Slc8a1 (solute carrier family 8 member A1) - Rat Genome Database
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Gene: Slc8a1 (solute carrier family 8 member A1) Rattus norvegicus
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Symbol: Slc8a1
Name: solute carrier family 8 member A1
RGD ID: 3717
Description: Exhibits calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration; calcium:sodium antiporter activity; and ion antiporter activity involved in regulation of postsynaptic membrane potential. Involved in several processes, including metal ion transport; regulation of heart contraction; and response to purine-containing compound. Localizes to several cellular components, including T-tubule; Z disc; and dendrite. Used to study brain ischemia. Biomarker of brain ischemia; congestive heart failure; hypertension; and status epilepticus. Human ortholog(s) of this gene implicated in hypertension. Orthologous to human SLC8A1 (solute carrier family 8 member A1); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (R)-noradrenaline; 1-[(2,3,4-trimethoxyphenyl)methyl]piperazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: na(+)/Ca(2+)-exchange protein 1; Na-Ca exchanger; Ncx; Ncx1; sodium/calcium exchanger 1; solute carrier family 8 (sodium/calcium exchanger) member 1; solute carrier family 8 (sodium/calcium exchanger), member 1; solute carrier family 8 member 1; solute carrier family 8, member 1
Orthologs:
Homo sapiens (human) : SLC8A1 (solute carrier family 8 member A1)  HGNC  Alliance
Mus musculus (house mouse) : Slc8a1 (solute carrier family 8 (sodium/calcium exchanger), member 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Slc8a1 (solute carrier family 8 member A1)
Pan paniscus (bonobo/pygmy chimpanzee) : SLC8A1 (solute carrier family 8 member A1)
Canis lupus familiaris (dog) : SLC8A1 (solute carrier family 8 member A1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Slc8a1 (solute carrier family 8 member A1)
Sus scrofa (pig) : SLC8A1 (solute carrier family 8 member A1)
Chlorocebus sabaeus (African green monkey) : SLC8A1 (solute carrier family 8 member A1)
Heterocephalus glaber (naked mole-rat) : Slc8a1 (solute carrier family 8 member A1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.064,244,076 - 4,564,262 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.064,208,126 - 4,495,690 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.464,421,046 - 4,691,716 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.164,421,045 - 4,691,719 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-noradrenaline  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(2,3,4-trimethoxyphenyl)methyl]piperazine  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-tert-Octylphenol  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP)
amiodarone  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
aspartame  (ISO)
atrazine  (EXP)
barium(0)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bepridil  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
calcitriol  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
cefaloridine  (EXP)
chrysene  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
D-glucose  (EXP)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
dextran sulfate  (ISO)
dichloroacetic acid  (ISO)
dioxygen  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
etoposide  (ISO)
flutamide  (ISO)
folic acid  (ISO)
fructose  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
glucose  (EXP)
glycidol  (EXP)
isoprenaline  (EXP,ISO)
maneb  (ISO)
methapyrilene  (ISO)
monosodium L-glutamate  (ISO)
nickel atom  (ISO)
O-methyleugenol  (ISO)
ouabain  (EXP,ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentanal  (ISO)
phenylephrine  (EXP,ISO)
phorbol 13-acetate 12-myristate  (EXP)
potassium chromate  (ISO)
progesterone  (ISO)
propranolol  (ISO)
pyridaben  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium atom  (ISO)
succimer  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
tetraphene  (ISO)
thalidomide  (ISO)
thapsigargin  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
uranium atom  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
calcium ion export  (IDA,ISO)
calcium ion homeostasis  (ISO)
calcium ion import  (IDA,ISO)
calcium ion import across plasma membrane  (IBA)
calcium ion transmembrane transport  (IDA,IGI,IMP,ISO)
calcium ion transport  (IEA,ISO,TAS)
calcium ion transport into cytosol  (IDA,ISO)
cardiac muscle cell development  (ISO)
cardiac muscle contraction  (ISO)
cell communication  (IEA)
cell communication by electrical coupling involved in cardiac conduction  (IDA)
cellular calcium ion homeostasis  (IGI,IMP)
cellular response to caffeine  (ISO)
cellular response to cAMP  (IDA)
cellular response to hypoxia  (IEP)
cellular response to reactive oxygen species  (IDA,ISO)
cellular sodium ion homeostasis  (ISO)
embryonic heart tube development  (ISO)
embryonic placenta development  (ISO)
heart morphogenesis  (ISO)
metal ion transport  (IBA)
muscle fiber development  (ISO)
negative regulation of cytosolic calcium ion concentration  (ISO)
negative regulation of protein serine/threonine kinase activity  (ISO)
positive regulation of bone mineralization  (ISO)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of fibroblast migration  (IMP)
positive regulation of the force of heart contraction  (ISO)
post-embryonic development  (ISO)
regulation of calcium ion transport  (IMP)
regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion  (IDA)
regulation of gene expression  (ISO)
regulation of heart rate  (ISO)
regulation of postsynaptic cytosolic calcium ion concentration  (IEA)
regulation of sodium ion transport  (IMP)
regulation of the force of heart contraction  (ISO)
relaxation of smooth muscle  (ISO)
response to ATP  (IDA)
response to drug  (IEP)
response to glucose  (IEP)
response to hydrogen peroxide  (IEP)
response to hypoxia  (IDA)
response to immobilization stress  (IEP)
response to muscle stretch  (ISO)
response to nutrient  (IEP)
sodium ion export across plasma membrane  (IDA,ISO)
sodium ion import across plasma membrane  (IDA,ISO)
sodium ion transmembrane transport  (IBA,IEA,ISO)
sodium ion transport  (IDA,ISO)
telencephalon development  (IEP)
vascular associated smooth muscle contraction  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
arrhythmogenic right ventricular cardiomyopathy pathway  (IEA)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium transport pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA,ISO)
carvedilol pharmacodynamics pathway  (ISO)
dilated cardiomyopathy pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
hypertrophic cardiomyopathy pathway  (IEA)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

References - curated
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Additional References at PubMed
PMID:1374913   PMID:1700476   PMID:8195112   PMID:8276763   PMID:8798769   PMID:9516469   PMID:10075718   PMID:10894800   PMID:10967099   PMID:11423561   PMID:11891588   PMID:12118014  
PMID:12391043   PMID:12477932   PMID:12502536   PMID:12502568   PMID:12527551   PMID:12722103   PMID:12754202   PMID:12767889   PMID:12882992   PMID:14535948   PMID:15075297   PMID:15105296  
PMID:15287883   PMID:15308581   PMID:15336980   PMID:15472108   PMID:15485817   PMID:15652482   PMID:15670870   PMID:15808841   PMID:16061478   PMID:16107787   PMID:16292983   PMID:16343035  
PMID:16407245   PMID:16679359   PMID:16820577   PMID:16921169   PMID:16977318   PMID:17178715   PMID:17490438   PMID:17872462   PMID:17934333   PMID:17935604   PMID:17962412   PMID:17977908  
PMID:18079274   PMID:18294620   PMID:18507397   PMID:18635667   PMID:18846343   PMID:19059659   PMID:19158404   PMID:19164785   PMID:19340563   PMID:19525383   PMID:19745171   PMID:19917219  
PMID:19966047   PMID:20018762   PMID:20118617   PMID:20353753   PMID:20610380   PMID:20622104   PMID:21293012   PMID:21302256   PMID:21311966   PMID:21321244   PMID:21734189   PMID:22245773  
PMID:22268447   PMID:22355118   PMID:22479505   PMID:22561287   PMID:22656960   PMID:22814700   PMID:22871113   PMID:23069678   PMID:23199000   PMID:23224895   PMID:23233681   PMID:23403180  
PMID:23564083   PMID:23990893   PMID:24474686   PMID:24632945   PMID:24725133   PMID:25315779   PMID:25336645   PMID:25416782   PMID:25445045   PMID:25589784   PMID:25633096   PMID:25839659  
PMID:26100674   PMID:26174834   PMID:26316108   PMID:26421717   PMID:27052156   PMID:27627464   PMID:27997906   PMID:28428550   PMID:28755400   PMID:29274751   PMID:29705161   PMID:29735991  
PMID:29788971   PMID:29947686   PMID:30466198   PMID:31673221  


Genomics

Comparative Map Data
Slc8a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.064,244,076 - 4,564,262 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.064,208,126 - 4,495,690 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.464,421,046 - 4,691,716 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.164,421,045 - 4,691,719 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBICelera
Cytogenetic Map6q12NCBI
SLC8A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl240,097,270 - 40,611,053 (-)EnsemblGRCh38hg38GRCh38
GRCh38240,094,523 - 40,512,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37240,339,286 - 40,739,575 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36240,192,790 - 40,510,948 (-)NCBINCBI36hg18NCBI36
Build 34240,253,795 - 40,569,095NCBI
Celera240,180,223 - 40,580,364 (-)NCBI
Cytogenetic Map2p22.1NCBI
HuRef240,078,719 - 40,478,536 (-)NCBIHuRef
CHM1_1240,269,776 - 40,669,965 (-)NCBICHM1_1
Slc8a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391781,680,534 - 82,045,816 (-)NCBI
GRCm381781,373,105 - 81,738,387 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1781,373,105 - 81,738,377 (-)EnsemblGRCm38mm10GRCm38
MGSCv371781,772,445 - 82,137,717 (-)NCBIGRCm37mm9NCBIm37
MGSCv361781,293,929 - 81,646,695 (-)NCBImm8
Celera1785,706,575 - 86,071,957 (-)NCBICelera
Cytogenetic Map17E3NCBI
cM Map1751.29NCBI
Slc8a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554417,656,031 - 7,957,640 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554417,653,107 - 8,037,784 (-)NCBIChiLan1.0ChiLan1.0
SLC8A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A40,936,799 - 41,444,963 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A40,939,900 - 41,363,038 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A40,169,339 - 40,586,546 (-)NCBIMhudiblu_PPA_v0panPan3
SLC8A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1732,005,245 - 32,307,700 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11732,004,207 - 32,381,399 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc8a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493650810,894,918 - 11,256,084 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC8A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl399,897,162 - 100,245,140 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1399,823,503 - 100,257,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23106,268,345 - 106,367,008 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC8A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11466,813,523 - 67,210,261 (+)NCBI
Slc8a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473821,648,277 - 22,026,385 (-)NCBI

Position Markers
RH128952  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.064,256,031 - 4,256,213NCBIRnor6.0
Rnor_5.064,217,887 - 4,218,069UniSTSRnor5.0
RGSC_v3.464,418,261 - 4,418,443UniSTSRGSC3.4
Celera613,226,677 - 13,226,859UniSTS
Cytogenetic Map6q12UniSTS
UniSTS:239208  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.064,519,958 - 4,520,604NCBIRnor6.0
Rnor_5.064,481,076 - 4,481,722UniSTSRnor5.0
RGSC_v3.464,691,039 - 4,691,685UniSTSRGSC3.4
Celera612,963,013 - 12,963,659UniSTS
Cytogenetic Map6q12UniSTS
PMC20271P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.064,519,867 - 4,520,503NCBIRnor6.0
Rnor_5.064,480,985 - 4,481,621UniSTSRnor5.0
RGSC_v3.464,690,948 - 4,691,584UniSTSRGSC3.4
Celera612,963,114 - 12,963,750UniSTS
Cytogenetic Map6q12UniSTS
Slc8a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.064,519,664 - 4,520,268NCBIRnor6.0
Rnor_5.064,480,782 - 4,481,386UniSTSRnor5.0
RGSC_v3.464,690,745 - 4,691,349UniSTSRGSC3.4
Celera612,963,349 - 12,963,953UniSTS
Cytogenetic Map6q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6123620518Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6125048718Rat
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)613505323600274Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:377
Count of miRNA genes:55
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000042230, ENSRNOT00000042251, ENSRNOT00000043870, ENSRNOT00000046246, ENSRNOT00000052367, ENSRNOT00000061940, ENSRNOT00000070918
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 42 15 2 19 2 4 4 66 35 34 10 4
Low 2 1 41 38 38 4 7 8 7 1 4
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_019268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07062708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07062709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07062710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07062711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07062712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07062713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01041800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF109163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF109164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF109165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF109166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF115506 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY033398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY245281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY245282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U95137 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U95138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X68191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X68812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X68813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y13036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y13037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042230   ⟹   ENSRNOP00000040751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000042251   ⟹   ENSRNOP00000040765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000043870   ⟹   ENSRNOP00000044094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000046246   ⟹   ENSRNOP00000043539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000052367   ⟹   ENSRNOP00000050918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000070918   ⟹   ENSRNOP00000064030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: NM_001270772   ⟹   NP_001257701
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270773   ⟹   NP_001257702
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270774   ⟹   NP_001257703
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270775   ⟹   NP_001257704
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270776   ⟹   NP_001257705
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270777   ⟹   NP_001257706
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270778   ⟹   NP_001257707
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270779   ⟹   NP_001257708
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: NM_019268   ⟹   NP_062141
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,255,699 - 4,520,638 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
RGSC_v3.464,421,046 - 4,691,716 (-)RGD
Celera612,962,979 - 13,227,191 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239660   ⟹   XP_006239722
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,534,717 (-)NCBI
Rnor_5.064,208,126 - 4,495,690 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764432   ⟹   XP_008762654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764433   ⟹   XP_008762655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,262 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764434   ⟹   XP_008762656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764435   ⟹   XP_008762657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764436   ⟹   XP_008762658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764437   ⟹   XP_008762659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764438   ⟹   XP_008762660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,260 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764439   ⟹   XP_008762661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594061   ⟹   XP_017449550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594062   ⟹   XP_017449551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594063   ⟹   XP_017449552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,260 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594064   ⟹   XP_017449553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.064,244,076 - 4,564,260 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001257701 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257702 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257703 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257704 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257705 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257706 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257707 (Get FASTA)   NCBI Sequence Viewer  
  NP_001257708 (Get FASTA)   NCBI Sequence Viewer  
  NP_062141 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239722 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762654 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762655 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762656 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762657 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762658 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762659 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762660 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762661 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449550 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449551 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449552 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449553 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA19125 (Get FASTA)   NCBI Sequence Viewer  
  AAA19126 (Get FASTA)   NCBI Sequence Viewer  
  AAA19127 (Get FASTA)   NCBI Sequence Viewer  
  AAA19128 (Get FASTA)   NCBI Sequence Viewer  
  AAA19129 (Get FASTA)   NCBI Sequence Viewer  
  AAB18825 (Get FASTA)   NCBI Sequence Viewer  
  AAB39952 (Get FASTA)   NCBI Sequence Viewer  
  AAD17214 (Get FASTA)   NCBI Sequence Viewer  
  AAD23386 (Get FASTA)   NCBI Sequence Viewer  
  AAD23387 (Get FASTA)   NCBI Sequence Viewer  
  AAD23388 (Get FASTA)   NCBI Sequence Viewer  
  AAD23389 (Get FASTA)   NCBI Sequence Viewer  
  AAH78698 (Get FASTA)   NCBI Sequence Viewer  
  AAK52307 (Get FASTA)   NCBI Sequence Viewer  
  AAO92265 (Get FASTA)   NCBI Sequence Viewer  
  AAO92266 (Get FASTA)   NCBI Sequence Viewer  
  CAA48273 (Get FASTA)   NCBI Sequence Viewer  
  CAA48707 (Get FASTA)   NCBI Sequence Viewer  
  CAA48708 (Get FASTA)   NCBI Sequence Viewer  
  EDM02742 (Get FASTA)   NCBI Sequence Viewer  
  EDM02743 (Get FASTA)   NCBI Sequence Viewer  
  EDM02744 (Get FASTA)   NCBI Sequence Viewer  
  EDM02745 (Get FASTA)   NCBI Sequence Viewer  
  EDM02746 (Get FASTA)   NCBI Sequence Viewer  
  EDM02747 (Get FASTA)   NCBI Sequence Viewer  
  EDM02748 (Get FASTA)   NCBI Sequence Viewer  
  EDM02749 (Get FASTA)   NCBI Sequence Viewer  
  EDM02750 (Get FASTA)   NCBI Sequence Viewer  
  EDM02751 (Get FASTA)   NCBI Sequence Viewer  
  Q01728 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062141   ⟸   NM_019268
- Peptide Label: isoform 1 precursor
- Sequence:
RefSeq Acc Id: NP_001257708   ⟸   NM_001270779
- Peptide Label: isoform 9 precursor
- UniProtKB: M0R3V7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257703   ⟸   NM_001270774
- Peptide Label: isoform 4 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257701   ⟸   NM_001270772
- Peptide Label: isoform 2 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257705   ⟸   NM_001270776
- Peptide Label: isoform 6 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257707   ⟸   NM_001270778
- Peptide Label: isoform 8 precursor
- Sequence:
RefSeq Acc Id: NP_001257706   ⟸   NM_001270777
- Peptide Label: isoform 7 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257704   ⟸   NM_001270775
- Peptide Label: isoform 5 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257702   ⟸   NM_001270773
- Peptide Label: isoform 3 precursor
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239722   ⟸   XM_006239660
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008762657   ⟸   XM_008764435
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008762655   ⟸   XM_008764433
- Peptide Label: isoform X2
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762654   ⟸   XM_008764432
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008762661   ⟸   XM_008764439
- Peptide Label: isoform X8
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762659   ⟸   XM_008764437
- Peptide Label: isoform X6
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762660   ⟸   XM_008764438
- Peptide Label: isoform X7
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762656   ⟸   XM_008764434
- Peptide Label: isoform X3
- UniProtKB: M0R3V7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762658   ⟸   XM_008764436
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017449551   ⟸   XM_017594062
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017449550   ⟸   XM_017594061
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017449553   ⟸   XM_017594064
- Peptide Label: isoform X12
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449552   ⟸   XM_017594063
- Peptide Label: isoform X11
- UniProtKB: Q01728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064030   ⟸   ENSRNOT00000070918
RefSeq Acc Id: ENSRNOP00000044094   ⟸   ENSRNOT00000043870
RefSeq Acc Id: ENSRNOP00000040751   ⟸   ENSRNOT00000042230
RefSeq Acc Id: ENSRNOP00000040765   ⟸   ENSRNOT00000042251
RefSeq Acc Id: ENSRNOP00000043539   ⟸   ENSRNOT00000046246
RefSeq Acc Id: ENSRNOP00000050918   ⟸   ENSRNOT00000052367
Protein Domains
Calx-beta   J

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)