
tributylstannane  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
valinomycin  (EXP)
valproic acid  (ISO)
vanoxerine dihydrochloride  (ISO)
zinc sulfate  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alves S, etal., Hum Mol Genet. 2008 Jul 15;17(14):2071-83. Epub 2008 Apr 1.
2. Bohnen NI, etal., J Cereb Blood Flow Metab. 2006 Sep;26(9):1198-212. Epub 2006 Jan 18.
3. Brunk I, etal., J Biol Chem. 2006 Nov 3;281(44):33373-85. Epub 2006 Aug 22.
4. Brunk I, etal., J Biol Chem. 2009 Jan 9;284(2):1050-6. Epub 2008 Nov 13.
5. Cartier EA, etal., J Biol Chem. 2010 Jan 15;285(3):1957-66. Epub 2009 Nov 10.
6. Cruz-Muros I, etal., Neurobiol Aging. 2008 Nov;29(11):1702-11. Epub 2007 Jun 19.
7. Erickson JD, etal., Proc Natl Acad Sci U S A 1992 Nov 15;89(22):10993-7.
8. Eyerman DJ and Yamamoto BK, J Neurochem. 2007 Nov;103(3):1219-27. Epub 2007 Aug 7.
9. Farnsworth SJ, etal., J Pharmacol Exp Ther. 2009 Mar;328(3):807-12. Epub 2008 Nov 26.
10. Fukui M, etal., J Neurosci. 2007 Sep 26;27(39):10520-9.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Glatt CE, etal., Hum Mol Genet. 2006 Jan 15;15(2):299-305. Epub 2005 Dec 8.
13. GOA data from the GO Consortium
14. Goland R, etal., J Nucl Med. 2009 Mar;50(3):382-9. Epub 2009 Feb 17.
15. Gros Y and Schuldiner S, J Biol Chem. 2010 Feb 12;285(7):5076-84. Epub 2009 Dec 10.
16. Gustafsson BI, etal., Scand J Gastroenterol. 2011 May;46(5):531-7. Epub 2011 Feb 23.
17. Kumar A, etal., Free Radic Res. 2010 Aug;44(8):950-65.
18. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
19. Lambrecht NW, etal., Physiol Genomics. 2007 Oct 22;31(2):183-92. Epub 2007 May 29.
20. Lee WY, etal., Exp Neurol. 2006 Jan;197(1):215-24. Epub 2005 Nov 2.
21. Li XM, etal., J Ethnopharmacol. 2011 Apr 12;134(3):768-74. Epub 2011 Feb 1.
22. Liu Y, etal., Cell 1992 Aug 21;70(4):539-51.
23. MGD data from the GO Consortium
24. Minton GO, etal., Neuropsychopharmacology. 2009 Sep;34(10):2265-74. Epub 2009 Jun 3.
25. Mooslehner KA, etal., Mol Cell Biol. 2001 Aug;21(16):5321-31.
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Nirenberg MJ, etal., J Neurosci. 1996 Jul 1;16(13):4135-45.
28. Nirenberg MJ, etal., Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8773-7.
29. Northrop NA, etal., J Pharmacol Exp Ther. 2011 Mar;336(3):900-7. Epub 2010 Dec 15.
30. Onoa B, etal., J Neurosci. 2010 Jun 9;30(23):7917-27.
31. Pipeline to import KEGG annotations from KEGG into RGD
32. Raffo A, etal., J Endocrinol. 2008 Jul;198(1):41-9.
33. Requena DF, etal., J Neurochem. 2009 Jul;110(2):581-94. Epub 2009 Apr 30.
34. RGD automated data pipeline
35. RGD automated import pipeline for gene-chemical interactions
36. Riezzo I, etal., J Neurosci Res. 2010 Mar;88(4):905-16.
37. Sevigny CP, etal., Eur J Neurosci. 2008 Oct;28(8):1536-44.
38. Souza F, etal., J Clin Invest. 2006 Jun;116(6):1506-13. Epub 2006 May 18.
39. Sriram K, etal., Arch Toxicol. 2010 Jul;84(7):521-40. Epub 2010 Mar 12.
40. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
41. Volz TJ, etal., J Neurosci Methods. 2009 Feb 15;177(1):177-82. Epub 2008 Oct 17.
Additional References at PubMed
PMID:8745292   PMID:9045708   PMID:9275230   PMID:9427251   PMID:12591135   PMID:15246838   PMID:15695065   PMID:16301178   PMID:16677634   PMID:16897727   PMID:17156758   PMID:17244889  
PMID:18287335   PMID:19021208   PMID:19429089   PMID:21046458   PMID:21705944   PMID:22570010   PMID:23160224   PMID:23404442   PMID:23504951   PMID:23530208   PMID:24062308   PMID:24161354  
PMID:24239562   PMID:24316448   PMID:24480406   PMID:25370842   PMID:25496994   PMID:25943760   PMID:26956479   PMID:27821772   PMID:31955909  


Genomics

Comparative Map Data
Slc18a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21258,413,748 - 258,449,143 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1258,413,959 - 258,448,325 (+)Ensembl
Rnor_6.01280,397,831 - 280,457,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1280,423,079 - 280,457,148 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01287,782,713 - 287,818,452 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41265,789,917 - 265,824,551 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11266,000,961 - 266,035,596 (+)NCBI
Celera1254,067,617 - 254,102,150 (+)NCBICelera
RH 3.4 Map11709.1RGD
Cytogenetic Map1q55NCBI
SLC18A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10117,241,093 - 117,279,430 (+)EnsemblGRCh38hg38GRCh38
GRCh3810117,241,114 - 117,279,430 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710119,000,625 - 119,038,941 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610118,990,706 - 119,027,085 (+)NCBINCBI36hg18NCBI36
Build 3410118,991,172 - 119,027,085NCBI
Celera10112,730,694 - 112,769,064 (+)NCBI
Cytogenetic Map10q25.3NCBI
HuRef10112,628,076 - 112,666,635 (+)NCBIHuRef
CHM1_110119,284,792 - 119,323,133 (+)NCBICHM1_1
Slc18a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391959,249,310 - 59,284,444 (+)NCBIGRCm39mm39
GRCm39 Ensembl1959,249,328 - 59,284,444 (+)Ensembl
GRCm381959,260,878 - 59,296,012 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1959,260,896 - 59,296,012 (+)EnsemblGRCm38mm10GRCm38
MGSCv371959,335,368 - 59,370,502 (+)NCBIGRCm37mm9NCBIm37
MGSCv361959,314,177 - 59,348,927 (+)NCBImm8
Celera1961,459,915 - 61,496,491 (+)NCBICelera
Cytogenetic Map19D3NCBI
cM Map1954.64NCBI
Slc18a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543121,949,576 - 21,979,679 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543121,949,553 - 21,979,679 (+)NCBIChiLan1.0ChiLan1.0
SLC18A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110117,250,639 - 117,290,064 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10117,250,639 - 117,290,064 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010113,823,005 - 113,862,451 (+)NCBIMhudiblu_PPA_v0panPan3
SLC18A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12827,731,709 - 27,809,341 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2827,731,004 - 27,767,993 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2827,875,180 - 27,989,296 (+)NCBI
ROS_Cfam_1.02828,261,416 - 28,375,583 (+)NCBI
UMICH_Zoey_3.12827,822,412 - 27,937,317 (+)NCBI
UNSW_CanFamBas_1.02827,836,195 - 27,950,801 (+)NCBI
UU_Cfam_GSD_1.02828,030,658 - 28,145,734 (+)NCBI
Slc18a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721318,450,220 - 18,486,469 (-)NCBI
SpeTri2.0NW_0049364867,075,373 - 7,108,984 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC18A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14127,357,555 - 127,396,533 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114127,357,605 - 127,394,242 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214138,758,819 - 138,800,217 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC18A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19110,039,783 - 110,078,822 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl9110,040,391 - 110,076,647 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604871,296,614 - 71,335,781 (+)NCBIVero_WHO_p1.0
Slc18a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473729,356,590 - 29,388,099 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94742  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21258,447,675 - 258,447,802 (+)MAPPERmRatBN7.2
Rnor_6.01280,456,499 - 280,456,625NCBIRnor6.0
Rnor_5.01287,816,983 - 287,817,109UniSTSRnor5.0
RGSC_v3.41265,823,902 - 265,824,028UniSTSRGSC3.4
Celera1254,101,501 - 254,101,627UniSTS
RH 3.4 Map11709.1UniSTS
Cytogenetic Map1q55UniSTS
D1Bda65  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21258,447,817 - 258,448,251 (+)MAPPERmRatBN7.2
Rnor_6.01280,456,641 - 280,457,074NCBIRnor6.0
Rnor_5.01287,817,125 - 287,817,558UniSTSRnor5.0
RGSC_v3.41265,824,044 - 265,824,477UniSTSRGSC3.4
Celera1254,101,643 - 254,102,076UniSTS
Cytogenetic Map1q55UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:184
Count of miRNA genes:113
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000011983
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 2 1 4 31 1
Low 3 28 48 33 15 33 8 10 41 17 24 11 8
Below cutoff 13 2 2 2 1 2 12 13

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011983   ⟹   ENSRNOP00000011983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1258,413,959 - 258,448,325 (+)Ensembl
Rnor_6.0 Ensembl1280,423,079 - 280,457,148 (+)Ensembl
RefSeq Acc Id: NM_013031   ⟹   NP_037163
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21258,413,959 - 258,448,325 (+)NCBI
Rnor_6.01280,423,079 - 280,457,148 (+)NCBI
Rnor_5.01287,782,713 - 287,818,452 (+)NCBI
RGSC_v3.41265,789,917 - 265,824,551 (+)RGD
Celera1254,067,617 - 254,102,150 (+)RGD
Sequence:
RefSeq Acc Id: XM_006231664   ⟹   XP_006231726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21258,413,748 - 258,449,143 (+)NCBI
Rnor_6.01280,397,831 - 280,457,968 (+)NCBI
Rnor_5.01287,782,713 - 287,818,452 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037163   ⟸   NM_013031
- UniProtKB: Q01827 (UniProtKB/Swiss-Prot),   A0A0G2JSJ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231726   ⟸   XM_006231664
- Peptide Label: isoform X1
- UniProtKB: Q01827 (UniProtKB/Swiss-Prot),   A0A0G2JSJ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011983   ⟸   ENSRNOT00000011983
Protein Domains
MFS

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)
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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
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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)
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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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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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
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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
PVG/Seac (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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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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)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 287798004 287798005 C G snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 265804628 265804629 C G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3694 AgrOrtholog
Ensembl Genes ENSRNOG00000008890 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011983 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011983 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Multidrug-R UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25549 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25549 ENTREZGENE
Pfam MFS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SLC18A2 RGD
PhenoGen Slc18a2 PhenoGen
PROSITE MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206310
TIGRFAMs 2_A_01_02 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSJ6 ENTREZGENE, UniProtKB/TrEMBL
  Q01827 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9QVP1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Slc18a2  solute carrier family 18 member A2  Slc18a2  solute carrier family 18 member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-25 Slc18a2  solute carrier family 18 member 2  Slc18a2  solute carrier family 18 (vesicular monoamine transporter), member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc18a2  solute carrier family 18 (vesicular monoamine transporter), member 2  Slc18a2  solute carrier family 18 (vesicular monoamine), member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc18a2  solute carrier family 18 (vesicular monoamine), member 2    solute carrier family 18, member 2  Name updated 1299863 APPROVED
2003-04-09 Slc18a2  solute carrier family 18, member 2    Solute carrier family 18 A2 (vesicular monoamine transporter 2)  Name updated 629478 APPROVED
2002-06-10 Slc18a2  Solute carrier family 18 A2 (vesicular monoamine transporter 2)      Symbol and Name status set to approved 70586 APPROVED