Th (tyrosine hydroxylase) - Rat Genome Database

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Gene: Th (tyrosine hydroxylase) Rattus norvegicus
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Symbol: Th
Name: tyrosine hydroxylase
RGD ID: 3853
Description: Enables several functions, including cation binding activity; tetrahydrobiopterin binding activity; and tyrosine 3-monooxygenase activity. Involved in several processes, including aminergic neurotransmitter loading into synaptic vesicle; carboxylic acid metabolic process; and cellular response to nicotine. Located in several cellular components, including cytoplasmic vesicle; perikaryon; and terminal bouton. Used to study Parkinson's disease. Biomarker of several diseases, including brain disease (multiple); hyperprolactinemia; hypoglycemia; polycystic ovary syndrome; and portal hypertension. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinsonism; hypertension; and obesity. Orthologous to human TH (tyrosine hydroxylase); PARTICIPATES IN aromatic L-amino acid decarboxylase deficiency pathway; catecholamine biosynthetic pathway; dopamine biosynthetic pathway; INTERACTS WITH (+)-sesamin; (-)-epigallocatechin 3-gallate; (-)-selegiline.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: The; tyrosine 3-hydroxylase; tyrosine 3-monooxygenase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21198,071,500 - 198,078,832 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1198,071,503 - 198,109,767 (-)Ensembl
Rnor_6.01216,073,034 - 216,080,287 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1216,073,031 - 216,080,287 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01222,935,462 - 222,942,715 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41203,164,253 - 203,171,506 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11203,317,712 - 203,324,972 (-)NCBI
Celera1195,642,057 - 195,649,203 (-)NCBICelera
RH 2.0 Map11080.1RGD
Cytogenetic Map1q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-sesamin  (EXP)
(-)-epigallocatechin 3-gallate  (EXP)
(-)-selegiline  (EXP)
(24S)-24-hydroxycholesterol  (ISO)
(R)-adrenaline  (EXP,ISO)
(R)-mevalonic acid  (ISO)
(R)-noradrenaline  (EXP,ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-amphetamine  (ISO)
(S)-nicotine  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-D  (EXP)
2-methyl-6-(phenylethynyl)pyridine  (EXP)
3,4-dihydroxyphenylacetaldehyde  (EXP)
3,5-dichloro-N-[[(2S)-1-ethyl-2-pyrrolidinyl]methyl]-2-hydroxy-6-methoxybenzamide  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-Amino-1-methyl-5H-pyrido[4,3-b]indole  (EXP)
3-methyladenine  (EXP)
3-phenylprop-2-enal  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-phenylbutyric acid  (ISO)
5-(2-chloroethyl)-4-methylthiazole  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7-NITROINDAZOLE  (ISO)
8-bromo-3',5'-cyclic GMP  (EXP)
acetic acid  (ISO)
acetylcholine  (EXP)
acrylamide  (EXP)
acrylonitrile  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
agmatine  (EXP)
albiflorin  (EXP)
all-trans-retinoic acid  (ISO)
AM-251  (EXP)
amentoflavone  (ISO)
aminoguanidine  (ISO)
amitraz  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP,ISO)
apigenin  (EXP)
apocynin  (EXP)
Aroclor 1254  (EXP,ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
Asiaticoside  (EXP)
atrazine  (EXP,ISO)
baicalein  (ISO)
Bardoxolone methyl  (ISO)
benzo[a]pyrene  (EXP,ISO)
bicuculline  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
BQ 123  (EXP)
bromochloroacetic acid  (ISO)
bucladesine  (EXP)
butanal  (ISO)
Butylparaben  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calcitriol  (EXP,ISO)
cannabidiol  (ISO)
carmustine  (EXP)
carnosic acid  (EXP)
Carnosol  (ISO)
carvedilol  (EXP)
chelerythrine  (EXP)
chitosan  (EXP)
Chloralose  (EXP)
chlorisondamine  (EXP)
chlorpyrifos  (EXP,ISO)
cisplatin  (ISO)
clonidine  (EXP)
clonidine (amino form)  (EXP)
clonidine (imino form)  (EXP)
clozapine  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP,ISO)
colforsin daropate hydrochloride  (EXP)
copper(II) sulfate  (EXP,ISO)
corticosterone  (ISO)
Cuprizon  (EXP)
curcumin  (EXP,ISO)
cyanazine  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
cytarabine  (ISO)
dabigatran  (EXP)
DDE  (EXP)
desferrioxamine B  (EXP)
desipramine  (EXP)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dichlorvos  (EXP)
dieldrin  (EXP)
diethyldithiocarbamic acid  (EXP)
dioxygen  (EXP)
dipyridamole  (EXP)
dopamine  (EXP,ISO)
edaravone  (EXP)
elemental selenium  (EXP)
enzacamene  (EXP)
epibatidine  (EXP)
ethanol  (EXP,ISO)
fasudil  (EXP)
fenvalerate  (EXP)
fipronil  (ISO)
flavonoids  (EXP)
fluoxetine  (EXP,ISO)
formaldehyde  (ISO)
fructose  (ISO)
ganglioside GM1  (EXP)
genistein  (EXP,ISO)
geraniol  (ISO)
ginkgetin  (ISO)
ginsenoside Re  (ISO)
glyburide  (ISO)
guanethidine  (EXP)
GW 1929  (EXP)
haloperidol  (EXP)
heptachlor  (ISO)
herbicide  (EXP)
hydrogen peroxide  (EXP,ISO)
icariin  (EXP)
idazoxan  (EXP)
imidacloprid  (EXP)
juglone  (ISO)
ketoconazole  (ISO)
KT 5720  (EXP)
L-ascorbic acid  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linalool  (EXP)
linuron  (EXP)
lipopolysaccharide  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
lovastatin  (ISO)
LY294002  (ISO)
maneb  (EXP,ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP,ISO)
manganese(II) sulfate  (EXP)
melatonin  (EXP,ISO)
mephedrone  (EXP,ISO)
mercaptopurine  (EXP)
methamphetamine  (EXP,ISO)
methoxychlor  (EXP)
methyllycaconitine  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
mifepristone  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (EXP)
montelukast  (EXP)
morphine  (EXP,ISO)
N(gamma)-nitro-L-arginine methyl ester  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (EXP)
N-ethyl-N-nitrosourea  (EXP)
N-ethylmaleimide  (EXP)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
naloxone  (EXP,ISO)
naltrexone  (ISO)
nickel atom  (EXP)
nickel dichloride  (ISO)
nicotine  (EXP,ISO)
nimodipine  (EXP)
nitroprusside  (EXP)
Norbinaltorphimine  (ISO)
olanzapine  (EXP)
oridonin  (EXP)
oxidopamine  (EXP,ISO)
P(1),P(4)-bis(5'-adenosyl) tetraphosphate  (EXP)
paracetamol  (EXP)
paraquat  (EXP,ISO)
pentanal  (ISO)
perfluorodecanoic acid  (ISO)
perfluorododecanoic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
perfluoroundecanoic acid  (ISO)
permethrin  (EXP)
phencyclidine  (ISO)
Phenelzine  (EXP)
phenethyl caffeate  (EXP)
phorbol 13-acetate 12-myristate  (EXP,ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (ISO)
pregabalin  (ISO)
probenecid  (ISO)
progesterone  (EXP)
propanal  (ISO)
propionic acid  (EXP)
propofol  (ISO)
purine-6-thiol  (EXP)
pyrrolidine dithiocarbamate  (ISO)
pyrroloquinoline quinone  (EXP)
quercetin  (EXP)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
reserpine  (EXP,ISO)
resveratrol  (ISO)
rimonabant  (EXP)
risperidone  (EXP)
rotenone  (EXP,ISO)
rottlerin  (EXP,ISO)
rutin  (EXP)
salubrinal  (EXP)
saxagliptin  (EXP)
SB 203580  (EXP)
SCH 23390  (ISO)
selenium atom  (EXP)
simazine  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (EXP)
spiperone  (EXP)
sulforaphane  (ISO)
sulpiride  (EXP,ISO)
Talipexole dihydrochloride  (ISO)
tamoxifen  (EXP,ISO)
taurine  (ISO)
telmisartan  (ISO)
testosterone  (EXP)
topiramate  (ISO)
trichloroethene  (EXP)
triprolidine  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (EXP)
valproic acid  (EXP,ISO)
vitamin D  (EXP)
vorinostat  (ISO)
WIN 55212-2  (EXP,ISO)
wortmannin  (EXP,ISO)
Y-27632  (ISO)
zearalenone  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)
zonisamide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aminergic neurotransmitter loading into synaptic vesicle  (IDA)
animal organ morphogenesis  (ISO)
catecholamine biosynthetic process  (IDA)
cellular response to alkaloid  (IEP)
cellular response to glucose stimulus  (IEP)
cellular response to growth factor stimulus  (IEP)
cellular response to manganese ion  (IEP)
cellular response to nicotine  (IEP)
cellular response to xenobiotic stimulus  (IEP)
cerebral cortex development  (IEP)
circadian sleep/wake cycle  (IEP)
cognition  (IEP)
dopamine biosynthetic process  (ISO)
dopamine biosynthetic process from tyrosine  (IBA,IDA,IMP,ISO)
eating behavior  (ISO)
embryonic camera-type eye morphogenesis  (ISO)
epinephrine biosynthetic process  (ISO)
eye photoreceptor cell development  (ISO)
fatty acid metabolic process  (IEP)
glycoside metabolic process  (IEP)
heart development  (IBA,IDA,ISO)
hyaloid vascular plexus regression  (ISO,ISS)
isoquinoline alkaloid metabolic process  (IEP)
learning  (ISO)
locomotory behavior  (ISO)
mating behavior  (ISO)
memory  (ISO)
multicellular organism aging  (IEP)
neurotransmitter biosynthetic process  (IEA)
norepinephrine biosynthetic process  (ISO)
phthalate metabolic process  (IEP)
phytoalexin metabolic process  (IEP)
regulation of heart contraction  (ISO)
response to activity  (IEP)
response to amphetamine  (IEP)
response to corticosterone  (IEP)
response to electrical stimulus  (IEP)
response to estradiol  (IEP)
response to ethanol  (IBA,IEP,ISO)
response to ether  (IEP)
response to growth factor  (IEP)
response to herbicide  (IEP)
response to hypoxia  (IBA,IDA,IEP,ISO)
response to immobilization stress  (IEP)
response to insecticide  (IEP)
response to isolation stress  (IEP)
response to light stimulus  (IEP)
response to lipopolysaccharide  (IEP)
response to metal ion  (IEP)
response to nicotine  (IEP)
response to nutrient levels  (IEP)
response to organic cyclic compound  (IEP)
response to peptide hormone  (IEP)
response to pyrethroid  (IEP)
response to salt stress  (IEP)
response to steroid hormone  (IEP)
response to water deprivation  (IEP)
response to xenobiotic stimulus  (IEP)
response to zinc ion  (IEP)
sensory perception of sound  (IEP)
social behavior  (IEP)
sphingolipid metabolic process  (IEP)
synaptic transmission, dopaminergic  (ISO)
terpene metabolic process  (IEP)
visual perception  (ISO)

Cellular Component

References

References - curated
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Additional References at PubMed
PMID:1672315   PMID:2857492   PMID:2882469   PMID:2884660   PMID:2889468   PMID:2896667   PMID:2905129   PMID:7518394   PMID:7592982   PMID:9228951   PMID:9520487   PMID:9753429  
PMID:9829800   PMID:10212311   PMID:10350535   PMID:10707987   PMID:10802666   PMID:10907721   PMID:11430814   PMID:11502746   PMID:11841594   PMID:11902120   PMID:11922614   PMID:12074840  
PMID:12130711   PMID:12147212   PMID:12423254   PMID:12457228   PMID:12538862   PMID:12604788   PMID:12631248   PMID:12675153   PMID:12742186   PMID:12929090   PMID:14651963   PMID:14660060  
PMID:14684249   PMID:14697237   PMID:14739357   PMID:15223360   PMID:15260122   PMID:15317940   PMID:15374756   PMID:15471880   PMID:15643613   PMID:15747353   PMID:15809070   PMID:15814794  
PMID:15860555   PMID:15935066   PMID:16076648   PMID:16165221   PMID:16195501   PMID:16338639   PMID:16445854   PMID:16452470   PMID:16503426   PMID:16584838   PMID:16618490   PMID:16805833  
PMID:17135716   PMID:17196177   PMID:17273802   PMID:17363452   PMID:17416971   PMID:17520326   PMID:17524356   PMID:17543899   PMID:17626271   PMID:17713852   PMID:17761882   PMID:17823252  
PMID:17900529   PMID:17951370   PMID:18032527   PMID:18047555   PMID:18072084   PMID:18185104   PMID:18258664   PMID:18343820   PMID:18536752   PMID:18572382   PMID:18589406   PMID:18772553  
PMID:18778785   PMID:19060113   PMID:19104749   PMID:19112418   PMID:19120093   PMID:19249909   PMID:19289463   PMID:19371093   PMID:19409439   PMID:19482560   PMID:19505538   PMID:19524553  
PMID:19581298   PMID:19703902   PMID:19756365   PMID:19818101   PMID:19844994   PMID:19945993   PMID:20037632   PMID:20102321   PMID:20143408   PMID:20170714   PMID:20620242   PMID:20811774  
PMID:20814066   PMID:20884338   PMID:21125428   PMID:21396433   PMID:21514317   PMID:21689789   PMID:21767616   PMID:21777029   PMID:21818658   PMID:21871514   PMID:22212880   PMID:22242182  
PMID:22372951   PMID:22815976   PMID:23153692   PMID:23321789   PMID:23327742   PMID:23368961   PMID:23608099   PMID:23680462   PMID:23868341   PMID:24117713   PMID:24317346   PMID:24480406  
PMID:24837549   PMID:25074751   PMID:25957836   PMID:26024204   PMID:26225746   PMID:26583134   PMID:26599339   PMID:26658810   PMID:26969276   PMID:27095027   PMID:27365397   PMID:27789384  
PMID:28132600   PMID:28630892   PMID:28637871   PMID:28726094   PMID:28750831   PMID:28887039   PMID:28984618   PMID:30056575   PMID:30634592   PMID:31279527   PMID:32697044  


Genomics

Comparative Map Data
Th
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21198,071,500 - 198,078,832 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1198,071,503 - 198,109,767 (-)Ensembl
Rnor_6.01216,073,034 - 216,080,287 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1216,073,031 - 216,080,287 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01222,935,462 - 222,942,715 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41203,164,253 - 203,171,506 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11203,317,712 - 203,324,972 (-)NCBI
Celera1195,642,057 - 195,649,203 (-)NCBICelera
RH 2.0 Map11080.1RGD
Cytogenetic Map1q41NCBI
TH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl112,163,929 - 2,171,815 (-)EnsemblGRCh38hg38GRCh38
GRCh38112,163,929 - 2,174,081 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37112,185,159 - 2,193,045 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,141,735 - 2,149,611 (-)NCBINCBI36hg18NCBI36
Build 34112,141,735 - 2,149,605NCBI
Celera112,221,752 - 2,229,624 (-)NCBI
Cytogenetic Map11p15.5NCBI
HuRef111,975,424 - 1,983,299 (-)NCBIHuRef
CHM1_1112,183,941 - 2,191,817 (-)NCBICHM1_1
Th
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397142,446,516 - 142,453,732 (-)NCBIGRCm39mm39
GRCm39 Ensembl7142,446,489 - 142,484,865 (-)Ensembl
GRCm387142,892,779 - 142,899,995 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7142,892,752 - 142,931,128 (-)EnsemblGRCm38mm10GRCm38
MGSCv377150,078,681 - 150,085,871 (-)NCBIGRCm37mm9NCBIm37
MGSCv367142,702,166 - 142,709,356 (-)NCBImm8
Celera7142,648,392 - 142,655,582 (-)NCBICelera
Cytogenetic Map7F5NCBI
cM Map788.06NCBI
Th
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542213,943,552 - 13,951,137 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542213,943,590 - 13,951,102 (-)NCBIChiLan1.0ChiLan1.0
TH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1112,234,095 - 2,242,030 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl112,231,248 - 2,242,433 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0112,204,820 - 2,212,750 (-)NCBIMhudiblu_PPA_v0panPan3
TH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11846,327,136 - 46,334,973 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1846,327,137 - 46,335,602 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1844,936,923 - 44,944,750 (-)NCBI
ROS_Cfam_1.01847,006,609 - 47,014,412 (-)NCBI
ROS_Cfam_1.0 Ensembl1847,006,611 - 47,014,441 (-)Ensembl
UMICH_Zoey_3.11846,455,359 - 46,462,897 (-)NCBI
UNSW_CanFamBas_1.01846,035,687 - 46,043,215 (-)NCBI
UU_Cfam_GSD_1.01846,782,129 - 46,789,967 (-)NCBI
Th
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049472,535,447 - 2,543,939 (-)NCBI
SpeTri2.0NW_004936794478,651 - 486,887 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl21,499,618 - 1,506,615 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.121,499,628 - 1,506,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111,969,194 - 1,977,263 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11,966,460 - 1,977,218 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603899,163,059 - 99,174,711 (-)NCBIVero_WHO_p1.0
Th
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476715,003,073 - 15,010,207 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Smu3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,081,083 - 198,081,184 (+)MAPPERmRatBN7.2
Rnor_6.01216,082,612 - 216,082,712NCBIRnor6.0
Rnor_5.01222,945,040 - 222,945,140UniSTSRnor5.0
RGSC_v3.41203,173,831 - 203,173,931UniSTSRGSC3.4
Celera1195,651,528 - 195,651,628UniSTS
Cytogenetic Map1q41UniSTS
M69200  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,071,580 - 198,071,684 (+)MAPPERmRatBN7.2
Rnor_6.01216,073,109 - 216,073,212NCBIRnor6.0
Rnor_5.01222,935,537 - 222,935,640UniSTSRnor5.0
RGSC_v3.41203,164,328 - 203,164,431UniSTSRGSC3.4
Celera1195,642,132 - 195,642,235UniSTS
Cytogenetic Map1q41UniSTS
PMC18740P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,072,757 - 198,073,166 (+)MAPPERmRatBN7.2
Rnor_6.01216,074,286 - 216,074,694NCBIRnor6.0
Rnor_5.01222,936,714 - 222,937,122UniSTSRnor5.0
RGSC_v3.41203,165,505 - 203,165,913UniSTSRGSC3.4
Celera1195,643,309 - 195,643,717UniSTS
Cytogenetic Map1q41UniSTS
RH94698  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,076,403 - 198,076,537 (+)MAPPERmRatBN7.2
Rnor_6.01216,077,932 - 216,078,065NCBIRnor6.0
Rnor_5.01222,940,360 - 222,940,493UniSTSRnor5.0
RGSC_v3.41203,169,151 - 203,169,284UniSTSRGSC3.4
Celera1195,646,955 - 195,647,088UniSTS
Cytogenetic Map1q41UniSTS
PMC151031P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,075,720 - 198,076,641 (+)MAPPERmRatBN7.2
Rnor_6.01216,077,249 - 216,078,169NCBIRnor6.0
Rnor_5.01222,939,677 - 222,940,597UniSTSRnor5.0
RGSC_v3.41203,168,468 - 203,169,388UniSTSRGSC3.4
Celera1195,646,272 - 195,647,192UniSTS
Cytogenetic Map1q41UniSTS
Th  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21198,075,568 - 198,076,698 (+)MAPPERmRatBN7.2
Rnor_6.01216,077,097 - 216,078,226NCBIRnor6.0
Rnor_5.01222,939,525 - 222,940,654UniSTSRnor5.0
RGSC_v3.41203,168,316 - 203,169,445UniSTSRGSC3.4
Celera1195,646,120 - 195,647,249UniSTS
Cytogenetic Map1q41UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)194494440198324465Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164747424209747424Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1164747424209747424Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118944897199050459Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1173108781218108781Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
631260Tcas2Tongue tumor susceptibility QTL 24.93tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)1192485903199050587Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1174133260219133260Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724559Pancm1Pancreatic morphology QTL 17.1islet of Langerhans morphology trait (VT:0005215)pancreatic islet damage composite score (CMO:0001156)1181759564214537555Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1169537671214537671Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)194494440198211706Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1181133855226133855Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1188377360224054420Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)194642722214537671Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1123350581201284552Rat
1302787Stl25Serum triglyceride level QTL 252.70.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1180359209210702199Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1143506580212458660Rat
2300161Bmd43Bone mineral density QTL 438.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2300174Bmd42Bone mineral density QTL 428.40.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)1171629477216629477Rat
2300187Bmd41Bone mineral density QTL 418.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1171629477216629477Rat
2293654Bss30Bone structure and strength QTL 3032.650.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1171629477216629477Rat
2293673Bss27Bone structure and strength QTL 2718.630.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)1171629477216629477Rat
2293677Bss41Bone structure and strength QTL 419.380.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1171629477216629477Rat
2293689Bss47Bone structure and strength QTL 477.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)1171629477216629477Rat
2293693Bss22Bone structure and strength QTL 2233.520.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1171629477216629477Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
634312Bp143Blood pressure QTL 14330.0002arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1182623426219932796Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
634338Hcar4Hepatocarcinoma resistance QTL 44.6liver integrity trait (VT:0010547)liver tumorous lesion number to liver area ratio (CMO:0001210)1193422268214537671Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1176550523221550523Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1185145134221264292Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1102813953201278233Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1151162512201278233Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1102813953201278233Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1156677124201278233Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512201278233Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1151162512201278233Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1151162512201278233Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354653Despr9Despair related QTL 90.00019locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1167909849212909849Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1359018Hrtrt20Heart rate QTL 203.08heart pumping trait (VT:2000009)heart rate (CMO:0000002)1185356336202902618Rat
1558658Bw59Body weight QTL 593.50.0003body mass (VT:0001259)body weight (CMO:0000012)1178784622223784622Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393213533942Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1181829673224569684Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1156677124218753816Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1154561505199561505Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1172609619217609619Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1358294Bw37Body weight QTL 3750.000011body mass (VT:0001259)body weight (CMO:0000012)1171310381216310381Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1169537671214537671Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1158633083203633083Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
4889428Stresp24Stress response QTL 240.05heart pumping trait (VT:2000009)absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)1155866514200866514Rat
6480777Insul17Insulin level QTL 173.86blood insulin amount (VT:0001560)blood insulin level area under curve (AUC) (CMO:0000351)1197260913198211706Rat
6480780Insul18Insulin level QTL 184.11blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1189607473200611765Rat
6480783Insul19Insulin level QTL 194.33blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1197489281200611765Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1180359209218108781Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1176869060221869060Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mirlet7drno-let-7d-5pMirtarbaseexternal_infoReporter assay;qRT-PCRFunctional MTI20557304

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:51
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000027682
Prediction methods: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 8 30 8
Low 2 2 2 2 44 10 16
Below cutoff 1 23 13 7 16 7 3 3 14 14 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027682   ⟹   ENSRNOP00000027682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1198,071,503 - 198,078,759 (-)Ensembl
Rnor_6.0 Ensembl1216,073,031 - 216,080,287 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105945   ⟹   ENSRNOP00000093950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1198,071,503 - 198,109,767 (-)Ensembl
RefSeq Acc Id: NM_012740   ⟹   NP_036872
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21198,071,506 - 198,078,759 (-)NCBI
Rnor_6.01216,073,034 - 216,080,287 (-)NCBI
Rnor_5.01222,935,462 - 222,942,715 (-)NCBI
RGSC_v3.41203,164,253 - 203,171,506 (-)RGD
Celera1195,642,057 - 195,649,203 (-)RGD
Sequence:
RefSeq Acc Id: XM_039101320   ⟹   XP_038957248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21198,071,500 - 198,078,829 (-)NCBI
RefSeq Acc Id: XM_039101324   ⟹   XP_038957252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21198,071,500 - 198,078,832 (-)NCBI
RefSeq Acc Id: XM_039101327   ⟹   XP_038957255
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21198,071,500 - 198,078,829 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036872   ⟸   NM_012740
- UniProtKB: P04177 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000027682   ⟸   ENSRNOT00000027682
RefSeq Acc Id: XP_038957252   ⟸   XM_039101324
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957255   ⟸   XM_039101327
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957248   ⟸   XM_039101320
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000093950   ⟸   ENSRNOT00000105945

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/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
LH/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
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)
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
M520/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
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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