Slc8a1 (solute carrier family 8 member A1) - Rat Genome Database

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Gene: Slc8a1 (solute carrier family 8 member A1) Rattus norvegicus
Analyze
Symbol: Slc8a1
Name: solute carrier family 8 member A1
RGD ID: 3717
Description: Enables 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. Located in several cellular components, including T-tubule; Z disc; and dendrite. Is integral component of postsynaptic membrane. 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: LOC108351162; 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; uncharacterized LOC108351162
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2613,194,609 - 13,547,369 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl613,194,662 - 13,535,628 (+)Ensembl
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)
aristolochic acid  (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)
Cuprizon  (EXP)
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)
PCB138  (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  (IEA,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 cell 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 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)
response to xenobiotic stimulus  (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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36. MGD data from the GO Consortium
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40. Pipeline to import KEGG annotations from KEGG into RGD
41. Pipeline to import SMPDB annotations from SMPDB into RGD
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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:31505169   PMID:31673221   PMID:31856086   PMID:32827867   PMID:33931586  


Genomics

Comparative Map Data
Slc8a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2613,194,609 - 13,547,369 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl613,194,662 - 13,535,628 (+)Ensembl
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
GRCh38240,097,270 - 40,512,435 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37240,321,663 - 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 (-)NCBIGRCm39mm39
GRCm39 Ensembl1781,680,534 - 82,045,806 (-)Ensembl
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
CanFam3.11732,004,207 - 32,381,399 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1732,005,245 - 32,307,700 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1731,772,774 - 32,072,461 (-)NCBI
ROS_Cfam_1.01732,669,189 - 33,057,808 (-)NCBI
UMICH_Zoey_3.11731,887,301 - 32,186,904 (-)NCBI
UNSW_CanFamBas_1.01731,956,496 - 32,256,674 (-)NCBI
UU_Cfam_GSD_1.01732,171,264 - 32,471,231 (-)NCBI
Slc8a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629239,466,272 - 39,841,883 (+)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11466,813,523 - 67,210,261 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604544,751,652 - 45,239,417 (-)NCBIVero_WHO_p1.0
Slc8a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473821,648,277 - 22,026,385 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128952  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2613,535,113 - 13,535,296 (-)MAPPERmRatBN7.2
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
mRatBN7.2613,271,254 - 13,271,901 (-)MAPPERmRatBN7.2
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
mRatBN7.2613,271,355 - 13,271,992 (-)MAPPERmRatBN7.2
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
mRatBN7.2613,271,590 - 13,272,195 (-)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
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)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
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)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
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)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6984331220338915Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat

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
  XM_039111865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111876 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111878 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide 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
  JACYVU010000163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04934 (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
mRatBN7.2 Ensembl613,194,662 - 13,535,628 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000042251   ⟹   ENSRNOP00000040765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,252,410 - 13,535,628 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000043870   ⟹   ENSRNOP00000044094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,251,011 - 13,535,628 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000046246   ⟹   ENSRNOP00000043539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,251,011 - 13,535,628 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000052367   ⟹   ENSRNOP00000050918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,252,410 - 13,535,628 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000070918   ⟹   ENSRNOP00000064030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,194,662 - 13,535,032 (+)Ensembl
Rnor_6.0 Ensembl64,258,991 - 4,520,604 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101103   ⟹   ENSRNOP00000093763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,251,011 - 13,535,628 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101881   ⟹   ENSRNOP00000077184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,251,011 - 13,535,628 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119744   ⟹   ENSRNOP00000082575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl613,251,011 - 13,535,628 (+)Ensembl
RefSeq Acc Id: NM_001270772   ⟹   NP_001257701
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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
mRatBN7.2613,271,221 - 13,535,628 (+)NCBI
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_008764432   ⟹   XP_008762654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,194,609 - 13,547,369 (+)NCBI
Rnor_6.064,244,076 - 4,564,261 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111865   ⟹   XP_038967793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111866   ⟹   XP_038967794
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111867   ⟹   XP_038967795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111868   ⟹   XP_038967796
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111869   ⟹   XP_038967797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111870   ⟹   XP_038967798
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111871   ⟹   XP_038967799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,866 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111872   ⟹   XP_038967800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111873   ⟹   XP_038967801
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,252,431 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111874   ⟹   XP_038967802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,252,431 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111875   ⟹   XP_038967803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,253,142 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111876   ⟹   XP_038967804
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111877   ⟹   XP_038967805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111878   ⟹   XP_038967806
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111879   ⟹   XP_038967807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111880   ⟹   XP_038967808
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,252,432 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111881   ⟹   XP_038967809
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111882   ⟹   XP_038967810
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,251,008 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111883   ⟹   XP_038967811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,865 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111884   ⟹   XP_038967812
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,866 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111885   ⟹   XP_038967813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,866 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111886   ⟹   XP_038967814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,252,432 - 13,547,369 (+)NCBI
RefSeq Acc Id: XM_039111887   ⟹   XP_038967815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,488,373 (+)NCBI
RefSeq Acc Id: XM_039111888   ⟹   XP_038967816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,479,486 (+)NCBI
RefSeq Acc Id: XM_039111889   ⟹   XP_038967817
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,867 - 13,318,188 (+)NCBI
RefSeq Acc Id: XR_005505449
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,488,280 (+)NCBI
RefSeq Acc Id: XR_005505450
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2613,223,864 - 13,488,303 (+)NCBI
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_008762654 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967793 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967794 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967795 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967796 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967797 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967798 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967799 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967800 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967801 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967802 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967803 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967804 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967805 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967806 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967807 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967808 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967809 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967810 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967811 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967812 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967813 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967814 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967815 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967816 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967817 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA19124 (Get FASTA)   NCBI Sequence Viewer  
  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_008762654   ⟸   XM_008764432
- Peptide Label: isoform X9
- 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
RefSeq Acc Id: XP_038967794   ⟸   XM_039111866
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038967805   ⟸   XM_039111877
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038967796   ⟸   XM_039111868
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967807   ⟸   XM_039111879
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038967815   ⟸   XM_039111887
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038967816   ⟸   XM_039111888
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038967793   ⟸   XM_039111865
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967804   ⟸   XM_039111876
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038967795   ⟸   XM_039111867
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038967806   ⟸   XM_039111878
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038967797   ⟸   XM_039111869
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038967809   ⟸   XM_039111881
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038967798   ⟸   XM_039111870
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038967811   ⟸   XM_039111883
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038967800   ⟸   XM_039111872
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038967799   ⟸   XM_039111871
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038967812   ⟸   XM_039111884
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038967813   ⟸   XM_039111885
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038967817   ⟸   XM_039111889
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038967810   ⟸   XM_039111882
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038967802   ⟸   XM_039111874
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038967801   ⟸   XM_039111873
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038967808   ⟸   XM_039111880
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038967814   ⟸   XM_039111886
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038967803   ⟸   XM_039111875
- Peptide Label: isoform X9
RefSeq Acc Id: ENSRNOP00000093763   ⟸   ENSRNOT00000101103
RefSeq Acc Id: ENSRNOP00000077184   ⟸   ENSRNOT00000101881
RefSeq Acc Id: ENSRNOP00000082575   ⟸   ENSRNOT00000119744
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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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
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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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
F344/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
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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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
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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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
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 (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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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