Sigmar1 (sigma non-opioid intracellular receptor 1) - Rat Genome Database

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Gene: Sigmar1 (sigma non-opioid intracellular receptor 1) Rattus norvegicus
Analyze
Symbol: Sigmar1
Name: sigma non-opioid intracellular receptor 1
RGD ID: 68364
Description: Enables G protein-coupled opioid receptor activity. Involved in nervous system development. Predicted to be located in membrane; nuclear envelope; and postsynaptic density. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 16 and distal spinal muscular atrophy 2. Orthologous to human SIGMAR1 (sigma non-opioid intracellular receptor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 3,3',5-triiodo-L-thyronine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: opioid receptor, sigma 1; Oprs1; sigma 1-type opioid receptor; sigma1-receptor; sigma1R
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2556,904,155 - 56,907,012 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl556,904,159 - 56,907,017 (-)Ensembl
Rnor_6.0558,121,824 - 58,124,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl558,121,786 - 58,124,681 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0562,645,887 - 62,648,735 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4559,162,537 - 59,165,315 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1559,162,715 - 59,165,489 (-)NCBI
Celera555,498,271 - 55,501,049 (-)NCBICelera
Cytogenetic Map5q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-alpha-phellandrene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[2-(3,4-dichlorophenyl)ethyl]-4-methylpiperazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acetylcholine  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-phellandrene  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
caffeine  (EXP)
carbon nanotube  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dextromethorphan  (EXP)
dibutyl phthalate  (EXP)
dimemorfan  (EXP)
dioxygen  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
flavonoids  (EXP)
fluoranthene  (ISO)
flutamide  (EXP)
hydrogen cyanide  (ISO)
ivermectin  (ISO)
kainic acid  (EXP)
linuron  (ISO)
manganese(II) chloride  (EXP)
methotrexate  (ISO)
methyl beta-cyclodextrin  (ISO)
N-\{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl\}-N-propylpropan-1-amine hydrochloride  (EXP)
N-nitrosodiethylamine  (EXP)
okadaic acid  (EXP)
paclitaxel  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
piperazines  (ISO)
pirinixic acid  (ISO)
potassium cyanide  (ISO)
pregnenolone  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
resveratrol  (ISO)
SCH 23390  (ISO)
scopolamine  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. The sigma receptor as a ligand-regulated auxiliary potassium channel subunit. Aydar E, etal., Neuron 2002 Apr 25;34(3):399-410.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Sigma-1 receptor chaperones at the ER-mitochondrion interface regulate Ca(2+) signaling and cell survival. Hayashi T and Su TP, Cell. 2007 Nov 2;131(3):596-610.
5. Dynamic interaction between sigma-1 receptor and Kv1.2 shapes neuronal and behavioral responses to cocaine. Kourrich S, etal., Cell. 2013 Jan 17;152(1-2):236-47. doi: 10.1016/j.cell.2012.12.004.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Cloning and functional characterization of a sigma receptor from rat brain. Seth P, etal., J Neurochem 1998 Mar;70(3):922-31.
12. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
13. Nerve growth factor-induced neurite sprouting in PC12 cells involves sigma-1 receptors: implications for antidepressants. Takebayashi M, etal., J Pharmacol Exp Ther 2002 Dec;303(3):1227-37.
14. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
15. Sigma receptors inhibit high-voltage-activated calcium channels in rat sympathetic and parasympathetic neurons. Zhang H and Cuevas J, J Neurophysiol 2002 Jun;87(6):2867-79.
Additional References at PubMed
PMID:9341151   PMID:10406945   PMID:10771347   PMID:11149946   PMID:11434908   PMID:11687279   PMID:11861817   PMID:12535781   PMID:14622179   PMID:15064136   PMID:15170821   PMID:15466698  
PMID:15489334   PMID:16522641   PMID:17545312   PMID:17964567   PMID:18641291   PMID:18723775   PMID:18946467   PMID:19213917   PMID:20018732   PMID:20167253   PMID:20223280   PMID:20404054  
PMID:20732358   PMID:21314692   PMID:21346735   PMID:21555866   PMID:21842496   PMID:21905129   PMID:22357973   PMID:22878224   PMID:23105111   PMID:23314020   PMID:23732704   PMID:23965801  
PMID:24015960   PMID:24508523   PMID:25273321   PMID:25848705   PMID:26031312   PMID:26234785   PMID:26792191   PMID:26860755   PMID:27042935   PMID:27339730   PMID:27373906   PMID:27735948  
PMID:27761593   PMID:28286226   PMID:28495886   PMID:28667101   PMID:28682953   PMID:28923416   PMID:29424796   PMID:29876881   PMID:29908082   PMID:30291362   PMID:31768847   PMID:32424233  
PMID:33098515   PMID:33459966   PMID:34176868  


Genomics

Comparative Map Data
Sigmar1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2556,904,155 - 56,907,012 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl556,904,159 - 56,907,017 (-)Ensembl
Rnor_6.0558,121,824 - 58,124,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl558,121,786 - 58,124,681 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0562,645,887 - 62,648,735 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4559,162,537 - 59,165,315 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1559,162,715 - 59,165,489 (-)NCBI
Celera555,498,271 - 55,501,049 (-)NCBICelera
Cytogenetic Map5q22NCBI
SIGMAR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38934,634,722 - 34,637,787 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl934,634,722 - 34,637,844 (-)EnsemblGRCh38hg38GRCh38
GRCh37934,634,719 - 34,637,784 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36934,624,719 - 34,627,768 (-)NCBINCBI36hg18NCBI36
Build 34934,624,719 - 34,627,768NCBI
Celera934,566,222 - 34,569,271 (-)NCBI
Cytogenetic Map9p13.3NCBI
HuRef934,589,001 - 34,592,050 (-)NCBIHuRef
CHM1_1934,634,494 - 34,637,538 (-)NCBICHM1_1
T2T-CHM13v2.0934,653,268 - 34,656,333 (-)NCBI
Sigmar1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39441,738,493 - 41,741,359 (-)NCBIGRCm39mm39
GRCm39 Ensembl441,738,493 - 41,756,157 (-)Ensembl
GRCm38441,738,493 - 41,741,359 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl441,738,493 - 41,756,157 (-)EnsemblGRCm38mm10GRCm38
MGSCv37441,685,369 - 41,688,186 (-)NCBIGRCm37mm9NCBIm37
MGSCv36441,927,007 - 41,929,824 (-)NCBImm8
Celera441,399,281 - 41,402,095 (-)NCBICelera
Cytogenetic Map4A5NCBI
Sigmar1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554721,493,896 - 1,496,377 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554721,493,896 - 1,496,377 (+)NCBIChiLan1.0ChiLan1.0
SIGMAR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1935,280,777 - 35,283,672 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0934,471,362 - 34,474,459 (-)NCBIMhudiblu_PPA_v0panPan3
SIGMAR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11151,310,672 - 51,313,426 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1151,311,085 - 51,313,400 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1149,939,025 - 49,941,785 (-)NCBI
ROS_Cfam_1.01152,251,407 - 52,254,167 (-)NCBI
ROS_Cfam_1.0 Ensembl1152,251,413 - 52,311,364 (-)Ensembl
UMICH_Zoey_3.11150,914,114 - 50,916,874 (-)NCBI
UNSW_CanFamBas_1.01150,782,279 - 50,785,039 (-)NCBI
UU_Cfam_GSD_1.01151,547,030 - 51,549,790 (-)NCBI
Sigmar1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947166,170,303 - 166,173,309 (-)NCBI
SpeTri2.0NW_0049365242,717,885 - 2,720,874 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIGMAR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1032,160,822 - 32,164,718 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11032,160,767 - 32,163,540 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21036,303,067 - 36,305,797 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sigmar1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473639,032,517 - 39,035,176 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473639,023,641 - 39,035,180 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127340  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2556,904,340 - 56,904,520 (+)MAPPERmRatBN7.2
Rnor_6.0558,122,008 - 58,122,187NCBIRnor6.0
Rnor_5.0562,646,073 - 62,646,252UniSTSRnor5.0
RGSC_v3.4559,162,719 - 59,162,898UniSTSRGSC3.4
Celera555,498,453 - 55,498,632UniSTS
Cytogenetic Map5q22UniSTS
AF004927  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2556,904,493 - 56,904,582 (+)MAPPERmRatBN7.2
Rnor_6.0558,122,161 - 58,122,249NCBIRnor6.0
Rnor_5.0562,646,226 - 62,646,314UniSTSRnor5.0
RGSC_v3.4559,162,872 - 59,162,960UniSTSRGSC3.4
Celera555,498,606 - 55,498,694UniSTS
Cytogenetic Map5q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:284
Count of miRNA genes:182
Interacting mature miRNAs:210
Transcripts:ENSRNOT00000019795
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 30 57 41 19 41 74 35 41 11
Low 13 8 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019795   ⟹   ENSRNOP00000019795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl556,904,159 - 56,907,017 (-)Ensembl
Rnor_6.0 Ensembl558,121,786 - 58,124,681 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112379   ⟹   ENSRNOP00000094001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl556,905,008 - 56,907,017 (-)Ensembl
RefSeq Acc Id: NM_030996   ⟹   NP_112258
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2556,904,159 - 56,906,937 (-)NCBI
Rnor_6.0558,121,826 - 58,124,604 (-)NCBI
Rnor_5.0562,645,887 - 62,648,735 (-)NCBI
RGSC_v3.4559,162,537 - 59,165,315 (-)RGD
Celera555,498,271 - 55,501,049 (-)RGD
Sequence:
RefSeq Acc Id: XR_001837835
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2556,904,155 - 56,907,012 (-)NCBI
Rnor_6.0558,121,824 - 58,124,687 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112258   ⟸   NM_030996
- Sequence:
RefSeq Acc Id: ENSRNOP00000019795   ⟸   ENSRNOT00000019795
RefSeq Acc Id: ENSRNOP00000094001   ⟸   ENSRNOT00000112379

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9R0C9-F1-model_v2 AlphaFold Q9R0C9 1-223 view protein structure

Transcriptome

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

Promoters
RGD ID:13693657
Promoter ID:EPDNEW_R4182
Type:initiation region
Name:Sigmar1_1
Description:sigma non-opioid intracellular receptor 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_6.0558,124,610 - 58,124,670EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68364 AgrOrtholog
BioCyc Gene G2FUF-41543 BioCyc
Ensembl Genes ENSRNOG00000014604 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019795 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000094001.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019795 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000112379.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5623693 IMAGE-MGC_LOAD
InterPro ERG2_sigma1_rcpt-like UniProtKB/Swiss-Prot
KEGG Report rno:29336 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72418 IMAGE-MGC_LOAD
NCBI Gene 29336 ENTREZGENE
PANTHER PTHR10868 UniProtKB/Swiss-Prot
Pfam ERG2_Sigma1R UniProtKB/Swiss-Prot
PhenoGen Sigmar1 PhenoGen
TIGR TC217595
UniProt A0A8I6AGV2_RAT UniProtKB/TrEMBL
  Q9R0C9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9R1J7 UniProtKB/Swiss-Prot
  Q9Z2W2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Sigmar1  sigma non-opioid intracellular receptor 1  Oprs1  opioid receptor, sigma 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Oprs1  opioid receptor, sigma 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference