Slc1a1 (solute carrier family 1 member 1) - Rat Genome Database

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Gene: Slc1a1 (solute carrier family 1 member 1) Rattus norvegicus
Analyze
Symbol: Slc1a1
Name: solute carrier family 1 member 1
RGD ID: 3696
Description: Enables amino acid transmembrane transporter activity; glutamate binding activity; and identical protein binding activity. Involved in L-glutamate transmembrane transport. Located in several cellular components, including dendrite; perikaryon; and perisynaptic space. Human ortholog(s) of this gene implicated in dicarboxylic aminoaciduria and schizophrenia 18. Orthologous to human SLC1A1 (solute carrier family 1 member 1); PARTICIPATES IN amiloride pharmacodynamics pathway; bendroflumethiazide pharmacodynamics pathway; bumetanide pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; (R)-lipoic acid; (S)-nicotine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Eaac1; Eaat3; excitatory amino acid carrier 1; excitatory amino acid transporter 3; excitatory amino acid transporter-3; excitatory amino-acid carrier 1; REAAC1; sodium-dependent glutamate/aspartate transporter 3; solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1; Solute carrier family 1 A1 (brain glutamate transporter); solute carrier family 1, member 1
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21226,549,932 - 226,631,925 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1226,549,842 - 226,630,402 (+)Ensembl
Rnor_6.01246,955,017 - 247,035,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1246,954,980 - 247,037,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01254,195,480 - 254,274,919 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41232,469,746 - 232,549,584 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11232,633,737 - 232,715,504 (+)NCBI
Celera1223,704,163 - 223,782,895 (+)NCBICelera
Cytogenetic Map1q52NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-lipoic acid  (EXP)
(S)-nicotine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3alpha-hydroxy-5beta-pregnan-20-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonia  (EXP)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (EXP)
arsenite(3-)  (ISO)
astemizole  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Butylparaben  (EXP)
caffeine  (EXP)
calcitriol  (ISO)
carbamazepine  (EXP,ISO)
carbon nanotube  (ISO)
chelerythrine  (EXP)
chloroprene  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clozapine  (EXP)
cobalt dichloride  (ISO)
cycloheximide  (EXP)
cyclosporin A  (ISO)
dexamethasone  (EXP)
dinophysistoxin 1  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (ISO)
fonofos  (ISO)
haloperidol  (EXP)
Ibotenic acid  (EXP)
ivermectin  (ISO)
kainic acid  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
lipoic acid  (EXP)
LY294002  (EXP)
menadione  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (EXP,ISO)
mitomycin C  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
nicotine  (EXP)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (EXP)
paraoxon  (EXP)
parathion  (ISO)
perfluorononanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregabalin  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
profenofos  (EXP)
progesterone  (EXP,ISO)
propofol  (EXP)
resveratrol  (EXP)
rotenone  (EXP,ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
staurosporine  (EXP)
sunitinib  (ISO)
tamibarotene  (EXP)
terbufos  (ISO)
tert-butyl hydroperoxide  (EXP,ISO)
thallium  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vorinostat  (ISO)
WIN 55212-2  (EXP)
wortmannin  (EXP)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zonisamide  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
activation of protein kinase B activity  (ISO)
adult behavior  (ISO)
behavioral fear response  (ISO)
blood vessel morphogenesis  (ISO)
brain development  (ISO)
cellular response to ammonium ion  (ISO)
cellular response to bisphenol A  (ISO)
cellular response to cocaine  (ISO)
cellular response to mercury ion  (ISO)
cellular response to organic cyclic compound  (ISO)
cellular response to oxidative stress  (ISO)
cellular zinc ion homeostasis  (ISO)
chloride transmembrane transport  (ISO,ISS)
conditioned place preference  (ISO)
cysteine transmembrane transport  (ISO)
cysteine transport  (ISO,ISS)
cytokine-mediated signaling pathway  (ISO)
D-aspartate import across plasma membrane  (ISO)
D-aspartate transport  (ISO)
dopamine metabolic process  (ISO)
dopamine receptor signaling pathway  (ISO)
establishment of protein localization  (ISO)
gene expression  (ISO)
glutamate homeostasis  (ISO)
glutamate receptor signaling pathway  (ISO)
glutathione biosynthetic process  (ISO)
glutathione metabolic process  (ISO)
grooming behavior  (ISO)
heart contraction  (ISO)
L-aspartate import across plasma membrane  (ISO,ISS)
L-aspartate transmembrane transport  (IBA,ISO)
L-glutamate import  (ISO)
L-glutamate import across plasma membrane  (IBA,ISO,ISS)
L-glutamate transmembrane transport  (IBA,IDA,ISO)
learning or memory  (ISO)
locomotory behavior  (ISO)
long-term synaptic potentiation  (ISO)
maintenance of blood-brain barrier  (ISO)
memory  (ISO)
motor behavior  (ISO)
motor neuron apoptotic process  (ISO)
negative regulation of neuron apoptotic process  (ISO)
neurogenesis  (ISO)
neuron death  (ISO)
neuron death in response to oxidative stress  (ISO)
neurotransmitter receptor transport to plasma membrane  (ISO)
peptidyl-serine phosphorylation  (ISO)
positive regulation of heart rate  (ISO)
regulation of heart rate  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of protein targeting to membrane  (ISO)
response to amphetamine  (ISO)
response to anesthetic  (ISO)
response to axon injury  (ISO)
response to decreased oxygen levels  (ISO)
response to morphine  (ISO)
response to xenobiotic stimulus  (ISO)
retina development in camera-type eye  (ISO)
retina layer formation  (ISO)
righting reflex  (ISO)
superoxide metabolic process  (ISO)
synapse organization  (ISO)
zinc ion transmembrane transport  (ISO)

References

References - curated
1. Bjoras M, etal., Brain Res Mol Brain Res 1996 Feb;36(1):163-8.
2. Conti F, etal., Cereb Cortex. 1998 Mar;8(2):108-16. doi: 10.1093/cercor/8.2.108.
3. Furuta A, etal., J Neurosci. 1997 Nov 1;17(21):8363-75.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Gonzalez MI, etal., J Neurochem. 2005 Sep;94(5):1180-8. Epub 2005 Jul 25.
7. Grewer C, etal., Biochemistry. 2005 Sep 6;44(35):11913-23.
8. Grewer C, etal., J Biol Chem 2003 Jan 24;278(4):2585-92.
9. He Y, etal., J Comp Neurol. 2000 Mar 13;418(3):255-69.
10. Kanai Y, etal., Neuroreport 1995 Nov 27;6(17):2357-62.
11. Liu Y, etal., J Biol Chem. 2008 Mar 7;283(10):6561-71. doi: 10.1074/jbc.M708096200. Epub 2007 Dec 20.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Pipeline to import SMPDB annotations from SMPDB into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sakurai T, etal., Biol Pharm Bull. 2015;38(7):1087-91. doi: 10.1248/bpb.b15-00226.
21. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
22. Ubhi K, etal., Eur J Neurosci. 2014 Mar;39(6):1026-41. doi: 10.1111/ejn.12444. Epub 2013 Dec 5.
23. Wiessner M, etal., Cell Tissue Res 2002 Oct;310(1):31-40.
Additional References at PubMed
PMID:7521911   PMID:7914198   PMID:8613726   PMID:8738164   PMID:8772431   PMID:8857541   PMID:11242046   PMID:12119102   PMID:12123836   PMID:12151387   PMID:12237337   PMID:12620282  
PMID:12843260   PMID:12875997   PMID:12923633   PMID:15009636   PMID:15197183   PMID:15489334   PMID:15736956   PMID:15737330   PMID:15914650   PMID:16368696   PMID:16417946   PMID:16442237  
PMID:16478724   PMID:16516346   PMID:16538232   PMID:16566829   PMID:16723357   PMID:16858406   PMID:16959903   PMID:17389249   PMID:17459877   PMID:17715130   PMID:17854777   PMID:18056970  
PMID:18079058   PMID:18400334   PMID:18671901   PMID:19056867   PMID:19804828   PMID:19843789   PMID:19922365   PMID:20378543   PMID:20493242   PMID:20521381   PMID:21123949   PMID:21127051  
PMID:21185901   PMID:21233495   PMID:22479505   PMID:22540959   PMID:22578356   PMID:23356950   PMID:23361868   PMID:23694703   PMID:24355585   PMID:25350110   PMID:25839761   PMID:26037264  
PMID:26092725   PMID:26599339   PMID:26690923   PMID:27358480   PMID:27507301   PMID:29350434   PMID:30840898   PMID:32827867  


Genomics

Comparative Map Data
Slc1a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21226,549,932 - 226,631,925 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1226,549,842 - 226,630,402 (+)Ensembl
Rnor_6.01246,955,017 - 247,035,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1246,954,980 - 247,037,056 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01254,195,480 - 254,274,919 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41232,469,746 - 232,549,584 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11232,633,737 - 232,715,504 (+)NCBI
Celera1223,704,163 - 223,782,895 (+)NCBICelera
Cytogenetic Map1q52NCBI
SLC1A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl94,490,468 - 4,587,469 (+)EnsemblGRCh38hg38GRCh38
GRCh3894,490,466 - 4,587,469 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3794,490,468 - 4,587,469 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3694,480,444 - 4,577,469 (+)NCBINCBI36hg18NCBI36
Build 3494,480,439 - 4,577,258NCBI
Celera94,412,118 - 4,509,171 (+)NCBI
Cytogenetic Map9p24.2NCBI
HuRef94,445,524 - 4,542,606 (+)NCBIHuRef
CHM1_194,490,396 - 4,587,442 (+)NCBICHM1_1
Slc1a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391928,812,535 - 28,891,360 (+)NCBIGRCm39mm39
GRCm39 Ensembl1928,812,449 - 28,891,360 (+)Ensembl
GRCm381928,835,135 - 28,913,960 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1928,835,049 - 28,913,960 (+)EnsemblGRCm38mm10GRCm38
MGSCv371928,909,656 - 28,988,450 (+)NCBIGRCm37mm9NCBIm37
MGSCv361928,901,163 - 28,979,957 (+)NCBImm8
Celera1929,610,074 - 29,689,176 (+)NCBICelera
Cytogenetic Map19C1NCBI
Slc1a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554348,790,685 - 8,879,757 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554348,790,685 - 8,879,757 (+)NCBIChiLan1.0ChiLan1.0
SLC1A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.194,511,491 - 4,608,337 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl94,511,491 - 4,608,337 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v094,323,124 - 4,420,193 (+)NCBIMhudiblu_PPA_v0panPan3
SLC1A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1192,898,274 - 92,978,260 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl192,898,274 - 92,978,260 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha193,370,688 - 93,450,612 (+)NCBI
ROS_Cfam_1.0193,451,994 - 93,532,207 (+)NCBI
ROS_Cfam_1.0 Ensembl193,451,891 - 93,532,204 (+)Ensembl
UMICH_Zoey_3.1193,083,822 - 93,163,810 (+)NCBI
UNSW_CanFamBas_1.0192,807,174 - 92,887,351 (+)NCBI
UU_Cfam_GSD_1.0193,572,134 - 93,652,376 (+)NCBI
Slc1a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947140,482,449 - 140,559,751 (+)NCBI
SpeTri2.0NW_004936503613,250 - 690,555 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC1A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1217,366,499 - 217,441,674 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11217,366,493 - 217,441,643 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21243,230,452 - 243,270,312 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC1A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11274,949,560 - 75,041,455 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1274,949,028 - 75,041,369 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603863,278,537 - 63,371,858 (-)NCBIVero_WHO_p1.0
Slc1a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247369,246,348 - 9,325,671 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130525  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21226,631,740 - 226,631,924 (+)MAPPERmRatBN7.2
Rnor_6.01247,036,873 - 247,037,056NCBIRnor6.0
Rnor_5.01254,276,633 - 254,276,816UniSTSRnor5.0
RGSC_v3.41232,551,298 - 232,551,481UniSTSRGSC3.4
Celera1223,784,609 - 223,784,792UniSTS
RH 3.4 Map11614.8UniSTS
Cytogenetic Map1q52UniSTS
BE120573  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21226,629,825 - 226,629,978 (+)MAPPERmRatBN7.2
Rnor_6.01247,034,958 - 247,035,110NCBIRnor6.0
Rnor_5.01254,274,718 - 254,274,870UniSTSRnor5.0
RGSC_v3.41232,549,383 - 232,549,535UniSTSRGSC3.4
Celera1223,782,694 - 223,782,846UniSTS
RH 3.4 Map11651.4UniSTS
Cytogenetic Map1q52UniSTS
BF399845  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21226,551,852 - 226,552,026 (+)MAPPERmRatBN7.2
Rnor_6.01246,956,938 - 246,957,111NCBIRnor6.0
Rnor_5.01254,197,401 - 254,197,574UniSTSRnor5.0
RGSC_v3.41232,471,667 - 232,471,840UniSTSRGSC3.4
Celera1223,706,084 - 223,706,257UniSTS
RH 3.4 Map11612.4UniSTS
Cytogenetic Map1q52UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
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
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
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
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1207702246228581766Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
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
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
634340Hcar5Hepatocarcinoma resistance QTL 58liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1214537555226660468Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
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
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
6480786Bw97Body weight QTL 975.03body mass (VT:0001259)body weight (CMO:0000012)1225126575227604520Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:146
Interacting mature miRNAs:155
Transcripts:ENSRNOT00000020272
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 1 54 29 4 11
Low 2 33 16 18 8 11 18 6 28 8
Below cutoff 10 18 18 1 18 2 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020272   ⟹   ENSRNOP00000020272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1226,549,842 - 226,630,401 (+)Ensembl
Rnor_6.0 Ensembl1246,954,980 - 247,037,056 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099702   ⟹   ENSRNOP00000096736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1226,550,021 - 226,630,402 (+)Ensembl
RefSeq Acc Id: NM_013032   ⟹   NP_037164
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21226,549,932 - 226,630,027 (+)NCBI
Rnor_6.01246,955,017 - 247,035,159 (+)NCBI
Rnor_5.01254,195,480 - 254,274,919 (+)NCBI
RGSC_v3.41232,469,746 - 232,549,584 (+)RGD
Celera1223,704,163 - 223,782,895 (+)RGD
Sequence:
RefSeq Acc Id: XM_039101858   ⟹   XP_038957786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21226,550,021 - 226,631,925 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037164   ⟸   NM_013032
- UniProtKB: P51907 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020272   ⟸   ENSRNOT00000020272
RefSeq Acc Id: XP_038957786   ⟸   XM_039101858
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000096736   ⟸   ENSRNOT00000099702

Transcriptome

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

Promoters
RGD ID:13690839
Promoter ID:EPDNEW_R1363
Type:single initiation site
Name:Slc1a1_1
Description:solute carrier family 1 member 1
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_6.01246,954,999 - 246,955,059EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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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
LEXF4/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
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3696 AgrOrtholog
Ensembl Genes ENSRNOG00000014816 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000020272 UniProtKB/Swiss-Prot
  ENSRNOP00000096736 ENTREZGENE
Ensembl Transcript ENSRNOT00000020272 UniProtKB/Swiss-Prot
  ENSRNOT00000099702 ENTREZGENE
Gene3D-CATH 1.10.3860.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599027 IMAGE-MGC_LOAD
InterPro Na-dicarboxylate_symporter UniProtKB/Swiss-Prot
  Na-dicarboxylate_symporter_CS UniProtKB/Swiss-Prot
  Na:dicarbo_symporter_sf UniProtKB/Swiss-Prot
KEGG Report rno:25550 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72260 IMAGE-MGC_LOAD
NCBI Gene 25550 ENTREZGENE
Pfam SDF UniProtKB/Swiss-Prot
PhenoGen Slc1a1 PhenoGen
PROSITE NA_DICARBOXYL_SYMP_1 UniProtKB/Swiss-Prot
  NA_DICARBOXYL_SYMP_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF118215 UniProtKB/Swiss-Prot
UniProt EAA3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O88389 UniProtKB/Swiss-Prot
  Q63727 UniProtKB/Swiss-Prot
  Q9JJP8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc1a1  solute carrier family 1 member 1  Slc1a1  solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc1a1  solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1    solute carrier family 1, member 1  Name updated 1299863 APPROVED
2003-04-09 Slc1a1  solute carrier family 1, member 1    Solute carrier family 1 A1 (brain glutamate transporter)  Name updated 629478 APPROVED
2002-06-10 Slc1a1  Solute carrier family 1 A1 (brain glutamate transporter)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process Glu-373 mediates proton binding and transmembrane proton transport 729828