Fdft1 (farnesyl diphosphate farnesyl transferase 1) - Rat Genome Database
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Gene: Fdft1 (farnesyl diphosphate farnesyl transferase 1) Rattus norvegicus
Analyze
Symbol: Fdft1
Name: farnesyl diphosphate farnesyl transferase 1
RGD ID: 61834
Description: Exhibits farnesyl-diphosphate farnesyltransferase activity. Involved in cholesterol biosynthetic process and farnesyl diphosphate metabolic process. Localizes to endoplasmic reticulum membrane. Used to study cataract. Orthologous to human FDFT1 (farnesyl-diphosphate farnesyltransferase 1); PARTICIPATES IN cholesterol biosynthetic pathway; alendronate pharmacodynamics pathway; cholesterol ester storage disease pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1-(3-(trifluoromethyl)phenyl)piperazine; 1-benzylpiperazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: farnesyl diphosphate farnesyltransferase; farnesyl-diphosphate farnesyltransferase; FPP:FPP farnesyltransferase; MGC93486; SQS; squalene synthase; squalene synthetase; SS
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SCR/Sscr  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21537,412,143 - 37,440,198 (-)NCBI
Rnor_6.0 Ensembl1546,339,249 - 46,367,302 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01546,339,248 - 46,367,302 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01550,104,042 - 50,132,096 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,425,336 - 42,453,390 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11542,442,550 - 42,469,109 (-)NCBI
Celera1537,096,417 - 37,124,524 (-)NCBICelera
Cytogenetic Map15p12NCBI
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
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
1-(3-(trifluoromethyl)phenyl)piperazine  (EXP)
1-benzylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (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)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
22-Hydroxycholesterol  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
antimony(0)  (ISO)
avobenzone  (ISO)
Azaspiracid  (ISO)
benzbromarone  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butan-1-ol  (ISO)
caffeine  (EXP)
captan  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
cholesterol  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (EXP)
cocaine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
dichloromethane  (ISO)
difenoconazole  (EXP)
dinophysistoxin 1  (ISO)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
farnesol  (ISO)
fenarimol  (EXP)
fenofibrate  (ISO)
fluoranthene  (ISO)
flusilazole  (EXP,ISO)
fluvastatin  (ISO)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
GW 4064  (ISO)
hexaconazole  (ISO)
hydrogen peroxide  (ISO)
isoflavones  (ISO)
isotretinoin  (ISO)
ketamine  (EXP)
ketoconazole  (EXP)
L-ethionine  (EXP)
lead nitrate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lovastatin  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
mitomycin C  (ISO)
mitoxantrone  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
omeprazole  (EXP)
ozone  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
perfluorobutanesulfonic acid  (EXP)
perfluorobutyric acid  (EXP)
perfluorododecanoic acid  (EXP)
perfluorohexanesulfonic acid  (EXP,ISO)
perfluorohexanoic acid  (EXP)
perfluorononanoic acid  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
perfluoroundecanoic acid  (EXP)
phencyclidine  (ISO)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
phenylpropanolamine  (ISO)
phosgene  (ISO)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
potassium dichromate  (ISO)
pravastatin  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propiconazole  (EXP)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
selenium atom  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (ISO)
triadimefon  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
Yessotoxin  (ISO)
zoledronic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:15489334   PMID:17460354  


Genomics

Comparative Map Data
Fdft1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21537,412,143 - 37,440,198 (-)NCBI
Rnor_6.0 Ensembl1546,339,249 - 46,367,302 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01546,339,248 - 46,367,302 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01550,104,042 - 50,132,096 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,425,336 - 42,453,390 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11542,442,550 - 42,469,109 (-)NCBI
Celera1537,096,417 - 37,124,524 (-)NCBICelera
Cytogenetic Map15p12NCBI
FDFT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl811,795,573 - 11,839,304 (+)EnsemblGRCh38hg38GRCh38
GRCh38811,795,582 - 11,839,309 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37811,653,091 - 11,696,818 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36811,697,599 - 11,734,227 (+)NCBINCBI36hg18NCBI36
Build 34811,697,663 - 11,734,215NCBI
Celera810,789,513 - 10,826,122 (+)NCBI
Cytogenetic Map8p23.1NCBI
HuRef810,591,147 - 10,627,774 (+)NCBIHuRef
CHM1_1811,718,559 - 11,762,299 (+)NCBICHM1_1
Fdft1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391463,382,599 - 63,419,136 (-)NCBIGRCm39mm39
GRCm39 Ensembl1463,382,599 - 63,417,027 (-)Ensembl
GRCm381463,145,150 - 63,181,687 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1463,145,150 - 63,179,578 (-)EnsemblGRCm38mm10GRCm38
MGSCv371463,763,987 - 63,796,630 (-)NCBIGRCm37mm9NCBIm37
MGSCv361462,099,260 - 62,131,903 (-)NCBImm8
Celera1460,907,922 - 60,941,524 (-)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1433.24NCBI
Fdft1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540353,067,637 - 53,081,499 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540353,068,011 - 53,081,499 (+)NCBIChiLan1.0ChiLan1.0
FDFT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v087,363,250 - 7,399,863 (-)NCBIMhudiblu_PPA_v0panPan3
FDFT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2526,060,386 - 26,093,582 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12526,060,031 - 26,093,515 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fdft1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366283,599,435 - 3,600,061 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FDFT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1414,967,273 - 15,104,179 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11414,976,259 - 15,010,701 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21416,164,964 - 16,199,406 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FDFT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.187,272,580 - 7,306,859 (-)NCBI
ChlSab1.1 Ensembl87,271,509 - 7,306,760 (-)Ensembl
Fdft1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475825,340,142 - 25,363,669 (+)NCBI

Position Markers
RH128506  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01546,339,330 - 46,339,516NCBIRnor6.0
Rnor_5.01550,104,124 - 50,104,310UniSTSRnor5.0
RGSC_v3.41542,425,418 - 42,425,604UniSTSRGSC3.4
Celera1537,096,499 - 37,096,685UniSTS
RH 3.4 Map15269.5UniSTS
Cytogenetic Map15p12UniSTS
RH133832  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01546,340,867 - 46,341,082NCBIRnor6.0
Rnor_5.01550,105,661 - 50,105,876UniSTSRnor5.0
RGSC_v3.41542,426,955 - 42,427,170UniSTSRGSC3.4
Celera1537,098,036 - 37,098,251UniSTS
Cytogenetic Map15p12UniSTS
BE105722  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01546,338,980 - 46,339,148NCBIRnor6.0
Rnor_5.01550,103,774 - 50,103,942UniSTSRnor5.0
RGSC_v3.41542,425,068 - 42,425,236UniSTSRGSC3.4
Celera1537,096,149 - 37,096,317UniSTS
RH 3.4 Map15272.2UniSTS
Cytogenetic Map15p12UniSTS
AI176781  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01546,338,903 - 46,339,102NCBIRnor6.0
Rnor_5.01550,103,697 - 50,103,896UniSTSRnor5.0
RGSC_v3.41542,424,991 - 42,425,190UniSTSRGSC3.4
Celera1537,096,072 - 37,096,271UniSTS
RH 3.4 Map15270.3UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154309747052831189Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat


Related Rat Strains
The following Strains have been annotated to Fdft1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:454
Count of miRNA genes:244
Interacting mature miRNAs:298
Transcripts:ENSRNOT00000032089
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032089   ⟹   ENSRNOP00000029808
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1546,339,249 - 46,367,302 (-)Ensembl
RefSeq Acc Id: NM_019238   ⟹   NP_062111
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21537,412,143 - 37,440,198 (-)NCBI
Rnor_6.01546,339,248 - 46,367,302 (-)NCBI
Rnor_5.01550,104,042 - 50,132,096 (-)NCBI
RGSC_v3.41542,425,336 - 42,453,390 (-)RGD
Celera1537,096,417 - 37,124,524 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062111   ⟸   NM_019238
- UniProtKB: Q02769 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000029808   ⟸   ENSRNOT00000032089

Transcriptome

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

Promoters
RGD ID:13699776
Promoter ID:EPDNEW_R10298
Type:initiation region
Name:Fdft1_1
Description:farnesyl diphosphate farnesyl transferase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01546,367,315 - 46,367,375EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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)
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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/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 (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)
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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/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
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 50111176 50111177 C A snv DOB/Oda (KyushuU)
15 50111177 50111178 T C snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61834 AgrOrtholog
Ensembl Genes ENSRNOG00000021314 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000029808 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000032089 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.600.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7188993 IMAGE-MGC_LOAD
InterPro Isoprenoid_synthase_dom_sf UniProtKB/Swiss-Prot
  Squ/phyt_synthse UniProtKB/Swiss-Prot
  Squal_synth-like UniProtKB/Swiss-Prot
  Squalene/phytoene_synthase_CS UniProtKB/Swiss-Prot
  Trans_IPPS_HH UniProtKB/Swiss-Prot
KEGG Report rno:29580 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93486 IMAGE-MGC_LOAD
NCBI Gene 29580 ENTREZGENE
PhenoGen Fdft1 PhenoGen
PROSITE SQUALEN_PHYTOEN_SYN_1 UniProtKB/Swiss-Prot
  SQUALEN_PHYTOEN_SYN_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48576 UniProtKB/Swiss-Prot
TIGR TC229595
TIGRFAMs squal_synth UniProtKB/Swiss-Prot
UniProt FDFT_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Fdft1  farnesyl diphosphate farnesyl transferase 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference