Fasn (fatty acid synthase) - Rat Genome Database

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Gene: Fasn (fatty acid synthase) Rattus norvegicus
Analyze
Symbol: Fasn
Name: fatty acid synthase
RGD ID: 620665
Description: Enables [acyl-carrier-protein] S-malonyltransferase activity and identical protein binding activity. Involved in acetyl-CoA metabolic process and fatty acid biosynthetic process. Located in cytoplasm. Orthologous to human FASN (fatty acid synthase); PARTICIPATES IN fatty acid biosynthetic pathway; insulin signaling pathway; INTERACTS WITH (+)-catechin; (-)-epigallocatechin 3-gallate; (R)-mevalonic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: type I FAS
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
mRatBN7.210106,072,093 - 106,090,259 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10106,072,091 - 106,090,261 (-)Ensembl
Rnor_6.010109,987,735 - 110,005,901 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10109,987,735 - 110,005,901 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,579,051 - 109,597,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10104,615,873 - 104,634,039 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP,ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(R)-mevalonic acid  (EXP)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
(S)-nicotine  (EXP,ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
1-(3-(trifluoromethyl)phenyl)piperazine  (EXP)
1-\{2-[(4-chlorobenzyl)sulfanyl]-2-(2,4-dichlorophenyl)ethyl\}-1H-imidazole  (ISO)
1-benzylpiperazine  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,5-hexanedione  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP,ISO)
4'-Methoxychalcone  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-nonylphenol  (EXP)
4-phenylbutyric acid  (ISO)
4-tert-Octylphenol  (EXP)
5-(2-chloroethyl)-4-methylthiazole  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
7,12-dimethyltetraphene  (EXP)
8'-apo-beta,psi-caroten-8'-al  (ISO)
9-cis-retinoic acid  (ISO)
acadesine  (ISO)
acarbose  (EXP)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP)
alcohol  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
alliin  (ISO)
allopurinol  (EXP,ISO)
alpha-linolenic acid  (EXP)
alpha-pinene  (ISO)
amiodarone  (ISO)
amlexanox  (ISO)
andrographolide  (ISO)
antimycin A  (ISO)
apigenin  (ISO)
arachidonic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (EXP,ISO)
ATP  (ISO)
atrazine  (EXP,ISO)
avobenzone  (ISO)
azoxystrobin  (ISO)
baicalein  (ISO)
Bardoxolone methyl  (ISO)
bathocuproine disulfonic acid  (ISO)
benzene  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
Benzyl parahydroxybenzoate  (ISO)
benzylpenicillin  (ISO)
beta-D-glucosamine  (ISO)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (ISO)
betulin  (ISO)
bexarotene  (EXP,ISO)
bezafibrate  (EXP,ISO)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
boric acid  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (ISO)
Butylparaben  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP,ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carvedilol  (EXP)
celecoxib  (ISO)
cerulenin  (ISO)
chenodeoxycholic acid  (ISO)
chitosan  (EXP)
chloroethene  (ISO)
chlorogenic acid  (ISO)
chlorohydrocarbon  (ISO)
chloropicrin  (ISO)
chlorothalonil  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (EXP,ISO)
ciguatoxin CTX1B  (ISO)
cis-caffeic acid  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
clozapine  (ISO)
cobalt dichloride  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cortisol  (ISO)
coumarin  (EXP)
crizotinib  (ISO)
curcumin  (EXP,ISO)
cyanocob(III)alamin  (EXP)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cyhalothrin  (EXP)
cyproconazole  (EXP,ISO)
D-glucose  (EXP,ISO)
dapagliflozin  (EXP)
DDE  (ISO)
DDT  (EXP)
decabromodiphenyl ether  (EXP)
deguelin  (ISO)
deoxypodophyllotoxin  (ISO)
dexamethasone  (EXP,ISO)
Di-n-hexyl phthalate  (ISO)
Diallyl sulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
diclofenac  (EXP)
dicrotophos  (ISO)
diethyl maleate  (EXP)
dihydroartemisinin  (ISO)
Diosbulbin B  (ISO)
dioxygen  (ISO)
dorsomorphin  (EXP,ISO)
doxorubicin  (ISO)
duvoglustat  (ISO)
elemental selenium  (EXP,ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
epoxiconazole  (EXP)
erythromycin A  (ISO)
erythromycin estolate  (EXP)
esculetin  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
eugenol  (ISO)
farnesol  (ISO)
fenofibrate  (EXP,ISO)
ferulic acid  (ISO)
fipronil  (ISO)
folic acid  (EXP,ISO)
folpet  (ISO)
formaldehyde  (ISO)
fructose  (EXP,ISO)
fulvestrant  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP,ISO)
gamma-hexachlorocyclohexane  (EXP)
Ganoderic acid A  (ISO)
Gastrodin  (ISO)
genistein  (ISO)
geraniol  (EXP)
gingerol  (ISO)
glafenine  (EXP)
glucagon  (ISO)
glucose  (EXP,ISO)
glutathione  (EXP,ISO)
glycine betaine  (EXP)
glyphosate  (ISO)
graphene oxide  (ISO)
guggulsterone  (ISO)
GW 3965  (ISO)
GW 4064  (ISO)
GW 6471  (ISO)
GW 7647  (ISO)
haloperidol  (ISO)
herbacetin  (ISO)
hesperidin  (ISO)
hexadecanoic acid  (EXP,ISO)
hydrazines  (ISO)
ibuprofen  (ISO)
indinavir  (ISO)
indometacin  (ISO)
isoflavones  (EXP)
isotretinoin  (ISO)
ivermectin  (ISO)
kahweol  (ISO)
L-methionine  (EXP,ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
linoleic acid  (EXP)
linsidomine  (EXP)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
losartan  (EXP)
lovastatin  (ISO)
luteolin  (ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP)
melatonin  (ISO)
metformin  (EXP,ISO)
methapyrilene  (EXP)
methimazole  (ISO)
methotrexate  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
Mitotane  (ISO)
mitoxantrone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (EXP,ISO)
motexafin gadolinium  (ISO)
myriocin  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
naloxone  (EXP)
naringin  (ISO)
nefazodone  (EXP)
nelfinavir  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (ISO)
nicotine  (EXP,ISO)
nicotinic acid  (ISO)
nimesulide  (EXP)
nitrofen  (EXP)
norethisterone  (ISO)
Norethynodrel  (ISO)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
olanzapine  (ISO)
olaparib  (ISO)
oleic acid  (EXP,ISO)
oleuropein  (EXP)
Olmesartan medoxomil  (EXP)
orlistat  (ISO)
oroxylin A  (ISO)
ozone  (EXP,ISO)
p-tert-Amylphenol  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
Paxilline  (ISO)
PD 0325901  (ISO)
penconazole  (ISO)
perfluorobutanesulfonic acid  (ISO)
perfluorobutyric acid  (EXP)
perfluorododecanoic acid  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
phosphatidylcholine  (ISO)
phosphocholine  (ISO)
phosphorylcholine chloride  (ISO)
pimecrolimus  (ISO)
pirinixic acid  (EXP,ISO)
platycodin D  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
procymidone  (ISO)
propamocarb  (ISO)
propiconazole  (ISO)
Propiverine  (EXP)
propylparaben  (ISO)
prostaglandin E2  (ISO)
protein kinase inhibitor  (ISO)
pterostilbene  (EXP)
puerarin  (ISO)
PX-866  (ISO)
pyrroloquinoline quinone  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
raffinose  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rimonabant  (ISO)
ritonavir  (EXP)
rotenone  (EXP,ISO)
S-allylcysteine  (ISO)
SB 431542  (ISO)
scopoletin  (EXP)
selenium atom  (EXP,ISO)
sildenafil citrate  (ISO)
silibinin  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP)
stavudine  (ISO)
steviol  (ISO)
streptozocin  (EXP,ISO)
sucrose  (ISO)
sulconazole  (ISO)
sulforaphane  (EXP)
sulindac  (ISO)
sunitinib  (ISO)
tamoxifen  (EXP,ISO)
taurine  (ISO)
tebuconazole  (ISO)
temozolomide  (ISO)
teriflunomide  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thiazolidinediones  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trametinib  (ISO)
trans-caffeic acid  (ISO)
tributylstannane  (ISO)
trichloroethene  (ISO)
triclocarban  (EXP)
triclosan  (EXP,ISO)
triolein  (ISO)
triphenyl phosphate  (EXP,ISO)
Triptolide  (ISO)
troglitazone  (EXP,ISO)
trovafloxacin  (EXP,ISO)
tungsten  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vemurafenib  (ISO)
vorinostat  (ISO)
yohimbine  (ISO)
zidovudine  (ISO)
zinc acetate  (ISO)
zinc atom  (EXP)
zinc dichloride  (ISO)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
cytosol  (ISO,TAS)
glycogen granule  (ISO)
Golgi apparatus  (IEA,ISO)
melanosome  (IEA)
plasma membrane  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alberdi G, etal., Nutr Metab (Lond). 2011 May 10;8(1):29. doi: 10.1186/1743-7075-8-29.
2. Amy CM, etal., Proc Natl Acad Sci U S A 1989 May;86(9):3114-8.
3. Asturias FJ, etal., Nat Struct Mol Biol. 2005 Mar;12(3):225-32. Epub 2005 Feb 13.
4. Beck KF, etal., DNA Seq 1992;2(6):359-86.
5. Brignole EJ, etal., Nat Struct Mol Biol. 2009 Feb;16(2):190-7. Epub 2009 Jan 18.
6. Chirala SS, etal., Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3104-8.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Huong DT and Ide T, Br J Nutr. 2008 Jul;100(1):79-87. Epub 2007 Dec 7.
9. Joshi AK, etal., Biochemistry. 1997 Feb 25;36(8):2316-22.
10. Menendez JA and Lupu R, Nat Rev Cancer. 2007 Oct;7(10):763-77.
11. Menendez JA, etal., Clin Chem. 2009 Mar;55(3):425-38. Epub 2009 Jan 30.
12. Moon YS, etal., J Lipid Res 2002 May;43(5):691-8.
13. Naggert J, etal., J Biol Chem 1988 Jan 25;263(3):1146-50.
14. Najjar SM, etal., Cell Metab. 2005 Jul;2(1):43-53.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pipeline to import SMPDB annotations from SMPDB into RGD
18. Rangan VS and Smith S, J Biol Chem. 1996 Dec 6;271(49):31749-55. doi: 10.1074/jbc.271.49.31749.
19. Rendina AR and Cheng D, Biochem J. 2005 Jun 15;388(Pt 3):895-903.
20. RGD automated data pipeline
21. RGD automated import pipeline for gene-chemical interactions
22. RGD comprehensive gene curation
23. Schweizer M, etal., Nucleic Acids Res 1989 Jan 25;17(2):567-86.
24. Silva SD, etal., Oral Dis. 2010 Nov;16(8):774-80. doi: 10.1111/j.1601-0825.2010.01687.x.
25. Witkowski A, etal., J Biol Chem. 1999 Apr 23;274(17):11557-63.
26. Wu M, etal., Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5378-83. doi: 10.1073/pnas.1002588108. Epub 2011 Mar 9.
Additional References at PubMed
PMID:1736293   PMID:2313386   PMID:3109907   PMID:9798653   PMID:12440974   PMID:12634446   PMID:12759350   PMID:12926246   PMID:15169678   PMID:15610851   PMID:15887043   PMID:15983196  
PMID:16210410   PMID:16800817   PMID:16834571   PMID:17313375   PMID:17709201   PMID:17823126   PMID:18079124   PMID:18096506   PMID:18239060   PMID:18280001   PMID:18380011   PMID:18614015  
PMID:19056867   PMID:19182904   PMID:19946888   PMID:20458337   PMID:20729114   PMID:22331133   PMID:22658674   PMID:22681889   PMID:22871113   PMID:23357280   PMID:23533145   PMID:24668799  
PMID:25046614   PMID:25468996   PMID:25565205   PMID:26246323   PMID:26287659   PMID:27923787   PMID:28027934   PMID:28810876   PMID:29097254   PMID:29476059   PMID:31465767   PMID:32357304  
PMID:33450132  


Genomics

Comparative Map Data
Fasn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210106,072,093 - 106,090,259 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10106,072,091 - 106,090,261 (-)Ensembl
Rnor_6.010109,987,735 - 110,005,901 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10109,987,735 - 110,005,901 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,579,051 - 109,597,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10104,615,873 - 104,634,039 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
FASN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1782,078,338 - 82,098,294 (-)EnsemblGRCh38hg38GRCh38
GRCh381782,078,338 - 82,098,303 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371780,036,214 - 80,056,112 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361777,629,503 - 77,649,395 (-)NCBINCBI36hg18NCBI36
Build 341777,629,503 - 77,649,395NCBI
Celera1776,630,560 - 76,648,850 (-)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1775,436,168 - 75,456,057 (-)NCBIHuRef
CHM1_11780,122,440 - 80,142,272 (-)NCBICHM1_1
Fasn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911120,696,784 - 120,715,992 (-)NCBIGRCm39mm39
GRCm39 Ensembl11120,696,672 - 120,715,373 (-)Ensembl
GRCm3811120,805,958 - 120,825,166 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,805,846 - 120,824,547 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711120,667,272 - 120,685,861 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611120,623,167 - 120,640,332 (-)NCBImm8
Celera11132,542,449 - 132,561,038 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1184.56NCBI
Fasn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555061,063,002 - 1,079,939 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555061,063,002 - 1,079,939 (+)NCBIChiLan1.0ChiLan1.0
FASN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11782,187,516 - 82,205,647 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1782,187,516 - 82,205,647 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01776,483,108 - 76,503,148 (-)NCBIMhudiblu_PPA_v0panPan3
FASN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.19233,105 - 249,573 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl9232,963 - 249,092 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha9835,096 - 852,365 (+)NCBI
ROS_Cfam_1.09826,552 - 843,813 (+)NCBI
UMICH_Zoey_3.19851,506 - 868,761 (+)NCBI
UNSW_CanFamBas_1.09978,401 - 995,678 (+)NCBI
UU_Cfam_GSD_1.091,056,702 - 1,073,992 (+)NCBI
Fasn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602802,978 - 820,174 (+)NCBI
SpeTri2.0NW_0049365945,591,785 - 5,609,886 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FASN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl12920,507 - 937,559 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.112922,405 - 937,560 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2121,023,512 - 1,032,662 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FASN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11673,988,410 - 74,008,374 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1673,982,899 - 74,006,551 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607745,523,735 - 45,543,679 (-)NCBIVero_WHO_p1.0
Fasn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480110,910,022 - 10,926,505 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129091  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210106,072,888 - 106,073,047 (+)MAPPERmRatBN7.2
Rnor_6.010109,988,531 - 109,988,689NCBIRnor6.0
Rnor_5.010109,579,847 - 109,580,005UniSTSRnor5.0
Celera10104,616,669 - 104,616,827UniSTS
RH141092  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210106,072,153 - 106,072,361 (+)MAPPERmRatBN7.2
Rnor_6.010109,987,796 - 109,988,003NCBIRnor6.0
Rnor_5.010109,579,112 - 109,579,319UniSTSRnor5.0
Celera10104,615,934 - 104,616,141UniSTS
PMC156147P10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210106,075,242 - 106,075,353 (+)MAPPERmRatBN7.2
Rnor_6.010109,990,885 - 109,990,995NCBIRnor6.0
Rnor_5.010109,582,201 - 109,582,311UniSTSRnor5.0
Celera10104,619,023 - 104,619,133UniSTS
PMC207565P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210106,084,121 - 106,084,204 (+)MAPPERmRatBN7.2
Rnor_6.010109,999,764 - 109,999,846NCBIRnor6.0
Rnor_5.010109,591,080 - 109,591,162UniSTSRnor5.0
Celera10104,627,902 - 104,627,984UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
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
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
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
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
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
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
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
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:601
Count of miRNA genes:277
Interacting mature miRNAs:330
Transcripts:ENSRNOT00000073321
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 3 2
Medium 3 30 49 36 17 36 4 4 74 33 40 11 4
Low 13 5 5 5 4 7 2 1 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073321   ⟹   ENSRNOP00000064445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,072,091 - 106,090,261 (-)Ensembl
Rnor_6.0 Ensembl10109,987,735 - 110,005,901 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100099   ⟹   ENSRNOP00000087318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,072,091 - 106,089,994 (-)Ensembl
RefSeq Acc Id: NM_017332   ⟹   NP_059028
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,072,093 - 106,090,259 (-)NCBI
Rnor_6.010109,987,735 - 110,005,901 (-)NCBI
Rnor_5.010109,579,051 - 109,597,217 (-)NCBI
Celera10104,615,873 - 104,634,039 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_059028   ⟸   NM_017332
- Sequence:
RefSeq Acc Id: ENSRNOP00000064445   ⟸   ENSRNOT00000073321
RefSeq Acc Id: ENSRNOP00000087318   ⟸   ENSRNOT00000100099
Protein Domains
Carrier

Transcriptome

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

Promoters
RGD ID:13697980
Promoter ID:EPDNEW_R8505
Type:single initiation site
Name:Fasn_1
Description:fatty acid synthase
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_6.010110,005,903 - 110,005,963EPDNEW

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)
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: 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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)