Lss (lanosterol synthase) - Rat Genome Database

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Gene: Lss (lanosterol synthase) Rattus norvegicus
Analyze
Symbol: Lss
Name: lanosterol synthase
RGD ID: 620955
Description: Exhibits lanosterol synthase activity. Involved in cholesterol biosynthetic process. Localizes to intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in alopecia-mental retardation syndrome; cataract 44; and hypotrichosis 14. Orthologous to human LSS (lanosterol synthase); PARTICIPATES IN cholesterol biosynthetic pathway; alendronate pharmacodynamics pathway; cholesterol ester storage disease pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 2,3-epoxysqualene--lanosterol cyclase; 2,3-oxidosqualene: lanosterol cyclase; lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase); LOC103690153; OSC; oxidosqualene--lanosterol cyclase; uncharacterized LOC103690153
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Lssem2Mcwi  
Genetic Models: SS-Lssem2Mcwi
Is Marker For: Strains:   SCR/Sscr  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22012,091,138 - 12,118,858 (-)NCBI
Rnor_6.0 Ensembl2012,842,884 - 12,870,497 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02012,844,522 - 12,870,474 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02015,337,114 - 15,338,473 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02015,000,298 - 15,027,581 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,507,575 - 12,534,612 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12012,507,801 - 12,534,839 (-)NCBI
Celera2013,590,952 - 13,616,816 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
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',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldrin  (ISO)
amiodarone  (EXP,ISO)
amitriptyline  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antimony(0)  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (EXP)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clarithromycin  (ISO)
clofibric acid  (EXP)
clomipramine  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
cyproconazole  (EXP)
dexamethasone  (EXP)
diazinon  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloromethane  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
doxepin  (ISO)
doxorubicin  (ISO)
epoxiconazole  (EXP)
erythromycin A  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
flecainide  (ISO)
fluoranthene  (ISO)
fluoxetine  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
folpet  (ISO)
formaldehyde  (ISO)
Ganoderic acid A  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexaconazole  (ISO)
hydroquinone  (ISO)
imipramine  (ISO)
indometacin  (ISO)
isoflavones  (ISO)
ketoconazole  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
Loratadine  (ISO)
metformin  (EXP)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methyltestosterone  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
obeticholic acid  (ISO)
ouabain  (ISO)
ozone  (EXP)
paracetamol  (ISO)
PCB138  (EXP)
pentamidine  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
perhexiline  (ISO)
phenobarbital  (EXP,ISO)
phenylpropanolamine  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
progesterone  (ISO)
quercetin  (ISO)
rotenone  (EXP,ISO)
sertraline  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sotalol  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thioridazine  (ISO)
titanium dioxide  (ISO)
triacsin C  (ISO)
triadimefon  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP,ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin K  (EXP)
vorinostat  (ISO)
Yessotoxin  (ISO)
yohimbine  (ISO)
zaragozic acid A  (EXP,ISO)
zimeldine  (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:7639730   PMID:14741744   PMID:17186944   PMID:17460354   PMID:18054775   PMID:19119143   PMID:19946888   PMID:21498505   PMID:22871113   PMID:30401459  


Genomics

Comparative Map Data
Lss
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22012,091,138 - 12,118,858 (-)NCBI
Rnor_6.0 Ensembl2012,842,884 - 12,870,497 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02012,844,522 - 12,870,474 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02015,337,114 - 15,338,473 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02015,000,298 - 15,027,581 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,507,575 - 12,534,612 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12012,507,801 - 12,534,839 (-)NCBI
Celera2013,590,952 - 13,616,816 (-)NCBICelera
Cytogenetic Map20p12NCBI
LSS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2146,188,141 - 46,228,824 (-)EnsemblGRCh38hg38GRCh38
GRCh382146,188,446 - 46,228,774 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372147,608,360 - 47,648,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,432,788 - 46,473,119 (-)NCBINCBI36hg18NCBI36
Build 342146,433,466 - 46,473,119NCBI
Celera2132,720,748 - 32,761,140 (-)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2132,990,213 - 33,031,026 (-)NCBIHuRef
CHM1_12147,167,889 - 47,208,226 (-)NCBICHM1_1
Lss
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,367,303 - 76,392,973 (+)NCBIGRCm39mm39
GRCm39 Ensembl1076,367,422 - 76,392,972 (+)Ensembl
GRCm381076,531,565 - 76,557,139 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,531,588 - 76,557,138 (+)EnsemblGRCm38mm10GRCm38
MGSCv371075,994,372 - 76,016,679 (+)NCBIGRCm37mm9NCBIm37
MGSCv361075,975,343 - 75,997,650 (+)NCBImm8
Celera1077,576,142 - 77,598,449 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.1NCBI
Lss
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,633,658 - 42,653,399 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,633,658 - 42,653,399 (-)NCBIChiLan1.0ChiLan1.0
LSS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12145,787,252 - 45,822,181 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,787,252 - 45,822,181 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02132,535,564 - 32,571,379 (-)NCBIMhudiblu_PPA_v0panPan3
LSS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,479,255 - 39,502,439 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3139,480,581 - 39,503,042 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,707,040 - 38,730,234 (-)NCBI
ROS_Cfam_1.03139,120,352 - 39,143,563 (-)NCBI
UMICH_Zoey_3.13138,982,033 - 39,005,248 (-)NCBI
UNSW_CanFamBas_1.03138,942,696 - 38,965,462 (-)NCBI
UU_Cfam_GSD_1.03139,460,908 - 39,484,125 (-)NCBI
Lss
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,779,602 - 38,807,151 (-)NCBI
SpeTri2.0NW_004936778323,120 - 351,100 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.213218,517,444 - 218,539,989 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,809,065 - 89,846,295 (-)NCBI
ChlSab1.1 Ensembl289,811,698 - 89,846,242 (-)Ensembl
Vero_WHO_p1.0NW_02366605418,194,151 - 18,231,629 (-)NCBI
Lss
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474531,301,648 - 31,325,283 (-)NCBI

Position Markers
RH140502  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,092,914 - 12,093,040 (+)MAPPER
Rnor_6.02013,183,368 - 13,183,493NCBIRnor6.0
Rnor_6.02012,844,661 - 12,844,786NCBIRnor6.0
Rnor_5.02015,337,253 - 15,337,378UniSTSRnor5.0
Rnor_5.02015,002,073 - 15,002,198UniSTSRnor5.0
RGSC_v3.42012,507,714 - 12,507,839UniSTSRGSC3.4
Celera2013,591,091 - 13,591,216UniSTS
RH 3.4 Map20154.34UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat


Related Rat Strains
The following Strains have been annotated to Lss


Genetic Models
This gene Lss is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:84
Count of miRNA genes:68
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000042499
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 16 48 33 14 33 74 35 34 11
Low 27 9 8 5 8 8 11 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078412   ⟹   ENSRNOP00000069432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,842,918 - 12,870,496 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081903   ⟹   ENSRNOP00000070074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,861,228 - 12,870,497 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084053   ⟹   ENSRNOP00000069968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,842,884 - 12,855,891 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085270   ⟹   ENSRNOP00000070008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,856,483 - 12,858,096 (-)Ensembl
RefSeq Acc Id: NM_031049   ⟹   NP_112311
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,092,776 - 12,118,739 (-)NCBI
Rnor_6.02012,844,522 - 12,870,474 (-)NCBI
Rnor_5.02015,337,114 - 15,338,473 (-)NCBI
RGSC_v3.42012,507,575 - 12,534,612 (-)RGD
Celera2013,590,952 - 13,616,816 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099120   ⟹   XP_038955048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,091,138 - 12,118,844 (-)NCBI
RefSeq Acc Id: XM_039099121   ⟹   XP_038955049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,091,138 - 12,118,858 (-)NCBI
RefSeq Acc Id: XM_039099122   ⟹   XP_038955050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,091,138 - 12,114,142 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112311   ⟸   NM_031049
- Sequence:
RefSeq Acc Id: ENSRNOP00000070008   ⟸   ENSRNOT00000085270
RefSeq Acc Id: ENSRNOP00000069432   ⟸   ENSRNOT00000078412
RefSeq Acc Id: ENSRNOP00000070074   ⟸   ENSRNOT00000081903
RefSeq Acc Id: ENSRNOP00000069968   ⟸   ENSRNOT00000084053
RefSeq Acc Id: XP_038955049   ⟸   XM_039099121
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955048   ⟸   XM_039099120
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955050   ⟸   XM_039099122
- Peptide Label: isoform X2
Protein Domains
SQHop_cyclase_C   SQHop_cyclase_N

Transcriptome

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

Promoters
RGD ID:13701516
Promoter ID:EPDNEW_R12040
Type:initiation region
Name:Lss_1
Description:lanosterol 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_6.02012,870,479 - 12,870,539EPDNEW

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)
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/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620955 AgrOrtholog
Ensembl Genes ENSRNOG00000054549 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069432 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069968 UniProtKB/TrEMBL
  ENSRNOP00000070008 UniProtKB/TrEMBL
  ENSRNOP00000070074 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078412 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081903 UniProtKB/TrEMBL
  ENSRNOT00000084053 UniProtKB/TrEMBL
  ENSRNOT00000085270 UniProtKB/TrEMBL
InterPro SQ_cyclase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SQ_cyclase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Squalene_cyclase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Terpene_synthase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Terpenoid_cyclase/PrenylTrfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81681 UniProtKB/Swiss-Prot
NCBI Gene 81681 ENTREZGENE
Pfam SQHop_cyclase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SQHop_cyclase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lss PhenoGen
PROSITE TERPENE_SYNTHASES UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs squalene_cyclas UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MJH3_RAT UniProtKB/TrEMBL
  A0A096MK55_RAT UniProtKB/TrEMBL
  A0A096MK62_RAT UniProtKB/TrEMBL
  A0A0G2JVC8_RAT UniProtKB/TrEMBL
  ERG7_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62811 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Lss  lanosterol synthase  LOC103690153  uncharacterized LOC103690153  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103690153  uncharacterized LOC103690153      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-18 Lss  lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)  Lss  lanosterol synthase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Lss  lanosterol synthase    2,3-oxidosqualene: lanosterol cyclase  Name updated 1299863 APPROVED
2002-08-07 Lss  2,3-oxidosqualene: lanosterol cyclase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains five QW motifs 728996