Xdh (xanthine dehydrogenase) - Rat Genome Database

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Gene: Xdh (xanthine dehydrogenase) Rattus norvegicus
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Symbol: Xdh
Name: xanthine dehydrogenase
RGD ID: 62043
Description: Enables several functions, including 2 iron, 2 sulfur cluster binding activity; molybdopterin cofactor binding activity; and oxidoreductase activity, acting on CH or CH2 groups. Involved in several processes, including cellular response to cytokine stimulus; purine nucleobase catabolic process; and response to aluminum ion. Located in cytosol; extracellular space; and peroxisome. Used to study several diseases, including hypertension; hyperuricemia; interstitial nephritis; kidney failure (multiple); and renal fibrosis. Biomarker of several diseases, including cholestasis; liver disease (multiple); obesity; pancreatitis; and peritonitis. Human ortholog(s) of this gene implicated in several diseases, including Lesch-Nyhan syndrome; cardiovascular system disease (multiple); chronic kidney disease; hyperuricemia; and xanthinuria. Orthologous to human XDH (xanthine dehydrogenase); PARTICIPATES IN adenine phoshoribosyltransferase deficiency pathway; adenosine monophosphate deaminase deficiency pathway; adenylosuccinate lyase deficiency pathway; INTERACTS WITH (R)-adrenaline; (R)-lipoic acid; (S)-nicotine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: xanthine dehydrogenase/oxidase; xanthine oxidase; xanthine oxidoreductase; XOR
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Xdhem1Mcwi   Xdhem2Mcwi  
Genetic Models: SS-Xdhem2Mcwi SS-Xdhem1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2621,530,463 - 21,592,172 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl621,530,113 - 21,592,268 (+)Ensembl
Rnor_6.0625,149,570 - 25,211,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl625,149,235 - 25,211,494 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0634,996,983 - 35,059,195 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4621,417,685 - 21,590,015 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1621,420,637 - 21,592,968 (+)NCBI
Celera621,081,179 - 21,143,279 (+)NCBICelera
Cytogenetic Map6q13-q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (IDA,ISO)
Acute Lung Injury  (IEP)
Animal Mammary Neoplasms  (ISO)
Arterial Thrombosis  (IMP)
autistic disorder  (ISO)
Autoinflammation with Infantile Enterocolitis  (ISO)
Brain Injuries  (IEP)
Carbon Monoxide Poisoning  (IEP,IMP)
carcinoma  (ISO)
cardiomyopathy  (IDA,IMP)
cardiovascular system disease  (ISO)
carotid artery disease  (ISO)
cataract  (IEP,ISO)
cholestasis  (IEP)
chronic kidney disease  (IDA,ISO)
Colonic Neoplasms  (IEP)
congestive heart failure  (ISO)
Diabetic Cardiomyopathies  (IDA)
Diabetic Nephropathies  (IDA,ISO)
Dwarfism  (ISO)
Eczema  (ISO)
Experimental Arthritis  (IEP)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Neoplasms  (IEP)
Fetal Growth Retardation  (ISO)
gout  (ISO)
heart disease  (ISO)
hepatocellular carcinoma  (IEP)
hydronephrosis  (ISO)
Hyperoxaluria  (IEP)
Hyperoxic Lung Injury  (IEP)
hypertension  (IDA,IEP,ISO)
hyperuricemia  (IDA,ISO)
Hypotension  (IEP)
interstitial nephritis  (IMP)
Intestinal Reperfusion Injury  (IEP)
ischemia  (ISO)
kidney failure  (ISO)
Kidney Reperfusion Injury  (IMP)
Left Ventricular Hypertrophy  (ISO)
Lesch-Nyhan syndrome  (ISO)
Liver Reperfusion Injury  (IEP)
major depressive disorder  (ISO)
Mammary Neoplasms, Experimental  (ISO)
middle cerebral artery infarction  (ISO)
Multiple Organ Failure  (ISO)
muscular disease  (IEP)
Myocardial Reperfusion Injury  (IEP)
Nerve Degeneration  (ISO)
neutropenia  (ISO)
obesity  (IEP)
pancreatitis  (IEP)
peritonitis  (IEP)
Pneumoperitoneum  (IDA)
portal hypertension  (IEP)
protein-losing enteropathy  (ISO)
pulmonary embolism  (ISO)
Puromycin Aminonucleoside Nephrosis  (IEP)
renal fibrosis  (IMP)
Renal Ischemia  (IEP)
Reperfusion Injury  (IDA,ISO)
Retina Reperfusion Injury  (IMP)
Sepsis  (IDA)
Shock  (IMP)
Spinal Cord Injuries  (IEP)
Testis Reperfusion Injury  (IDA)
thrombocytopenia  (ISO)
Transplant Rejection  (IMP)
Urachal Cyst  (ISO)
urinary bladder cancer  (ISO)
Wounds, Penetrating  (IEP)
xanthinuria  (ISO,ISS)
Xanthinuria, Type I  (ISO)
Xanthinuria, Type II  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (ISO)
(R)-adrenaline  (EXP)
(R)-lipoic acid  (EXP)
(S)-nicotine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-dithiothreitol  (EXP)
1-methyl-7H-xanthine  (ISO)
1-methyluric acid  (ISO)
1-naphthyl isothiocyanate  (ISO)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
2-nitroanisole  (ISO)
2-nitrofluorene  (EXP,ISO)
3',5'-cyclic GMP  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (EXP,ISO)
3-phenylprop-2-enal  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP,ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (EXP,ISO)
7H-xanthine  (EXP,ISO)
9H-xanthine  (EXP,ISO)
acetaldehyde  (ISO)
acetic acid  (ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
allantoin  (EXP)
allopurinol  (EXP,ISO)
alloxan  (EXP)
alloxanthine  (EXP)
aluminium atom  (EXP)
aluminium(0)  (EXP)
ammonium acetate  (EXP)
ammonium chloride  (EXP)
anthocyanin  (EXP)
apocynin  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
aspartame  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
Benzoyl peroxide  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
bezafibrate  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bosentan  (ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbon monoxide  (EXP)
carbon nanotube  (ISO)
carboplatin  (EXP)
Chloramine  (EXP)
chloroprene  (ISO)
chlorpyrifos  (EXP)
chlorzoxazone  (ISO)
chromium(6+)  (ISO)
cis-caffeic acid  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
curcumin  (EXP)
cycloartenol  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
D-glucose  (EXP)
DDT  (EXP)
dehydroepiandrosterone  (EXP)
dexamethasone  (EXP,ISO)
dextromethorphan  (ISO)
diethylstilbestrol  (EXP,ISO)
diisopropyl fluorophosphate  (EXP)
diosmin  (EXP,ISO)
dioxygen  (EXP,ISO)
diuron  (EXP)
dizocilpine maleate  (EXP)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
enzyme inhibitor  (EXP)
erdosteine  (EXP)
ethanol  (EXP,ISO)
ethylenediaminetetraacetic acid  (ISO)
flavonoids  (EXP)
fluocinolone acetonide  (ISO)
fluoranthene  (ISO)
formaldehyde  (ISO)
fructose  (EXP,ISO)
genistein  (ISO)
glucose  (EXP)
glutathione  (EXP)
glyburide  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroxyl  (ISO)
hydroxytyrosol  (EXP)
hypoxanthine  (EXP,ISO)
indometacin  (EXP,ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
L-1,4-dithiothreitol  (EXP)
L-ascorbic acid  (ISO)
L-glutamine  (EXP)
L-methionine  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
lipoic acid  (EXP)
Lithospermic acid  (EXP)
lupeol  (ISO)
mercaptopurine  (EXP)
methamphetamine  (ISO)
methapyrilene  (EXP)
methylisothiazolinone  (ISO)
mitomycin C  (ISO)
monosodium L-glutamate  (ISO)
myo-inositol hexakisphosphate  (EXP)
myricetin  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nicorandil  (EXP,ISO)
nicotine  (EXP)
nitric oxide  (ISO)
nitroprusside  (EXP)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (ISO)
palytoxin  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentachlorophenol  (ISO)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP,ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
potassium bromate  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (EXP,ISO)
propanal  (ISO)
propiconazole  (ISO)
purine-6-thiol  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
reactive oxygen species  (EXP,ISO)
resveratrol  (EXP)
rotenone  (EXP,ISO)
rutin  (EXP)
SB 203580  (EXP)
Senkirkine  (ISO)
serotonin  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium acetate trihydrate  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium benzoate  (EXP)
sodium fluoride  (ISO)
sodium nitrate  (ISO)
sodium tungstate  (EXP)
streptozocin  (EXP)
superoxide  (ISO)
taurine  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
toluene  (EXP)
trans-caffeic acid  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (ISO)
tubocurarine  (EXP)
tungsten  (EXP,ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
zinc atom  (EXP,ISO)
zinc sulfate  (EXP)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
adenosine catabolic process  (IEA,ISO)
aging  (IEP)
allantoin metabolic process  (IDA,IEA,ISO)
AMP catabolic process  (IEA,ISO)
cellular response to interleukin-1  (IEP)
cellular response to tumor necrosis factor  (IEP)
dAMP catabolic process  (IEA,ISO)
deoxyadenosine catabolic process  (IEA,ISO)
deoxyguanosine catabolic process  (IEA,ISO)
deoxyinosine catabolic process  (IEA,ISO)
dGMP catabolic process  (IEA,ISO)
GMP catabolic process  (IEA,ISO)
guanine catabolic process  (IDA,IEA,ISO)
hypoxanthine catabolic process  (IDA,IEA,ISO)
IMP catabolic process  (IEA,ISO)
inosine catabolic process  (IEA,ISO)
iron-sulfur cluster assembly  (IEA,ISO)
lactation  (IEA,ISO)
negative regulation of endothelial cell differentiation  (IEA,ISO)
negative regulation of endothelial cell proliferation  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of protein kinase B signaling  (IEA,ISO)
negative regulation of protein phosphorylation  (IEA,ISO)
negative regulation of vascular endothelial growth factor signaling pathway  (IEA,ISO)
negative regulation of vasculogenesis  (IEA,ISO)
positive regulation of p38MAPK cascade  (IEA,ISO)
positive regulation of reactive oxygen species metabolic process  (IEA,ISO)
regulation of epithelial cell differentiation  (ISO)
response to aluminum ion  (IDA)
response to azide  (IEP)
response to carbon monoxide  (IEP)
response to heat  (IEP)
response to hydrogen peroxide  (IEP)
response to lipopolysaccharide  (IEP)
xanthine catabolic process  (IBA,IDA,IEA,ISO,ISS)

Cellular Component
cytosol  (IDA,IEA,ISO)
extracellular space  (IBA,IDA)
peroxisome  (IDA,IEA)
sarcoplasmic reticulum  (IEA,ISO)

References

References - curated
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87. Yi LT, etal., Pharm Biol. 2012 Nov;50(11):1423-7. doi: 10.3109/13880209.2012.683115. Epub 2012 Sep 11.
88. Zhang Y, etal., Urology. 2013 Jun 12. pii: S0090-4295(13)00472-X. doi: 10.1016/j.urology.2013.04.016.
Additional References at PubMed
PMID:8670112   PMID:12502743   PMID:12969896   PMID:14588143   PMID:15201549   PMID:15201667   PMID:15932896   PMID:16109514   PMID:16407880   PMID:16502470   PMID:17031261   PMID:17301076  
PMID:17301077   PMID:17370312   PMID:17440754   PMID:17597094   PMID:17765919   PMID:17920330   PMID:18083771   PMID:18386220   PMID:18424432   PMID:18487445   PMID:18818408   PMID:18974366  
PMID:19800018   PMID:20167676   PMID:20399619   PMID:20555367   PMID:21077683   PMID:21295134   PMID:22231435   PMID:22648241   PMID:22688000   PMID:24014679   PMID:24448833   PMID:25486021  
PMID:25751622   PMID:25817260   PMID:26119820   PMID:26663724   PMID:27078869   PMID:27198514   PMID:27573711   PMID:27585949   PMID:28025796   PMID:30059711  


Genomics

Comparative Map Data
Xdh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2621,530,463 - 21,592,172 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl621,530,113 - 21,592,268 (+)Ensembl
Rnor_6.0625,149,570 - 25,211,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl625,149,235 - 25,211,494 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0634,996,983 - 35,059,195 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4621,417,685 - 21,590,015 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1621,420,637 - 21,592,968 (+)NCBI
Celera621,081,179 - 21,143,279 (+)NCBICelera
Cytogenetic Map6q13-q14NCBI
XDH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl231,334,321 - 31,414,742 (-)EnsemblGRCh38hg38GRCh38
GRCh38231,334,320 - 31,414,777 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37231,557,187 - 31,637,608 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36231,410,692 - 31,491,115 (-)NCBINCBI36hg18NCBI36
Build 34231,470,146 - 31,549,264NCBI
Celera231,399,873 - 31,481,045 (-)NCBI
Cytogenetic Map2p23.1NCBI
HuRef231,294,906 - 31,375,846 (-)NCBIHuRef
CHM1_1231,487,808 - 31,568,252 (-)NCBICHM1_1
Xdh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391774,190,890 - 74,257,369 (-)NCBIGRCm39mm39
GRCm39 Ensembl1774,190,890 - 74,257,191 (-)Ensembl
GRCm381773,883,895 - 73,950,397 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1773,883,895 - 73,950,196 (-)EnsemblGRCm38mm10GRCm38
MGSCv371774,233,248 - 74,299,522 (-)NCBIGRCm37mm9NCBIm37
MGSCv361773,788,790 - 73,855,081 (-)NCBImm8
Celera1778,175,030 - 78,239,710 (-)NCBICelera
Cytogenetic Map17E2NCBI
cM Map1745.25NCBI
XDH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A31,425,183 - 31,504,455 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A31,425,183 - 31,504,455 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A31,356,011 - 31,435,111 (-)NCBIMhudiblu_PPA_v0panPan3
XDH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11724,900,708 - 24,960,748 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1724,901,447 - 24,971,935 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1724,694,965 - 24,754,929 (-)NCBI
ROS_Cfam_1.01725,464,496 - 25,524,534 (-)NCBI
UMICH_Zoey_3.11724,767,742 - 24,827,816 (-)NCBI
UNSW_CanFamBas_1.01724,830,189 - 24,890,224 (-)NCBI
UU_Cfam_GSD_1.01724,929,639 - 24,989,647 (-)NCBI
Xdh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629269,015,034 - 69,076,787 (-)NCBI
SpeTri2.0NW_0049364931,762,814 - 1,824,501 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XDH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3107,986,528 - 108,080,151 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13107,987,060 - 108,052,043 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23114,732,427 - 114,796,636 (+)NCBISscrofa10.2Sscrofa10.2susScr3
XDH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11476,084,693 - 76,162,840 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1476,085,368 - 76,163,936 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604535,902,856 - 35,979,384 (-)NCBIVero_WHO_p1.0
Xdh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473813,116,317 - 13,180,935 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D6Rat74  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2621,420,196 - 21,420,428 (-)MAPPERmRatBN7.2
mRatBN7.2621,420,196 - 21,420,428 (+)MAPPERmRatBN7.2
Rnor_6.0625,321,298 - 25,321,529NCBIRnor6.0
Rnor_6.0622,591,778 - 22,592,009NCBIRnor6.0
Rnor_5.0635,169,195 - 35,169,426UniSTSRnor5.0
Rnor_5.0632,478,223 - 32,478,454UniSTSRnor5.0
RGSC_v3.4621,447,493 - 21,447,724UniSTSRGSC3.4
RGSC_v3.4621,447,492 - 21,447,724RGDRGSC3.4
RGSC_v3.1621,450,277 - 21,450,691RGD
Celera620,970,862 - 20,971,109UniSTS
SHRSP x BN Map620.6398RGD
SHRSP x BN Map620.6398UniSTS
Cytogenetic Map6q13UniSTS
RH136872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2621,592,194 - 21,592,392 (-)MAPPERmRatBN7.2
Rnor_6.0625,149,350 - 25,149,547NCBIRnor6.0
Rnor_5.0634,996,763 - 34,996,960UniSTSRnor5.0
RGSC_v3.4621,590,038 - 21,590,235UniSTSRGSC3.4
Celera621,143,302 - 21,143,499UniSTS
Cytogenetic Map6q13UniSTS
BE120616  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2621,456,451 - 21,456,635 (-)MAPPERmRatBN7.2
Rnor_6.0625,285,094 - 25,285,277NCBIRnor6.0
Rnor_5.0635,132,991 - 35,133,174UniSTSRnor5.0
RGSC_v3.4621,483,767 - 21,483,950UniSTSRGSC3.4
Celera621,007,206 - 21,007,389UniSTS
Cytogenetic Map6q13UniSTS


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
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
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
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)61653614027261739Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat


Genetic Models
This gene Xdh is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:48
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000009634
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 14 37 23 17 23 7 10 17 12 11 7
Low 1 19 16 14 2 14 1 1 37 16 22 1
Below cutoff 10 4 4 4 35 2 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC128261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH000836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ104432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB789770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB794695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB798942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB811713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB848248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB866510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB885376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB890763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB896523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB659829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB664754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB669001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB681772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB718307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB736569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB755435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB760822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB766582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J05579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U08123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009634   ⟹   ENSRNOP00000009634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl621,530,481 - 21,592,268 (+)Ensembl
Rnor_6.0 Ensembl625,149,235 - 25,211,494 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101107   ⟹   ENSRNOP00000076909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl621,530,113 - 21,589,971 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110434   ⟹   ENSRNOP00000079949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl621,541,111 - 21,592,268 (+)Ensembl
RefSeq Acc Id: NM_017154   ⟹   NP_058850
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2621,530,463 - 21,592,172 (+)NCBI
Rnor_6.0625,149,570 - 25,211,273 (-)NCBI
Rnor_5.0634,996,983 - 35,059,195 (-)NCBI
RGSC_v3.4621,417,685 - 21,590,015 (+)RGD
Celera621,081,179 - 21,143,279 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058850   ⟸   NM_017154
- Sequence:
RefSeq Acc Id: ENSRNOP00000009634   ⟸   ENSRNOT00000009634
RefSeq Acc Id: ENSRNOP00000076909   ⟸   ENSRNOT00000101107
RefSeq Acc Id: ENSRNOP00000079949   ⟸   ENSRNOT00000110434
Transcriptome

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

Promoters
RGD ID:13694425
Promoter ID:EPDNEW_R4950
Type:initiation region
Name:Xdh_1
Description:xanthine dehydrogenase
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_6.0625,211,266 - 25,211,326EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62043 AgrOrtholog
Ensembl Genes ENSRNOG00000007081 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009634 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009634 UniProtKB/TrEMBL
InterPro 2Fe-2S-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2Fe-2S-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2Fe-2S_ferredoxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2Fe-2S_ferredoxin-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2Fe2S_fd_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_Oxase/Xan_DH_a/b UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_Oxase/Xan_DH_a/b_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_Oxase/xanthine_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AldOxase/xan_DH_Mopterin-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AldOxase/xan_DH_Mopterin-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CO_DH_flav_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CO_DH_flav_C_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD-bd_PCMH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD-bd_PCMH-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Mopterin_DH_FAD-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OxRdtase_Mopterin_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Xanthine_DH_ssu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:497811 UniProtKB/Swiss-Prot
NCBI Gene 497811 ENTREZGENE
Pfam Ald_Xan_dh_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_Xan_dh_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CO_deh_flav_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD_binding_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fer2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fer2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB XDH RGD
PhenoGen Xdh PhenoGen
PIRSF Xanthine_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE 2FE2S_FER_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2FE2S_FER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD_PCMH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MOLYBDOPTERIN_EUK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Ald_Xan_dh_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CO_deh_flav_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47741 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54292 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54665 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55447 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56003 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56176 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs xanthine_xdhA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LQS6_RAT UniProtKB/TrEMBL
  P22985 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q63157 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Xdh  xanthine dehydrogenase      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference