Slc1a3 (solute carrier family 1 member 3) - Rat Genome Database
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Gene: Slc1a3 (solute carrier family 1 member 3) Rattus norvegicus
Analyze
Symbol: Slc1a3
Name: solute carrier family 1 member 3
RGD ID: 3698
Description: Exhibits high-affinity glutamate transmembrane transporter activity. Involved in amino acid import across plasma membrane; malate-aspartate shuttle; and response to inorganic substance. Localizes to several cellular components, including basal plasma membrane; dendritic spine; and neuronal cell body. Human ortholog(s) of this gene implicated in episodic ataxia type 6. Orthologous to human SLC1A3 (solute carrier family 1 member 3); PARTICIPATES IN nicotinamide adenine dinucleotide metabolic pathway; glutamate signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: EAAT1; excitatory amino acid transporter 1; GLAST; GLAST-1; glial glutamate transporter; GluT-1; glutamate transporter; glutamate/aspartate transporter; sodium-dependent glutamate/aspartate transporter 1; solute carrier family 1 (glial high affinity glutamate transporter), member 3; solute carrier family 1, member 3
Orthologs:
Homo sapiens (human) : SLC1A3 (solute carrier family 1 member 3)  HGNC  Alliance
Mus musculus (house mouse) : Slc1a3 (solute carrier family 1 (glial high affinity glutamate transporter), member 3)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Slc1a3 (solute carrier family 1 member 3)
Pan paniscus (bonobo/pygmy chimpanzee) : SLC1A3 (solute carrier family 1 member 3)
Canis lupus familiaris (dog) : SLC1A3 (solute carrier family 1 member 3)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Slc1a3 (solute carrier family 1 member 3)
Sus scrofa (pig) : SLC1A3 (solute carrier family 1 member 3)
Chlorocebus sabaeus (African green monkey) : SLC1A3 (solute carrier family 1 member 3)
Heterocephalus glaber (naked mole-rat) : Slc1a3 (solute carrier family 1 member 3)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0257,860,881 - 57,935,363 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl257,860,834 - 57,935,363 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0279,348,443 - 79,422,645 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4258,270,236 - 58,347,613 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1258,198,470 - 58,275,846 (-)NCBI
Celera253,367,866 - 53,442,429 (-)NCBICelera
Cytogenetic Map2q16NCBI
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-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-chloroethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acrolein  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
agathisflavone  (EXP)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
atorvastatin calcium  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
bromobenzene  (EXP)
Butylparaben  (EXP)
butyric acid  (ISO)
calcidiol  (EXP)
calcitriol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP,ISO)
cholesterol  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP)
D-glucose  (EXP)
dexamethasone  (ISO)
diazepam  (EXP)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dioxygen  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enzacamene  (EXP)
ethanol  (EXP,ISO)
excitatory amino acid agonist  (EXP)
folpet  (ISO)
furan  (EXP)
genistein  (ISO)
glucose  (EXP)
haloperidol  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
kanamycin A  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
manganese(II) sulfate  (EXP)
medroxyprogesterone acetate  (ISO)
methamphetamine  (EXP)
methylmercury chloride  (EXP)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
oxidopamine  (EXP)
ozone  (ISO)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraoxon  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenylephrine  (EXP)
pirinixic acid  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (EXP)
raloxifene  (EXP)
resveratrol  (EXP)
Riluzole  (EXP)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (EXP,ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
XL147  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7521911   PMID:7903437   PMID:8123008   PMID:8521863   PMID:9364068   PMID:9539795   PMID:9671661   PMID:9753165   PMID:11102482   PMID:11133151   PMID:12440940   PMID:12957496  
PMID:12971893   PMID:14723703   PMID:15305132   PMID:15337311   PMID:15390100   PMID:15615843   PMID:15661376   PMID:15862894   PMID:15965470   PMID:16093329   PMID:16123171   PMID:16738240  
PMID:16775204   PMID:16855093   PMID:16868771   PMID:16959378   PMID:17048262   PMID:17179860   PMID:17346885   PMID:17590480   PMID:17684014   PMID:18028233   PMID:18671901   PMID:18720515  
PMID:19323820   PMID:19440835   PMID:19551376   PMID:19553454   PMID:19570219   PMID:19717015   PMID:19728998   PMID:19804828   PMID:20477940   PMID:20521381   PMID:20531390   PMID:21233495  
PMID:21971915   PMID:22026960   PMID:22134673   PMID:22252783   PMID:22339645   PMID:22871113   PMID:22886112   PMID:23070469   PMID:23392471   PMID:23638698   PMID:24692063   PMID:25454285  
PMID:26037264   PMID:26269591   PMID:26690923   PMID:26920805   PMID:27003918   PMID:27769869   PMID:27889915   PMID:28032905   PMID:28104249   PMID:29476059  


Genomics

Comparative Map Data
Slc1a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0257,860,881 - 57,935,363 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl257,860,834 - 57,935,363 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0279,348,443 - 79,422,645 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4258,270,236 - 58,347,613 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1258,198,470 - 58,275,846 (-)NCBI
Celera253,367,866 - 53,442,429 (-)NCBICelera
Cytogenetic Map2q16NCBI
SLC1A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl536,606,355 - 36,688,334 (+)EnsemblGRCh38hg38GRCh38
GRCh38536,606,606 - 36,688,334 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37536,606,457 - 36,688,436 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36536,642,446 - 36,724,191 (+)NCBINCBI36hg18NCBI36
Build 34536,642,447 - 36,724,197NCBI
Celera536,493,385 - 36,575,353 (+)NCBI
Cytogenetic Map5p13.2NCBI
HuRef536,559,517 - 36,641,481 (+)NCBIHuRef
CHM1_1536,609,230 - 36,691,155 (+)NCBICHM1_1
Slc1a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39158,663,608 - 8,742,648 (-)NCBI
GRCm38158,634,124 - 8,710,807 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl158,634,124 - 8,710,764 (-)EnsemblGRCm38mm10GRCm38
MGSCv37158,584,124 - 8,660,807 (-)NCBIGRCm37mm9NCBIm37
MGSCv36158,581,339 - 8,657,945 (-)NCBImm8
Celera158,479,667 - 8,556,633 (-)NCBICelera
Cytogenetic Map15A1NCBI
cM Map153.82NCBI
Slc1a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542621,371,985 - 21,451,069 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542621,371,985 - 21,450,749 (+)NCBIChiLan1.0ChiLan1.0
SLC1A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1578,960,797 - 79,042,694 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl578,960,797 - 79,042,694 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0573,679,841 - 73,761,591 (-)NCBIMhudiblu_PPA_v0panPan3
SLC1A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl471,936,126 - 72,014,173 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1471,936,128 - 72,014,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc1a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365185,216,343 - 5,291,107 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC1A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1621,873,691 - 21,968,671 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11621,873,691 - 21,965,315 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21622,924,641 - 23,007,781 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC1A3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl435,473,658 - 35,557,138 (+)Ensembl
ChlSab1.1435,473,425 - 35,557,118 (+)NCBI
Slc1a3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475918,325,272 - 18,400,447 (-)NCBI

Position Markers
AI504299  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0257,912,870 - 57,912,961NCBIRnor6.0
Rnor_5.0279,400,231 - 79,400,322UniSTSRnor5.0
RGSC_v3.4258,325,197 - 58,325,288UniSTSRGSC3.4
Celera253,419,930 - 53,420,021UniSTS
Cytogenetic Map2q16UniSTS
RH143474  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0257,893,532 - 57,893,749NCBIRnor6.0
Rnor_5.0279,381,094 - 79,381,311UniSTSRnor5.0
RGSC_v3.4258,302,892 - 58,303,109UniSTSRGSC3.4
Celera253,400,521 - 53,400,738UniSTS
Cytogenetic Map2q16UniSTS
RH139535  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0257,861,064 - 57,861,254NCBIRnor6.0
Rnor_5.0279,348,626 - 79,348,816UniSTSRnor5.0
RGSC_v3.4258,270,419 - 58,270,609UniSTSRGSC3.4
Celera253,368,049 - 53,368,239UniSTS
Cytogenetic Map2q16UniSTS
RH 3.4 Map2333.7UniSTS
RH140370  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0257,861,131 - 57,861,261NCBIRnor6.0
Rnor_5.0279,348,693 - 79,348,823UniSTSRnor5.0
RGSC_v3.4258,270,486 - 58,270,616UniSTSRGSC3.4
Celera253,368,116 - 53,368,246UniSTS
Cytogenetic Map2q16UniSTS
AU049927  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0257,871,378 - 57,871,605NCBIRnor6.0
Rnor_5.0279,358,940 - 79,359,167UniSTSRnor5.0
RGSC_v3.4258,280,735 - 58,280,962UniSTSRGSC3.4
Celera253,378,363 - 53,378,590UniSTS
Cytogenetic Map2q16UniSTS
GDB:335409  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01131,837,545 - 31,837,713NCBIRnor6.0
Rnor_6.0257,873,107 - 57,873,273NCBIRnor6.0
Rnor_5.01135,446,278 - 35,446,446UniSTSRnor5.0
Rnor_5.0279,360,669 - 79,360,835UniSTSRnor5.0
RGSC_v3.41131,651,927 - 31,652,095UniSTSRGSC3.4
RGSC_v3.4258,282,464 - 58,282,630UniSTSRGSC3.4
Celera1130,590,374 - 30,590,542UniSTS
Celera253,380,092 - 53,380,258UniSTS
Cytogenetic Map11q11UniSTS
Cytogenetic Map2q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)23127638105149020Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)2944467968866454Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21423783059237830Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21901646564016465Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22027698165276981Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22064137165641371Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22261295267612952Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22328064775687607Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)223837491149614623Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22618609783819822Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226186097135654963Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226186097142053534Rat
12879841Cm87Cardiac mass QTL 870.026heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)227161361148295267Rat
12879842Cm88Cardiac mass QTL 880.042heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)227161361148295267Rat
12879843Am3Aortic mass QTL 30.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)227161361148295267Rat
12879844Kidm62Kidney mass QTL 620.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227161361148295267Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22776030172760301Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23127237976272379Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23408817591101903Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23513320280133202Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)236245223112175725Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240171834105089682Rat
1300155Bp174Blood pressure QTL 1744.09arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)24277691662238534Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916169852800Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243141290114164944Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243141290114164944Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243141290154583160Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)24314978885642672Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
1354592Rf50Renal function QTL 503.5urine output (VT:0003620)timed urine volume (CMO:0000260)25443669875687607Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)25673640160325686Rat
1582246Cm60Cardiac mass QTL 605.8heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)25771560378466260Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:818
Count of miRNA genes:256
Interacting mature miRNAs:326
Transcripts:ENSRNOT00000022319, ENSRNOT00000035821
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 2 15 2 12 2 72 8 28 11
Low 3 41 36 33 7 33 8 10 2 27 13 8
Below cutoff 6 6 6 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001289941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001289942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001289943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_019225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07008423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07008424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01013589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01013590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF265360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM094687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ082713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ097869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ085382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ085383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S59158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S75687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022319   ⟹   ENSRNOP00000022319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl257,860,834 - 57,935,334 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000035821   ⟹   ENSRNOP00000036554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl257,860,883 - 57,935,363 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077790   ⟹   ENSRNOP00000073634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl257,860,883 - 57,935,352 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085599   ⟹   ENSRNOP00000075509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl257,860,883 - 57,935,352 (-)Ensembl
RefSeq Acc Id: NM_001289941   ⟹   NP_001276870
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,860,881 - 57,935,363 (-)NCBI
Celera253,367,866 - 53,442,429 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001289942   ⟹   NP_001276871
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,860,881 - 57,935,352 (-)NCBI
Celera253,367,866 - 53,442,418 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001289943   ⟹   NP_001276872
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,860,881 - 57,935,352 (-)NCBI
Celera253,367,866 - 53,442,418 (-)NCBI
Sequence:
RefSeq Acc Id: NM_019225   ⟹   NP_062098
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,860,881 - 57,935,342 (-)NCBI
Rnor_5.0279,348,443 - 79,422,645 (-)NCBI
RGSC_v3.4258,270,236 - 58,347,613 (-)RGD
Celera253,367,866 - 53,442,408 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017590721   ⟹   XP_017446210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,860,881 - 57,935,115 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062098   ⟸   NM_019225
- Peptide Label: isoform 1
- UniProtKB: P24942 (UniProtKB/Swiss-Prot),   G3V846 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276870   ⟸   NM_001289941
- Peptide Label: isoform 2
- UniProtKB: P24942 (UniProtKB/Swiss-Prot),   A0A0G2JSU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276872   ⟸   NM_001289943
- Peptide Label: isoform 4
- UniProtKB: P24942 (UniProtKB/Swiss-Prot),   A0A0G2K611 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276871   ⟸   NM_001289942
- Peptide Label: isoform 3
- UniProtKB: P24942 (UniProtKB/Swiss-Prot),   A0A0G2KAS7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017446210   ⟸   XM_017590721
- Peptide Label: isoform X1
- UniProtKB: G3V846 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036554   ⟸   ENSRNOT00000035821
RefSeq Acc Id: ENSRNOP00000075509   ⟸   ENSRNOT00000085599
RefSeq Acc Id: ENSRNOP00000073634   ⟸   ENSRNOT00000077790
RefSeq Acc Id: ENSRNOP00000022319   ⟸   ENSRNOT00000022319

Transcriptome

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

Promoters
RGD ID:13691177
Promoter ID:EPDNEW_R1701
Type:initiation region
Name:Slc1a3_1
Description:solute carrier family 1 member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0257,935,309 - 57,935,369EPDNEW

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 57933536 57933537 T C snv F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3698 AgrOrtholog
Ensembl Genes ENSRNOG00000016163 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022319 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000036554 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073634 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075509 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022319 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000035821 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077790 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085599 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.3860.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Na-dicarboxylate_symporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na-dicarboxylate_symporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na:dicarbo_symporter_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29483 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29483 ENTREZGENE
Pfam SDF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc1a3 PhenoGen
PROSITE NA_DICARBOXYL_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_DICARBOXYL_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF118215 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.34134 ENTREZGENE
UniProt A0A0G2JSU1 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K611 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KAS7 ENTREZGENE, UniProtKB/TrEMBL
  EAA1_RAT UniProtKB/Swiss-Prot
  G3V846 ENTREZGENE, UniProtKB/TrEMBL
  P24942 ENTREZGENE
UniProt Secondary Q9JK43 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc1a3  solute carrier family 1 member 3  Slc1a3  solute carrier family 1 (glial high affinity glutamate transporter), member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc1a3  solute carrier family 1 (glial high affinity glutamate transporter), member 3    solute carrier family 1, member 3  Name updated 1299863 APPROVED
2002-06-10 Slc1a3  solute carrier family 1, member 3      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the cerebellar Purkinje cell layer, possibly in Bergmann glia cells 70007