Fdps (farnesyl diphosphate synthase) - Rat Genome Database
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Gene: Fdps (farnesyl diphosphate synthase) Rattus norvegicus
Analyze
Symbol: Fdps
Name: farnesyl diphosphate synthase
RGD ID: 68953
Description: Exhibits geranyltranstransferase activity. Involved in several processes, including farnesyl diphosphate biosynthetic process; positive regulation of cell growth involved in cardiac muscle cell development; and positive regulation of cholesterol biosynthetic process. Localizes to mitochondrial matrix and peroxisome. Human ortholog(s) of this gene implicated in porokeratosis. Orthologous to human FDPS (farnesyl diphosphate synthase); PARTICIPATES IN alendronate pharmacodynamics pathway; cholesterol biosynthetic pathway; cholesterol ester storage disease pathway; INTERACTS WITH 1-(3-(trifluoromethyl)phenyl)piperazine; 1-benzylpiperazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: (2E,6E)-farnesyl diphosphate synthase; Ac2-125; cholesterol-regulated 39 kDa protein; CR 39; dimethylallyltranstransferase; farensyl diphosphate synthase; farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase); farnesyl diphosphate synthetase; farnesyl pyrophosphate synthase; farnesyl pyrophosphate synthetase; Farnesyldiphosphate synthase; FPP synthase; FPP synthetase; FPS; geranyltranstransferase; testis-specific farnesyl pyrophosphate synthetase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22174,497,402 - 174,507,031 (-)NCBI
Rnor_6.0 Ensembl2188,392,858 - 188,413,219 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02188,403,595 - 188,413,219 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02207,816,332 - 207,826,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42181,138,474 - 181,177,903 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12181,119,007 - 181,128,009 (-)NCBI
Celera2168,441,483 - 168,451,110 (-)NCBICelera
Cytogenetic Map2q34NCBI
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-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-(3-(trifluoromethyl)phenyl)piperazine  (EXP)
1-benzylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (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)
2,4-diaminotoluene  (ISO)
2,4-dinitrotoluene  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
3H-1,2-dithiole-3-thione  (EXP,ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
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)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
Actein  (EXP)
aflatoxin B1  (ISO)
alachlor  (EXP)
alendronic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
antimony(0)  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
Azaspiracid  (ISO)
benzbromarone  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
chloroethene  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clozapine  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichloromethane  (ISO)
diethylstilbestrol  (ISO)
dinophysistoxin 1  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
glafenine  (EXP)
hexaconazole  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
iodide salt  (EXP)
isopentenyl diphosphate  (ISO)
isotretinoin  (ISO)
L-ethionine  (EXP)
lead nitrate  (EXP)
lovastatin  (ISO)
manganese(II) chloride  (EXP)
methyl methanesulfonate  (ISO)
methyltestosterone  (ISO)
miconazole  (ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monosodium L-glutamate  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (ISO)
N-nitrosomorpholine  (EXP)
nickel dichloride  (ISO)
obeticholic acid  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
omeprazole  (EXP)
ozone  (EXP)
paclitaxel  (ISO)
pamidronate  (EXP,ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenylpropanolamine  (ISO)
pinosylvin  (ISO)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
quinolin-8-ol  (ISO)
resveratrol  (ISO)
Risedronate sodium  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
trans-pinosylvin  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
zoledronic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Ashby MN and Edwards PA, J Biol Chem. 1989 Jan 5;264(1):635-40.
2. CIBICKOVA L, etal., Physiol Res. 2009;58(3):455-8. Epub 2008 Jul 18.
3. Clarke CF, etal., Mol Cell Biol 1987 Sep;7(9):3138-46.
4. Dracheva SV, etal., Genomics 2000 Jan 15;63(2):202-26.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Gupta SD, etal., J Lipid Res. 1999 Sep;40(9):1572-84.
8. Heemers H, etal., Mol Cell Endocrinol. 2003 Jul 31;205(1-2):21-31.
9. KEGG
10. Kovacs WJ, etal., Histochem Cell Biol. 2007 Mar;127(3):273-90. Epub 2006 Dec 19.
11. Krisans SK, etal., J Biol Chem. 1994 May 13;269(19):14165-9.
12. Le Jossic-Corcos C, etal., Biochem J. 2005 Feb 1;385(Pt 3):787-94.
13. Le Jossic-Corcos C, etal., J Steroid Biochem Mol Biol. 2004 Feb;88(2):203-11.
14. Nazian SJ, etal., J Androl. 1991 Jul-Aug;12(4):264-72.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. OMIM Disease Annotation Pipeline
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Pipeline to import SMPDB annotations from SMPDB into RGD
19. Remmers EF, etal., Transplant Proc 1999 May;31(3):1549-54.
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Runquist M, etal., J Biol Chem. 1994 Feb 25;269(8):5804-9.
24. Spear DH, etal., J Biol Chem 1992 Jul 15;267(20):14462-9.
25. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
26. Teruya JH, etal., Biol Reprod. 1991 Apr;44(4):663-71.
27. Teruya JH, etal., Mol Cell Biol 1990 May;10(5):2315-26.
28. Waterham HR FEBS Lett. 2006 Oct 9;580(23):5442-9. Epub 2006 Jul 20.
29. Ye Y, etal., FEBS Lett. 2009 Sep 17;583(18):2997-3003. Epub 2009 Aug 28.
Additional References at PubMed
PMID:18614015   PMID:19800872   PMID:22658674   PMID:24527834   PMID:24625528   PMID:25847782  


Genomics

Comparative Map Data
Fdps
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22174,497,402 - 174,507,031 (-)NCBI
Rnor_6.0 Ensembl2188,392,858 - 188,413,219 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02188,403,595 - 188,413,219 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02207,816,332 - 207,826,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42181,138,474 - 181,177,903 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12181,119,007 - 181,128,009 (-)NCBI
Celera2168,441,483 - 168,451,110 (-)NCBICelera
Cytogenetic Map2q34NCBI
FDPS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1155,308,748 - 155,320,666 (+)EnsemblGRCh38hg38GRCh38
GRCh381155,308,801 - 155,320,665 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371155,278,657 - 155,290,456 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361153,545,374 - 153,557,080 (+)NCBINCBI36hg18NCBI36
Build 341152,092,649 - 152,103,529NCBI
Celera1128,351,680 - 128,363,599 (+)NCBI
Cytogenetic Map1q22NCBI
HuRef1126,640,838 - 126,652,759 (+)NCBIHuRef
CHM1_11156,673,976 - 156,685,898 (+)NCBICHM1_1
Fdps
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39389,000,895 - 89,009,274 (-)NCBIGRCm39mm39
GRCm39 Ensembl389,000,895 - 89,009,266 (-)Ensembl
GRCm38389,093,588 - 89,101,967 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl389,093,588 - 89,101,959 (-)EnsemblGRCm38mm10GRCm38
MGSCv37388,897,510 - 88,905,867 (-)NCBIGRCm37mm9NCBIm37
MGSCv36389,179,515 - 89,187,872 (-)NCBImm8
Celera389,132,279 - 89,140,636 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map339.01NCBI
Fdps
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555451,757,418 - 1,765,028 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555451,757,090 - 1,765,028 (+)NCBIChiLan1.0ChiLan1.0
FDPS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11134,258,881 - 134,270,237 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1134,258,968 - 134,270,237 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01130,653,316 - 130,665,196 (+)NCBIMhudiblu_PPA_v0panPan3
FDPS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl742,241,107 - 42,250,225 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1742,241,086 - 42,250,373 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fdps
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365804,799,354 - 4,808,406 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FDPS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl494,489,215 - 94,518,408 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1494,500,140 - 94,514,820 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24103,291,797 - 103,304,940 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FDPS
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1208,514,311 - 8,526,363 (-)NCBI
Fdps
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624885942,998 - 949,529 (+)NCBI

Position Markers
D2Arb36  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02188,413,570 - 188,413,781NCBIRnor6.0
Rnor_5.02207,826,699 - 207,826,910UniSTSRnor5.0
RGSC_v3.42181,178,253 - 181,178,466RGDRGSC3.4
RGSC_v3.42181,178,254 - 181,178,466UniSTSRGSC3.4
RGSC_v3.12181,128,359 - 181,128,572RGD
Celera2168,451,461 - 168,451,672UniSTS
Cytogenetic Map2q34UniSTS
RH127967  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q34UniSTS
AA408288  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02188,394,145 - 188,394,315NCBIRnor6.0
Rnor_5.02207,806,504 - 207,806,674UniSTSRnor5.0
RGSC_v3.42181,157,880 - 181,158,050UniSTSRGSC3.4
Celera2168,432,196 - 168,432,366UniSTS
Cytogenetic Map2q34UniSTS
AW534365  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02188,394,529 - 188,394,647NCBIRnor6.0
Rnor_5.02207,806,888 - 207,807,006UniSTSRnor5.0
RGSC_v3.42181,158,264 - 181,158,382UniSTSRGSC3.4
Celera2168,432,580 - 168,432,698UniSTS
RH 3.4 Map21160.7UniSTS
Cytogenetic Map2q34UniSTS
RH128237  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02188,394,246 - 188,394,426NCBIRnor6.0
Rnor_5.02207,806,605 - 207,806,785UniSTSRnor5.0
RGSC_v3.42181,157,981 - 181,158,161UniSTSRGSC3.4
Celera2168,432,297 - 168,432,477UniSTS
RH 3.4 Map21156.2UniSTS
Cytogenetic Map2q34UniSTS
BQ193911  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02188,392,886 - 188,393,044NCBIRnor6.0
Rnor_5.02207,805,245 - 207,805,403UniSTSRnor5.0
RGSC_v3.42181,156,621 - 181,156,779UniSTSRGSC3.4
Celera2168,430,937 - 168,431,095UniSTS
RH 3.4 Map21162.0UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2157914311204022555Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2140566078217498545Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2147522550217498710Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
61473Bp19Blood pressure QTL 196.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2186611811189857032Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141583337217498710Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2142053350204585731Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2157914409217498545Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2186611811198704485Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2169852800217498545Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2161745602206745602Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
2301415Cm67Cardiac mass QTL 670.003heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683189857032Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2138901276217498710Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2158159186217498710Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2158159186217498710Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181987080199696953Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2118446646200453484Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2118446646200453484Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2169852670207612467Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2159585731204585731Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2149614623198704357Rat
7488904Bp363Blood pressure QTL 3630.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2186889035189857032Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2143447078188447078Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2174160958219160958Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2177339806222339806Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2149614466205573168Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2149614466205573168Rat
12879846Cm90Cardiac mass QTL 900.011heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)2172795683189857032Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683199696953Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683199696953Rat
11565181Bw176Body weight QTL 1760.002body mass (VT:0001259)body weight (CMO:0000012)2172795683189857032Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683199696953Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2172795683199696953Rat
12879845Cm89Cardiac mass QTL 890.008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683189857032Rat
11565180Kidm56Kidney mass QTL 560.003kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683189857032Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683199696953Rat
12879847Am4Aortic mass QTL 40.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683189857032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:176
Count of miRNA genes:142
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000033917, ENSRNOT00000065065
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 3 41 57 41 19 41 8 11 74 35 41 11 8
Low 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC059125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M17300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M34477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M89945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000033917   ⟹   ENSRNOP00000031191
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2188,392,858 - 188,412,329 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000065065   ⟹   ENSRNOP00000058918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2188,403,595 - 188,413,219 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080185   ⟹   ENSRNOP00000070394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2188,403,583 - 188,412,362 (-)Ensembl
RefSeq Acc Id: NM_031840   ⟹   NP_114028
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22174,497,402 - 174,507,031 (-)NCBI
Rnor_6.02188,403,595 - 188,413,219 (-)NCBI
Rnor_5.02207,816,332 - 207,826,348 (-)NCBI
RGSC_v3.42181,138,474 - 181,177,903 (-)RGD
Celera2168,441,483 - 168,451,110 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_114028 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40960 (Get FASTA)   NCBI Sequence Viewer  
  AAA41143 (Get FASTA)   NCBI Sequence Viewer  
  AAH59125 (Get FASTA)   NCBI Sequence Viewer  
  EDM00669 (Get FASTA)   NCBI Sequence Viewer  
  P05369 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_114028   ⟸   NM_031840
- UniProtKB: P05369 (UniProtKB/Swiss-Prot),   F1LND7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000031191   ⟸   ENSRNOT00000033917
RefSeq Acc Id: ENSRNOP00000070394   ⟸   ENSRNOT00000080185
RefSeq Acc Id: ENSRNOP00000058918   ⟸   ENSRNOT00000065065
Protein Domains
RUN   SH3

Transcriptome

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

Promoters
RGD ID:13691456
Promoter ID:EPDNEW_R1981
Type:initiation region
Name:Fdps_1
Description:farnesyl diphosphate 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_6.02188,413,113 - 188,413,173EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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)
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
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/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)
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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 188405697 188405698 C T snv WN/N (MCW), CDR, CDS, SS/JrHsdMcwi (MCW), WKY/N (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SBH/Ygl (MCW), BN/SsN (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW)
2 188405720 188405721 C T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), CDR, WKY/N (MCW), CDS
2 188405742 188405743 T G snv CDS, CDR
2 188405846 188405847 G T snv CDS, CDR
2 188405894 188405895 C T snv SBH/Ygl (MCW), Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), BN/SsN (MCW), ACI/N (MCW), CDR, GH/OmrMcwi (MCW), CDS
2 188405913 188405914 T A snv CDR, CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68953 AgrOrtholog
Ensembl Genes ENSRNOG00000043377 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000031191 UniProtKB/TrEMBL
  ENSRNOP00000058918 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070394 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033917 UniProtKB/TrEMBL
  ENSRNOT00000065065 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080185 UniProtKB/TrEMBL
Gene3D-CATH 1.10.600.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.58.900 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6919326 IMAGE-MGC_LOAD
InterPro Isoprenoid_synthase_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Polyprenyl_synt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Polyprenyl_synt_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Run UniProtKB/TrEMBL
  Run_dom_sf UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
KEGG Report rno:83791 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72758 IMAGE-MGC_LOAD
NCBI Gene 83791 ENTREZGENE
Pfam polyprenyl_synt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RUN UniProtKB/TrEMBL
  SH3_9 UniProtKB/TrEMBL
PharmGKB FDPS RGD
PhenoGen Fdps PhenoGen
PROSITE POLYPRENYL_SYNTHASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POLYPRENYL_SYNTHASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RUN UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
SMART RUN UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
Superfamily-SCOP SH3 UniProtKB/TrEMBL
  SSF140741 UniProtKB/TrEMBL
  SSF48576 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JXT3_RAT UniProtKB/TrEMBL
  F1LND7 ENTREZGENE, UniProtKB/TrEMBL
  FPPS_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q7TPK0_RAT UniProtKB/TrEMBL
UniProt Secondary F1LMQ2 UniProtKB/TrEMBL
  Q6GT82 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Fdps  farnesyl diphosphate synthase  Fdps  farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Fdps  farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)  Fdps  farnesyl diphosphate synthetase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Fdps  farnesyl diphosphate synthetase  Fdps  farnesyl diphosphate synthase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-09-11   farnesyl diphosphate synthase  Fdps  farensyl diphosphate synthase  Name updated 1299863 APPROVED
2002-06-10 Fdps  farensyl diphosphate synthase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function catalyzes the formation of geranyl- and farnesylpyrophosphate from the condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate  
gene_pathway part of isoprene biosynthetic pathway, which provides the cell with cholesterol, ubiquinone, dolichol, and other nonsterol metabolites 61515
gene_process functions in the isoprene biosynthetic pathway  
gene_regulation co-regulated with HMG-CoA synthase and HMG-CoA reductase 61515