Mapt (microtubule-associated protein tau) - Rat Genome Database

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Gene: Mapt (microtubule-associated protein tau) Rattus norvegicus
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Symbol: Mapt
Name: microtubule-associated protein tau
RGD ID: 69329
Description: Enables several functions, including Hsp90 protein binding activity; chaperone binding activity; and enzyme binding activity. Involved in several processes, including intrinsic apoptotic signaling pathway in response to oxidative stress; mRNA transport; and positive regulation of long-term synaptic depression. Located in several cellular components, including axon; cytoplasmic side of plasma membrane; and neuronal cell body. Colocalizes with microtubule. Used to study brain disease (multiple); cognitive disorder (multiple); obesity; and tauopathy (multiple). Biomarker of middle cerebral artery infarction. Human ortholog(s) of this gene implicated in dementia (multiple); neurodegenerative disease (multiple); progressive supranuclear palsy; and temporal lobe epilepsy. Orthologous to human MAPT (microtubule associated protein tau); PARTICIPATES IN Reelin signaling pathway; Alzheimer's disease pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC156663; Mtapt; neurofibrillary tangle protein; paired helical filament-tau; PHF-tau; pTau; RNPTAU; Tau; Tau microtubule-associated protein
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
mRatBN7.21089,138,644 - 89,236,137 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1089,138,627 - 89,236,129 (+)Ensembl
Rnor_6.01092,289,002 - 92,386,517 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1092,288,910 - 92,386,517 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01092,050,754 - 92,147,840 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41093,411,098 - 93,508,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11093,425,375 - 93,523,128 (+)NCBI
Celera1087,832,730 - 87,930,191 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
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
(S)-colchicine  (ISO)
(Z)-ligustilide  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-(4-methoxybenzyl)-3-(5-nitro-1,3-thiazol-2-yl)urea  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,5-hexanedione  (EXP)
2-methyl-6-(phenylethynyl)pyridine  (EXP)
2-methylcholine  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-nitropropanoic acid  (EXP)
3alpha-hydroxy-5beta-pregnan-20-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
5alpha-pregnane-3,20-dione  (EXP)
8-azaguanine  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
agmatine  (ISO)
albendazole  (ISO)
alexidine  (ISO)
all-trans-retinoic acid  (EXP,ISO)
aluminium atom  (EXP)
aluminium sulfate (anhydrous)  (EXP)
aluminium(0)  (EXP)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
ascomycin  (EXP,ISO)
astemizole  (ISO)
ATP  (EXP)
benfotiamine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (EXP)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
Calpeptin  (EXP)
camptothecin  (ISO)
cannabidiol  (EXP)
carbon nanotube  (ISO)
CCCP  (EXP)
chelidonine  (ISO)
chlordecone  (ISO)
chloroquine  (EXP)
chlorpyrifos  (ISO)
cholesterol  (EXP)
ciclopirox  (ISO)
ciguatoxin CTX1B  (ISO)
cilostazol  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
cordycepin  (EXP)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP,ISO)
D-aspartic acid  (EXP)
daunorubicin  (ISO)
decabromodiphenyl ether  (ISO)
diaziquone  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
dipicolinic acid  (ISO)
dizocilpine maleate  (EXP,ISO)
dopamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (EXP)
emetine  (ISO)
emodin  (ISO)
endosulfan  (EXP,ISO)
ethanol  (ISO)
fasudil  (EXP)
fenbendazole  (ISO)
fisetin  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
Formyl-N-acetyl-5-methoxykynurenamine  (EXP)
fulvestrant  (ISO)
genistein  (EXP)
glyoxal  (ISO)
griseofulvin  (ISO)
harmine  (ISO)
heparin  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
ionomycin  (EXP,ISO)
ivermectin  (ISO)
ketamine  (ISO)
L-ascorbic acid  (EXP)
L-serine  (EXP)
lansoprazole  (ISO)
lasalocid  (ISO)
lead diacetate  (EXP,ISO)
lead tetraacetate  (ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
leflunomide  (ISO)
liraglutide  (ISO)
lithium atom  (ISO)
lithium chloride  (EXP,ISO)
lithium hydride  (ISO)
losartan  (EXP)
LY294002  (ISO)
malonaldehyde  (ISO)
maneb  (ISO)
manganese(II) chloride  (EXP)
mebendazole  (ISO)
melatonin  (EXP,ISO)
mercury dichloride  (ISO)
methamphetamine  (EXP,ISO)
methylene blue  (ISO)
methylglyoxal  (ISO)
methylmercury chloride  (EXP,ISO)
methylseleninic acid  (ISO)
microcystin  (EXP)
microcystin LF  (ISO)
microcystin-LR  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (EXP)
mycophenolic acid  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nocodazole  (ISO)
norethisterone  (ISO)
okadaic acid  (EXP,ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP)
ozone  (ISO)
paclitaxel  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentachlorophenol  (ISO)
pentanal  (ISO)
pentetrazol  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenylarsine oxide  (EXP,ISO)
PhIP  (ISO)
phosgene  (ISO)
picoxystrobin  (ISO)
piericidin A  (ISO)
pirinixic acid  (ISO)
podophyllotoxin  (ISO)
potassium chloride  (EXP)
pravastatin  (EXP,ISO)
proanthocyanidin  (EXP)
progesterone  (EXP)
propanal  (ISO)
pyrithione  (EXP)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (EXP,ISO)
quinolinic acid  (ISO)
resveratrol  (EXP,ISO)
Ro 31-8220  (ISO)
rotenone  (EXP,ISO)
sarin  (ISO)
SB 203580  (EXP,ISO)
SB 431542  (ISO)
scopolamine  (EXP)
selenium atom  (EXP)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
Soman  (EXP)
staurosporine  (EXP,ISO)
streptozocin  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
tebufenpyrad  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetrathiomolybdate(2-)  (ISO)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
tributylstannane  (EXP,ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
Tryptanthrine  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
WIN 55212-2  (ISO)
wortmannin  (ISO)
Y-27632  (EXP)
zaragozic acid A  (EXP,ISO)
zinc acetate  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult walking behavior  (ISO)
amyloid fibril formation  (IEA,ISO)
apoptotic process  (IDA)
axo-dendritic transport  (ISO)
axon extension  (ISO)
axonogenesis  (ISO)
brain development  (IEP)
female pregnancy  (IEP)
intracellular distribution of mitochondria  (IEA,ISO)
intrinsic apoptotic signaling pathway in response to oxidative stress  (IDA)
learning or memory  (ISO)
memory  (IEA,IEP,ISO)
microtubule cytoskeleton organization  (IBA,IEA,ISO,ISS)
microtubule polymerization  (ISO)
microtubule-based process  (NAS)
mitochondrion transport along microtubule  (ISO)
mRNA transport  (IMP)
negative regulation of establishment of protein localization to mitochondrion  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of intracellular transport  (ISO)
negative regulation of kinase activity  (IEA,ISO)
negative regulation of mitochondrial fission  (IEA,ISO)
negative regulation of mitochondrial membrane potential  (IEA,ISO)
negative regulation of tubulin deacetylation  (IEA,ISO)
neuron differentiation  (NAS)
neuron migration  (ISO)
neuron projection development  (IBA)
positive regulation of axon extension  (IEA,ISO,ISS)
positive regulation of long-term synaptic depression  (IMP)
positive regulation of microtubule polymerization  (IEA,ISO,ISS)
positive regulation of neuron death  (IEA,ISO)
positive regulation of neuron projection development  (IMP)
positive regulation of protein localization  (IEA,ISO)
positive regulation of protein localization to synapse  (IEA,ISO)
positive regulation of superoxide anion generation  (IEA,ISO)
protein homooligomerization  (ISO)
protein polymerization  (IEA,ISO)
regulation of autophagy  (IEA,ISO)
regulation of calcium-mediated signaling  (IEA,ISO)
regulation of cellular response to heat  (IEA,ISO)
regulation of microtubule cytoskeleton organization  (ISO)
regulation of microtubule polymerization or depolymerization  (ISO)
regulation of microtubule-based movement  (ISO)
regulation of response to DNA damage stimulus  (IEA,ISO)
response to lead ion  (IDA)
response to nutrient  (IDA)
response to organic substance  (IDA)
supramolecular fiber organization  (ISO)
synapse assembly  (ISO)
synapse organization  (IEA,ISO)

Cellular Component
axolemma  (IEA,ISO)
axon  (IDA,IEA,ISO,ISS)
axonal growth cone  (IDA)
axoneme  (ISO)
cell body  (ISO)
cytoplasm  (IDA,ISO,ISS)
cytoplasmic ribonucleoprotein granule  (IEA,ISO)
cytoplasmic side of plasma membrane  (IDA)
cytosol  (IDA,IEA,ISO)
dendrite  (IDA,IEA,ISO,ISS)
extracellular region  (IEA)
glial cell projection  (ISO)
growth cone  (IEA,ISO,ISS)
main axon  (IDA)
membrane  (ISO)
membrane raft  (ISO)
microtubule  (IDA,IEA)
microtubule cytoskeleton  (IDA,ISO)
neurofibrillary tangle  (IEA,ISO)
neuron projection  (IBA,IDA)
neuronal cell body  (IDA,IEA,ISO)
nuclear periphery  (IEA,ISO)
nuclear speck  (IEA,ISO)
nucleus  (ISO)
plasma membrane  (IDA,IEA,ISO,ISS)
postsynaptic density  (ISO)
somatodendritic compartment  (ISO)
tubulin complex  (IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:1057175   PMID:1389180   PMID:1421571   PMID:1918161   PMID:2484340   PMID:2504728   PMID:2560640   PMID:3147150   PMID:7566652   PMID:7706316   PMID:7929085   PMID:7964751  
PMID:7972031   PMID:8202139   PMID:8245007   PMID:8408300   PMID:8522593   PMID:8642405   PMID:8855335   PMID:8889548   PMID:8990203   PMID:9736630   PMID:9763511   PMID:11826099  
PMID:11891784   PMID:12074840   PMID:12477932   PMID:12715101   PMID:12888622   PMID:14769047   PMID:15073173   PMID:15121898   PMID:15147841   PMID:15475565   PMID:15525651   PMID:15632090  
PMID:15654759   PMID:15834957   PMID:15939536   PMID:15975079   PMID:16137567   PMID:16176937   PMID:16446437   PMID:16536727   PMID:16554463   PMID:16714296   PMID:16753151   PMID:16816118  
PMID:16816120   PMID:16882358   PMID:16923168   PMID:16930434   PMID:17114649   PMID:17270732   PMID:17517623   PMID:17535890   PMID:17537547   PMID:17562708   PMID:17906291   PMID:18007203  
PMID:18202255   PMID:18272392   PMID:18289510   PMID:18289787   PMID:18403053   PMID:18424437   PMID:18460467   PMID:18506390   PMID:18725189   PMID:19004860   PMID:19046381   PMID:19071093  
PMID:19074461   PMID:19101570   PMID:19157893   PMID:19368808   PMID:19457097   PMID:19457109   PMID:19555739   PMID:19591849   PMID:19648118   PMID:19692427   PMID:19695252   PMID:19815707  
PMID:20045398   PMID:20061514   PMID:20232114   PMID:20338169   PMID:20379729   PMID:20398714   PMID:20503426   PMID:20508838   PMID:20513368   PMID:20568963   PMID:20655099   PMID:20659131  
PMID:20706749   PMID:20720012   PMID:20736167   PMID:20829454   PMID:20965859   PMID:21047784   PMID:21061060   PMID:21131359   PMID:21281610   PMID:21281635   PMID:21482827   PMID:21489990  
PMID:21613497   PMID:21633390   PMID:21683086   PMID:21756775   PMID:21854751   PMID:21983102   PMID:22055774   PMID:22456537   PMID:22460328   PMID:22528735   PMID:22767602   PMID:22833681  
PMID:22871113   PMID:22892311   PMID:22910909   PMID:22920254   PMID:22982863   PMID:23134599   PMID:23164821   PMID:23254634   PMID:23362255   PMID:23412472   PMID:23469846   PMID:23632019  
PMID:23666762   PMID:23906983   PMID:24251416   PMID:24270208   PMID:24722055   PMID:24983010   PMID:25051234   PMID:25079367   PMID:25079798   PMID:25165145   PMID:25212465   PMID:25217135  
PMID:25378699   PMID:25436420   PMID:25620700   PMID:25891085   PMID:26014385   PMID:26232997   PMID:26436840   PMID:26496899   PMID:26671463   PMID:26704708   PMID:26858248   PMID:26996940  
PMID:27044754   PMID:27185631   PMID:27255602   PMID:27356871   PMID:27428544   PMID:27699791   PMID:27760323   PMID:27914953   PMID:28104351   PMID:28132394   PMID:28258221   PMID:28271723  
PMID:28372990   PMID:28377597   PMID:28416463   PMID:28492240   PMID:28552936   PMID:28877993   PMID:29705343   PMID:30142893   PMID:30158706   PMID:30166454   PMID:30274285   PMID:30660367  
PMID:30894745   PMID:31189515   PMID:31201283   PMID:31344367   PMID:31698056   PMID:31918031   PMID:32247043   PMID:32357304   PMID:32385548   PMID:32737201   PMID:32881772   PMID:33564035  
PMID:33604685   PMID:33809910   PMID:34656177  


Genomics

Comparative Map Data
Mapt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21089,138,644 - 89,236,137 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1089,138,627 - 89,236,129 (+)Ensembl
Rnor_6.01092,289,002 - 92,386,517 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1092,288,910 - 92,386,517 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01092,050,754 - 92,147,840 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41093,411,098 - 93,508,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11093,425,375 - 93,523,128 (+)NCBI
Celera1087,832,730 - 87,930,191 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
MAPT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1745,894,527 - 46,028,334 (+)EnsemblGRCh38hg38GRCh38
GRCh381745,894,538 - 46,028,334 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371743,971,920 - 44,105,700 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361741,327,624 - 41,461,547 (+)NCBINCBI36hg18NCBI36
Build 341741,327,623 - 41,458,611NCBI
Celera1740,619,037 - 40,753,014 (+)NCBI
Cytogenetic Map17q21.31NCBI
HuRef1739,635,406 - 39,768,427 (+)NCBIHuRef
CHM1_11744,218,591 - 44,352,524 (+)NCBICHM1_1
Mapt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911104,120,235 - 104,222,916 (+)NCBIGRCm39mm39
GRCm39 Ensembl11104,122,216 - 104,222,916 (+)Ensembl
GRCm3811104,229,409 - 104,332,090 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11104,231,390 - 104,332,090 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711104,092,750 - 104,193,410 (+)NCBIGRCm37mm9NCBIm37
MGSCv3611104,047,526 - 104,148,186 (+)NCBImm8
Celera11115,951,246 - 116,057,990 (+)NCBICelera
Cytogenetic Map11E1NCBI
cM Map1167.79NCBI
Mapt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547810,225,823 - 10,271,442 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547810,222,439 - 10,271,439 (-)NCBIChiLan1.0ChiLan1.0
MAPT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11711,458,159 - 11,590,626 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1711,458,159 - 11,523,129 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01711,373,220 - 11,506,669 (+)NCBIMhudiblu_PPA_v0panPan3
MAPT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.199,572,174 - 9,674,082 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl99,570,557 - 9,674,349 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha910,679,514 - 10,725,761 (+)NCBI
ROS_Cfam_1.0911,161,388 - 11,263,326 (-)NCBI
UMICH_Zoey_3.1910,175,159 - 10,221,409 (-)NCBI
UNSW_CanFamBas_1.0917,303,033 - 17,349,281 (+)NCBI
UU_Cfam_GSD_1.0917,249,716 - 17,295,984 (+)NCBI
Mapt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560216,714,614 - 16,813,155 (-)NCBI
SpeTri2.0NW_0049365412,381,411 - 2,479,984 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MAPT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1217,095,587 - 17,211,368 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11217,098,259 - 17,211,483 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21217,123,502 - 17,234,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MAPT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11659,894,400 - 60,020,723 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1659,890,221 - 59,955,612 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607730,612,597 - 30,742,938 (-)NCBIVero_WHO_p1.0
Mapt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248492,320,887 - 2,421,099 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D10Wox21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,135,845 - 89,135,975 (+)MAPPERmRatBN7.2
Rnor_6.01092,286,199 - 92,286,328NCBIRnor6.0
Rnor_5.01092,047,951 - 92,048,080UniSTSRnor5.0
RGSC_v3.41093,408,294 - 93,408,423UniSTSRGSC3.4
Celera1087,829,949 - 87,830,068UniSTS
Cytogenetic Map10q32.1UniSTS
D10Chm236  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,163,076 - 89,163,326 (+)MAPPERmRatBN7.2
Rnor_6.01092,313,428 - 92,313,677NCBIRnor6.0
Rnor_5.01092,075,180 - 92,075,429UniSTSRnor5.0
RGSC_v3.41093,435,526 - 93,435,775UniSTSRGSC3.4
Celera1087,857,142 - 87,857,391UniSTS
Cytogenetic Map10q32.1UniSTS
Mapt  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10q32.1UniSTS
RH127601  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,235,748 - 89,235,937 (+)MAPPERmRatBN7.2
Rnor_6.01092,386,129 - 92,386,317NCBIRnor6.0
Rnor_5.01092,147,452 - 92,147,640UniSTSRnor5.0
RGSC_v3.41093,508,374 - 93,508,562UniSTSRGSC3.4
Celera1087,929,803 - 87,929,991UniSTS
RH 3.4 Map10924.29UniSTS
Cytogenetic Map10q32.1UniSTS
RH134050  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,148,207 - 89,148,400 (+)MAPPERmRatBN7.2
Rnor_6.01092,298,561 - 92,298,753NCBIRnor6.0
Rnor_5.01092,060,313 - 92,060,505UniSTSRnor5.0
RGSC_v3.41093,420,659 - 93,420,851UniSTSRGSC3.4
Celera1087,842,273 - 87,842,465UniSTS
RH 3.4 Map10917.3UniSTS
Cytogenetic Map10q32.1UniSTS
RH134151  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1087,916,504 - 87,916,712UniSTS
RH 3.4 Map10924.49UniSTS
Cytogenetic Map10q32.1UniSTS
AW532191  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,151,304 - 89,152,011 (+)MAPPERmRatBN7.2
Rnor_6.01092,301,658 - 92,302,364NCBIRnor6.0
Rnor_5.01092,063,410 - 92,064,116UniSTSRnor5.0
RGSC_v3.41093,423,756 - 93,424,462UniSTSRGSC3.4
Celera1087,845,372 - 87,846,078UniSTS
RH 3.4 Map10919.9UniSTS
Cytogenetic Map10q32.1UniSTS
BF405908  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,218,207 - 89,218,396 (+)MAPPERmRatBN7.2
Rnor_6.01092,368,555 - 92,368,743NCBIRnor6.0
Rnor_5.01092,130,307 - 92,130,495UniSTSRnor5.0
RGSC_v3.41093,490,661 - 93,490,849UniSTSRGSC3.4
Celera1087,912,281 - 87,912,469UniSTS
RH 3.4 Map10925.09UniSTS
Cytogenetic Map10q32.1UniSTS
RH135345  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,232,469 - 89,232,672 (+)MAPPERmRatBN7.2
Rnor_6.01092,382,850 - 92,383,052NCBIRnor6.0
Rnor_5.01092,144,168 - 92,144,370UniSTSRnor5.0
RGSC_v3.41093,505,060 - 93,505,262UniSTSRGSC3.4
Celera1087,926,522 - 87,926,726UniSTS
RH 3.4 Map10929.4UniSTS
Cytogenetic Map10q32.1UniSTS
RH138894  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,141,732 - 89,141,904 (+)MAPPERmRatBN7.2
Rnor_6.01092,292,087 - 92,292,258NCBIRnor6.0
Rnor_5.01092,053,839 - 92,054,010UniSTSRnor5.0
RGSC_v3.41093,414,183 - 93,414,354UniSTSRGSC3.4
Celera1087,835,815 - 87,835,986UniSTS
RH 3.4 Map10918.59UniSTS
Cytogenetic Map10q32.1UniSTS
G35712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,167,621 - 89,167,884 (+)MAPPERmRatBN7.2
Rnor_6.01092,317,973 - 92,318,235NCBIRnor6.0
Rnor_5.01092,079,725 - 92,079,987UniSTSRnor5.0
RGSC_v3.41093,440,071 - 93,440,333UniSTSRGSC3.4
Celera1087,861,687 - 87,861,949UniSTS
Cytogenetic Map10q32.1UniSTS
UniSTS:224586  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21089,233,403 - 89,233,568 (+)MAPPERmRatBN7.2
Rnor_6.01092,383,784 - 92,383,948NCBIRnor6.0
Rnor_5.01092,145,107 - 92,145,271UniSTSRnor5.0
RGSC_v3.41093,506,029 - 93,506,193UniSTSRGSC3.4
Celera1087,927,458 - 87,927,622UniSTS
Cytogenetic Map10q32.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
2313856Bp342Blood pressure QTL 3424.40.0001life span trait (VT:0005372)age at time of death (CMO:0001193)108730761796121100Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:349
Count of miRNA genes:90
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000006856, ENSRNOT00000006947, ENSRNOT00000042984, ENSRNOT00000043604, ENSRNOT00000045127, ENSRNOT00000045134, ENSRNOT00000050070
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 8 4 7 68 23 11 4
Low 3 25 49 33 19 33 4 4 6 12 40 4
Below cutoff 10 8 8 8 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085748 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC126095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG373604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA945776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB556982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB581821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB615367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB726905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB744947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO394225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO394568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO405139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO405815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D30628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D30629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ177309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY311887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M84156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X79321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X94916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006947   ⟹   ENSRNOP00000006947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,627 - 89,236,129 (+)Ensembl
Rnor_6.0 Ensembl1092,288,910 - 92,386,517 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042984   ⟹   ENSRNOP00000042392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,753 - 89,233,239 (+)Ensembl
Rnor_6.0 Ensembl1092,337,879 - 92,382,637 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000045127   ⟹   ENSRNOP00000051451
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,753 - 89,232,343 (+)Ensembl
Rnor_6.0 Ensembl1092,288,956 - 92,382,691 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000050070   ⟹   ENSRNOP00000040951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,753 - 89,232,343 (+)Ensembl
Rnor_6.0 Ensembl1092,289,107 - 92,382,723 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,159,541 - 89,192,808 (+)Ensembl
Rnor_6.0 Ensembl1092,289,055 - 92,343,176 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,195,202 - 89,232,311 (+)Ensembl
Rnor_6.0 Ensembl1092,344,292 - 92,364,061 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100910   ⟹   ENSRNOP00000077141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,627 - 89,236,129 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111184   ⟹   ENSRNOP00000079242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,753 - 89,232,343 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115998   ⟹   ENSRNOP00000097333
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1089,138,666 - 89,236,129 (+)Ensembl
RefSeq Acc Id: NM_017212   ⟹   NP_058908
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,648 - 89,236,137 (+)NCBI
Rnor_6.01092,289,002 - 92,386,517 (+)NCBI
Rnor_5.01092,050,754 - 92,147,840 (+)NCBI
RGSC_v3.41093,411,098 - 93,508,762 (+)RGD
Celera1087,832,730 - 87,930,191 (+)RGD
Sequence:
RefSeq Acc Id: XM_008768268   ⟹   XP_008766490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,042 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768269   ⟹   XP_008766491
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,048 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768270   ⟹   XP_008766492
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,042 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768272   ⟹   XP_008766494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,232,314 (+)NCBI
Rnor_6.01092,289,042 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768273   ⟹   XP_008766495
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,042 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768277   ⟹   XP_008766499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,232,257 (+)NCBI
Rnor_6.01092,289,048 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768278   ⟹   XP_008766500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,002 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768279   ⟹   XP_008766501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,048 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768280   ⟹   XP_008766502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,002 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768281   ⟹   XP_008766503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,232,310 (+)NCBI
Rnor_6.01092,289,002 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768282   ⟹   XP_008766504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
Rnor_6.01092,289,042 - 92,386,512 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085742   ⟹   XP_038941670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085743   ⟹   XP_038941671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085744   ⟹   XP_038941672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085745   ⟹   XP_038941673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085746   ⟹   XP_038941674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085747   ⟹   XP_038941675
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085748   ⟹   XP_038941676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085749   ⟹   XP_038941677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085750   ⟹   XP_038941678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085751   ⟹   XP_038941679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085752   ⟹   XP_038941680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085753   ⟹   XP_038941681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085754   ⟹   XP_038941682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085755   ⟹   XP_038941683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085756   ⟹   XP_038941684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,187,553 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085759   ⟹   XP_038941687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,191,567 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085760   ⟹   XP_038941688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,194,541 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085761   ⟹   XP_038941689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,202,520 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085762   ⟹   XP_038941690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,187,584 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085763   ⟹   XP_038941691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XM_039085764   ⟹   XP_038941692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,236,132 (+)NCBI
RefSeq Acc Id: XR_005489770
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21089,138,644 - 89,210,310 (+)NCBI
Protein Sequences
Protein RefSeqs NP_058908 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766490 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766491 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766492 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766494 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766495 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766499 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766500 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766501 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766502 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766503 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766504 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941670 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941671 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941672 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941673 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941674 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941675 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941676 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941677 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941678 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941679 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941680 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941681 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941682 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941683 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941684 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941687 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941688 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941689 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941690 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941691 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941692 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42204 (Get FASTA)   NCBI Sequence Viewer  
  AAI26096 (Get FASTA)   NCBI Sequence Viewer  
  ABA02201 (Get FASTA)   NCBI Sequence Viewer  
  CAA55889 (Get FASTA)   NCBI Sequence Viewer  
  EDM06297 (Get FASTA)   NCBI Sequence Viewer  
  EDM06298 (Get FASTA)   NCBI Sequence Viewer  
  EDM06299 (Get FASTA)   NCBI Sequence Viewer  
  EDM06300 (Get FASTA)   NCBI Sequence Viewer  
  EDM06301 (Get FASTA)   NCBI Sequence Viewer  
  EDM06302 (Get FASTA)   NCBI Sequence Viewer  
  EDM06303 (Get FASTA)   NCBI Sequence Viewer  
  EDM06304 (Get FASTA)   NCBI Sequence Viewer  
  EDM06305 (Get FASTA)   NCBI Sequence Viewer  
  EDM06306 (Get FASTA)   NCBI Sequence Viewer  
  EDM06307 (Get FASTA)   NCBI Sequence Viewer  
  EDM06308 (Get FASTA)   NCBI Sequence Viewer  
  EDM06309 (Get FASTA)   NCBI Sequence Viewer  
  EDM06310 (Get FASTA)   NCBI Sequence Viewer  
  P19332 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058908   ⟸   NM_017212
- UniProtKB: A0JN25 (UniProtKB/TrEMBL),   D3ZKD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766504   ⟸   XM_008768282
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008766492   ⟸   XM_008768270
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008766490   ⟸   XM_008768268
- Peptide Label: isoform X2
- UniProtKB: F1LST4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766491   ⟸   XM_008768269
- Peptide Label: isoform X27
- Sequence:
RefSeq Acc Id: XP_008766494   ⟸   XM_008768272
- Peptide Label: isoform X8
- UniProtKB: D4A1Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766495   ⟸   XM_008768273
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008766501   ⟸   XM_008768279
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_008766499   ⟸   XM_008768277
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_008766500   ⟸   XM_008768278
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_008766502   ⟸   XM_008768280
- Peptide Label: isoform X22
- Sequence:
RefSeq Acc Id: XP_008766503   ⟸   XM_008768281
- Peptide Label: isoform X26
- UniProtKB: A0JN25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000051451   ⟸   ENSRNOT00000045127
RefSeq Acc Id: ENSRNOP00000006947   ⟸   ENSRNOT00000006947
RefSeq Acc Id: ENSRNOP00000042392   ⟸   ENSRNOT00000042984
RefSeq Acc Id: ENSRNOP00000040951   ⟸   ENSRNOT00000050070
RefSeq Acc Id: XP_038941671   ⟸   XM_039085743
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038941673   ⟸   XM_039085745
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038941674   ⟸   XM_039085746
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038941678   ⟸   XM_039085750
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038941670   ⟸   XM_039085742
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941692   ⟸   XM_039085764
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038941675   ⟸   XM_039085747
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038941680   ⟸   XM_039085752
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038941676   ⟸   XM_039085748
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038941681   ⟸   XM_039085753
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038941672   ⟸   XM_039085744
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038941677   ⟸   XM_039085749
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038941682   ⟸   XM_039085754
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038941679   ⟸   XM_039085751
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038941683   ⟸   XM_039085755
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038941691   ⟸   XM_039085763
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038941684   ⟸   XM_039085756
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038941690   ⟸   XM_039085762
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038941687   ⟸   XM_039085759
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038941688   ⟸   XM_039085760
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038941689   ⟸   XM_039085761
- Peptide Label: isoform X24
RefSeq Acc Id: ENSRNOP00000097333   ⟸   ENSRNOT00000115998
RefSeq Acc Id: ENSRNOP00000079242   ⟸   ENSRNOT00000111184
RefSeq Acc Id: ENSRNOP00000077141   ⟸   ENSRNOT00000100910

Transcriptome

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

Promoters
RGD ID:13697820
Promoter ID:EPDNEW_R8344
Type:multiple initiation site
Name:Mapt_1
Description:microtubule-associated protein tau
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_6.01092,288,999 - 92,289,059EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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