Slc2a1 (solute carrier family 2 member 1) - Rat Genome Database

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Gene: Slc2a1 (solute carrier family 2 member 1) Rattus norvegicus
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Symbol: Slc2a1
Name: solute carrier family 2 member 1
RGD ID: 3704
Description: Enables several functions, including D-glucose transmembrane transporter activity; dehydroascorbic acid transmembrane transporter activity; and kinase binding activity. Involved in several processes, including cellular hyperosmotic response; cellular response to mechanical stimulus; and dehydroascorbic acid transport. Located in several cellular components, including Z disc; basolateral plasma membrane; and intercalated disc. Colocalizes with sarcolemma. Biomarker of hypertension; hypothyroidism; and middle cerebral artery infarction. Human ortholog(s) of this gene implicated in brain disease (multiple); carbohydrate metabolic disorder; myelomeningocele; obesity; and type 2 diabetes mellitus. Orthologous to human SLC2A1 (solute carrier family 2 member 1); PARTICIPATES IN facilitative sugar transporter mediated glucose transport pathway; Glut1 deficiency syndrome pathway; hypoxia inducible factor pathway; INTERACTS WITH (-)-epigallocatechin 3-gallate; 1-[(2,3,4-trimethoxyphenyl)methyl]piperazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: glucose transporter type 1, erythrocyte/brain; GLUT-1; Glut1; GLUTB; GTG1; Gtg3; RATGTG1; solute carrier family 2 (facilitated glucose transporter) member 1; solute carrier family 2 (facilitated glucose transporter), member 1; Solute carrier family 2 a 1 (facilitated glucose transporter) brain; solute carrier family 2, facilitated glucose transporter member 1; solute carrier family 2, member 1; solute carrier family 2,member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Bp103  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25132,717,196 - 132,745,416 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5132,717,196 - 132,745,416 (+)Ensembl
Rnor_6.05138,154,677 - 138,182,897 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,154,673 - 138,182,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05141,964,114 - 141,992,634 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45139,690,801 - 139,719,021 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15139,696,029 - 139,724,247 (+)NCBI
Celera5131,243,786 - 131,272,021 (+)NCBICelera
RH 3.4 Map5865.0RGD
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Alzheimer's disease  (ISO)
Ataxia  (ISO)
benign epilepsy with centrotemporal spikes  (ISO)
Breast Neoplasms  (ISO)
cataract  (ISO)
cerebellar ataxia  (ISO)
Charcot-Marie-Tooth disease dominant intermediate C  (ISO)
childhood absence epilepsy  (ISO)
childhood onset GLUT1 deficiency syndrome 2  (ISO)
Colonic Neoplasms  (ISO)
Developmental Disabilities  (ISO)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (IEP,ISO)
Ductal Carcinoma  (ISO)
ductal carcinoma in situ  (ISO)
dystonia  (ISO)
dystonia 9  (ISO)
epilepsy  (ISO)
Experimental Diabetes Mellitus  (IEP)
Fetal Growth Retardation  (IEP)
genetic disease  (ISO)
glomerulosclerosis  (ISO)
GLUT1 Deficiency Syndrome  (ISO)
hemangioma  (ISO)
hepatocellular carcinoma  (ISO)
Hirschsprung's disease  (ISO)
hypertension  (IEP)
hypothyroidism  (IEP)
idiopathic generalized epilepsy 12  (ISO)
Infantile Capillary Hemangioma  (ISO)
inherited metabolic disorder  (ISO)
intellectual disability  (ISO)
Liver Neoplasms  (ISO)
malignant mesothelioma  (ISO)
microcephaly  (ISO)
middle cerebral artery infarction  (IEP)
migraine  (ISO)
myelomeningocele  (ISO)
Myocardial Reperfusion Injury  (IEP)
Neoplastic Cell Transformation  (ISO)
nephroblastoma  (ISO)
nervous system disease  (ISO)
obesity  (ISO)
osteoarthritis  (ISO)
Ovarian Neoplasms  (ISO)
Peritoneal Neoplasms  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IEP)
Stomatin-Deficient Cryohydrocytosis with Mental Retardation, Seizures, Cataracts, and Massive Hepatosplenomegaly  (ISO)
type 2 diabetes mellitus  (ISO)
visual epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(E)-cinnamyl alcohol  (ISO)
(E)-Dacarbazine  (ISO)
(S)-naringenin  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-[(2,3,4-trimethoxyphenyl)methyl]piperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dinitrophenol  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-deoxy-2-((18)F)fluoro-D-glucose  (ISO)
2-deoxy-D-glucose  (ISO)
2-methoxy-17beta-estradiol  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-dihydroxybenzoic acid  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-bromopyruvic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
3-methylcholanthrene  (EXP)
3-O-methyl-D-glucose  (ISO)
3-Phenyl-1-propanol  (ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5-fluorouracil  (ISO)
7-hydroxyflavone  (ISO)
acadesine  (ISO)
acarbose  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-naphthoflavone  (ISO)
aluminium atom  (ISO)
aluminium(0)  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthracene-1,8,9-triol  (ISO)
antirheumatic drug  (ISO)
Apaziquone  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
ATP  (ISO)
atrazine  (ISO)
Azaspiracid  (ISO)
azide  (EXP)
barbiturates  (ISO)
beauvericin  (ISO)
benzaldehyde  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
bucladesine  (ISO)
butan-1-ol  (ISO)
butylated hydroxyanisole  (ISO)
butyric acid  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbon nanotube  (ISO)
celecoxib  (ISO)
chloral hydrate  (ISO)
chloroacetaldehyde  (ISO)
chloroform  (EXP)
chloropicrin  (ISO)
chloroprene  (ISO)
cholic acid  (ISO)
chromium atom  (EXP)
chromium(6+)  (ISO)
cidofovir anhydrous  (ISO)
cinnamyl alcohol  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP,ISO)
crotonaldehyde  (ISO)
cumene  (ISO)
curcumin  (ISO)
Cyclofenil  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
cytochalasin B  (ISO)
D-glucose  (EXP,ISO)
dacarbazine  (ISO)
daidzein  (ISO)
DDT  (ISO)
deguelin  (ISO)
dehydroascorbic acid  (EXP,ISO)
Deoxycorticosterone acetate  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
diazepam  (ISO)
dibenz[a,h]anthracene  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
Dihydrotanshinone I  (ISO)
dinophysistoxin 1  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enniatin  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
Fusaric acid  (ISO)
Genipin  (ISO)
genistein  (EXP,ISO)
gentamycin C  (ISO)
glucose  (EXP,ISO)
glycine  (ISO)
glyphosate  (ISO)
hexadecanoic acid  (ISO)
hydrazine  (EXP)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroquinone  (EXP)
ibuprofen  (ISO)
ifosfamide  (ISO)
indometacin  (ISO)
iron dichloride  (ISO)
isoliquiritigenin  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
kaempferide  (ISO)
kaempferol  (ISO)
L-ascorbic acid  (EXP)
L-cysteine  (ISO)
L-dehydroascorbic acid  (EXP,ISO)
L-mimosine  (EXP,ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
leflunomide  (ISO)
lipopolysaccharide  (EXP)
lithocholic acid  (ISO)
LY294002  (ISO)
menadione  (ISO)
mercaptoethanol  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
methylarsonic acid  (EXP,ISO)
methylene blue  (ISO)
methylmercury chloride  (EXP,ISO)
Mezerein  (ISO)
mifepristone  (ISO)
minocycline  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monosodium L-glutamate  (ISO)
myricetin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
nickel subsulfide  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
Niflumic acid  (ISO)
nimesulide  (ISO)
Nonidet P-40  (ISO)
ochratoxin A  (ISO)
ofloxacin  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
organoselenium compound  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
palytoxin  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
pentachlorophenol  (ISO)
pentobarbital  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenobarbital  (ISO)
phenylarsine oxide  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phloretin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
probenecid  (ISO)
prochloraz  (ISO)
progesterone  (EXP,ISO)
promethazine  (EXP)
propanal  (ISO)
prostaglandin E2  (ISO)
protoporphyrin  (ISO)
puerarin  (EXP)
Pyridostigmine bromide  (ISO)
pyrithiamine  (EXP)
quercetin  (ISO)
ranitidine  (EXP)
resveratrol  (ISO)
rofecoxib  (ISO)
rotenone  (ISO)
saccharin  (ISO)
sarpogrelate  (EXP)
SB 431542  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (EXP,ISO)
sodium azide  (ISO)
sodium chloride  (EXP,ISO)
sodium dichromate  (ISO)
streptozocin  (EXP)
sulfadimethoxine  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
tetraethylenepentamine  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
tin(II) chloride (anhydrous)  (ISO)
tolbutamide  (ISO)
tolfenamic acid  (ISO)
toluene  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (EXP,ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (EXP,ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
Yessotoxin  (ISO)
zidovudine  (ISO)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
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40. MGD data from the GO Consortium
41. NCBI rat LocusLink and RefSeq merged data July 26, 2002
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46. OMIM Disease Annotation Pipeline
47. Pearson-Leary J and McNay EC, J Neurosci. 2016 Nov 23;36(47):11851-11864. doi: 10.1523/JNEUROSCI.1700-16.2016.
48. Pipeline to import KEGG annotations from KEGG into RGD
49. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
50. Pipeline to import SMPDB annotations from SMPDB into RGD
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53. RGD automated data pipeline
54. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
55. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:1429721   PMID:1714544   PMID:3198639   PMID:7589840   PMID:7593639   PMID:8457197   PMID:9751501   PMID:10198040   PMID:10227690   PMID:10394363   PMID:10862609   PMID:11172003  
PMID:11259273   PMID:11681785   PMID:12002265   PMID:12506324   PMID:12531786   PMID:14519432   PMID:14729246   PMID:14741039   PMID:15166316   PMID:15359219   PMID:15489334   PMID:15808844  
PMID:15811071   PMID:15855808   PMID:15975910   PMID:16091581   PMID:16140905   PMID:16162661   PMID:16449286   PMID:16461188   PMID:17189352   PMID:17369047   PMID:17369472   PMID:17878754  
PMID:18196278   PMID:18245775   PMID:18347014   PMID:18474279   PMID:18511518   PMID:18650261   PMID:18787834   PMID:18797165   PMID:18802725   PMID:18957618   PMID:19546347   PMID:19681047  
PMID:19841136   PMID:19950593   PMID:20375116   PMID:20458337   PMID:21069159   PMID:21141602   PMID:21562080   PMID:21605500   PMID:21613414   PMID:21624469   PMID:21773965   PMID:21791420  
PMID:22125125   PMID:22258767   PMID:22433294   PMID:22516433   PMID:22579067   PMID:22871113   PMID:23265586   PMID:23280796   PMID:23680377   PMID:23975336   PMID:24062089   PMID:24329691  
PMID:24382486   PMID:24610532   PMID:24726496   PMID:24739976   PMID:25101238   PMID:25982116   PMID:26347179   PMID:26590355   PMID:26953753   PMID:27078104   PMID:28495754   PMID:28993322  
PMID:29476059   PMID:29490264   PMID:30335140   PMID:30837370   PMID:31162576   PMID:31765739   PMID:32445055   PMID:33856052  


Genomics

Comparative Map Data
Slc2a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25132,717,196 - 132,745,416 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5132,717,196 - 132,745,416 (+)Ensembl
Rnor_6.05138,154,677 - 138,182,897 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,154,673 - 138,182,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05141,964,114 - 141,992,634 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45139,690,801 - 139,719,021 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15139,696,029 - 139,724,247 (+)NCBI
Celera5131,243,786 - 131,272,021 (+)NCBICelera
RH 3.4 Map5865.0RGD
Cytogenetic Map5q36NCBI
SLC2A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl142,925,353 - 42,958,893 (-)EnsemblGRCh38hg38GRCh38
GRCh38142,925,353 - 42,958,868 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37143,391,024 - 43,424,539 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36143,164,102 - 43,197,088 (-)NCBINCBI36hg18NCBI36
Build 34143,060,611 - 43,093,594NCBI
Celera141,673,133 - 41,706,939 (-)NCBI
Cytogenetic Map1p34.2NCBI
HuRef141,511,000 - 41,544,561 (-)NCBIHuRef
CHM1_1143,507,796 - 43,541,586 (-)NCBICHM1_1
Slc2a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394118,965,942 - 118,994,527 (+)NCBIGRCm39mm39
GRCm39 Ensembl4118,965,908 - 118,995,180 (+)Ensembl
GRCm384119,108,745 - 119,137,330 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4119,108,711 - 119,137,983 (+)EnsemblGRCm38mm10GRCm38
MGSCv374118,781,350 - 118,809,935 (+)NCBIGRCm37mm9NCBIm37
MGSCv364118,606,700 - 118,635,259 (+)NCBImm8
Celera4117,836,249 - 117,864,839 (+)NCBICelera
Cytogenetic Map4D2.1NCBI
cM Map455.34NCBI
Slc2a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555372,408,042 - 2,439,511 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555372,408,042 - 2,438,788 (-)NCBIChiLan1.0ChiLan1.0
SLC2A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1143,600,733 - 43,634,143 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl143,600,733 - 43,634,143 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0142,224,273 - 42,257,184 (-)NCBIMhudiblu_PPA_v0panPan3
SLC2A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.115463,307 - 493,145 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl15463,237 - 493,140 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha15719,928 - 748,675 (+)NCBI
ROS_Cfam_1.015546,520 - 575,271 (+)NCBI
UMICH_Zoey_3.115456,107 - 484,827 (+)NCBI
UNSW_CanFamBas_1.015515,411 - 544,075 (+)NCBI
UU_Cfam_GSD_1.015532,601 - 561,334 (+)NCBI
Slc2a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505858,381,102 - 58,411,854 (-)NCBI
SpeTri2.0NW_00493647424,205,878 - 24,236,611 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC2A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12089,974,567 - 90,007,977 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2090,002,030 - 90,008,033 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603326,904,125 - 26,937,791 (-)NCBIVero_WHO_p1.0
Slc2a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248922,110,310 - 2,148,023 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Wox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,743,341 - 132,743,469 (+)MAPPERmRatBN7.2
Rnor_6.05138,180,823 - 138,180,950NCBIRnor6.0
Rnor_5.05141,990,560 - 141,990,687UniSTSRnor5.0
RGSC_v3.45139,716,946 - 139,717,074RGDRGSC3.4
RGSC_v3.45139,716,947 - 139,717,074UniSTSRGSC3.4
RGSC_v3.15139,722,172 - 139,722,300RGD
Celera5131,269,936 - 131,270,074UniSTS
RH 3.4 Map5868.7UniSTS
RH 3.4 Map5868.7RGD
RH 2.0 Map5861.1RGD
Cytogenetic Map5q36.1UniSTS
D5Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,744,136 - 132,744,368 (+)MAPPERmRatBN7.2
Rnor_6.05138,181,618 - 138,181,849NCBIRnor6.0
Rnor_5.05141,991,355 - 141,991,586UniSTSRnor5.0
RGSC_v3.45139,717,741 - 139,717,973RGDRGSC3.4
RGSC_v3.45139,717,742 - 139,717,973UniSTSRGSC3.4
RGSC_v3.15139,722,967 - 139,723,199RGD
Celera5131,270,742 - 131,270,973UniSTS
RH 3.4 Map5867.2RGD
RH 3.4 Map5867.2UniSTS
RH 2.0 Map5860.2RGD
SHRSP x BN Map570.6499RGD
Cytogenetic Map5q36.1UniSTS
Cytogenetic Map5q36UniSTS
Slc2a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,744,921 - 132,745,113 (+)MAPPERmRatBN7.2
Rnor_6.05138,182,403 - 138,182,594NCBIRnor6.0
Rnor_5.05141,992,140 - 141,992,331UniSTSRnor5.0
RGSC_v3.45139,718,527 - 139,718,718UniSTSRGSC3.4
Celera5131,271,527 - 131,271,718UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map5q36.1UniSTS
Slc2a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,740,566 - 132,741,330 (+)MAPPERmRatBN7.2
Rnor_6.05138,178,048 - 138,178,811NCBIRnor6.0
Rnor_5.05141,987,785 - 141,988,548UniSTSRnor5.0
RGSC_v3.45139,714,172 - 139,714,935UniSTSRGSC3.4
Celera5131,267,161 - 131,267,924UniSTS
Cytogenetic Map5q36.1UniSTS
Slc2a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,743,856 - 132,745,113 (+)MAPPERmRatBN7.2
Rnor_6.05138,181,338 - 138,182,594NCBIRnor6.0
Rnor_5.05141,991,075 - 141,992,331UniSTSRnor5.0
Celera5131,270,462 - 131,271,718UniSTS
Cytogenetic Map5q36.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5128033842133011550Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:456
Count of miRNA genes:236
Interacting mature miRNAs:280
Transcripts:ENSRNOT00000064452
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 3 29 23 18 13 18 74 35 39 10
Low 14 34 23 6 23 8 11 2 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064452   ⟹   ENSRNOP00000061340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5132,717,196 - 132,745,416 (+)Ensembl
Rnor_6.0 Ensembl5138,154,673 - 138,182,897 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083700   ⟹   ENSRNOP00000072351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5132,728,277 - 132,745,416 (+)Ensembl
Rnor_6.0 Ensembl5138,164,480 - 138,182,011 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106473   ⟹   ENSRNOP00000090216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5132,728,055 - 132,745,416 (+)Ensembl
RefSeq Acc Id: NM_138827   ⟹   NP_620182
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25132,717,196 - 132,745,416 (+)NCBI
Rnor_6.05138,154,677 - 138,182,897 (+)NCBI
Rnor_5.05141,964,114 - 141,992,634 (+)NCBI
RGSC_v3.45139,690,801 - 139,719,021 (+)RGD
Celera5131,243,786 - 131,272,021 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_620182 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41248 (Get FASTA)   NCBI Sequence Viewer  
  AAA41297 (Get FASTA)   NCBI Sequence Viewer  
  AAH61873 (Get FASTA)   NCBI Sequence Viewer  
  EDL90143 (Get FASTA)   NCBI Sequence Viewer  
  P11167 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_620182   ⟸   NM_138827
- UniProtKB: P11167 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072351   ⟸   ENSRNOT00000083700
RefSeq Acc Id: ENSRNOP00000061340   ⟸   ENSRNOT00000064452
RefSeq Acc Id: ENSRNOP00000090216   ⟸   ENSRNOT00000106473
Protein Domains
MFS

Transcriptome

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

Promoters
RGD ID:13693972
Promoter ID:EPDNEW_R4497
Type:multiple initiation site
Name:Slc2a1_1
Description:solute carrier family 2 member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05138,154,734 - 138,154,794EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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