Sod3 (superoxide dismutase 3) - Rat Genome Database

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Gene: Sod3 (superoxide dismutase 3) Rattus norvegicus
Analyze
Symbol: Sod3
Name: superoxide dismutase 3
RGD ID: 3733
Description: Exhibits superoxide dismutase activity. Involved in blood vessel diameter maintenance; response to copper ion; and response to oxidative stress. Localizes to several cellular components, including collagen-containing extracellular matrix; extracellular space; and nucleus. Used to study hypertension. Human ortholog(s) of this gene implicated in several diseases, including coronary artery disease (multiple); diabetes mellitus (multiple); diabetic retinopathy; lung disease (multiple); and polyneuropathy. Orthologous to human SOD3 (superoxide dismutase 3); PARTICIPATES IN cardiovascular system disease pathway; diabetes mellitus pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: EC-SOD; ECSODPT; extracellular superoxide dismutase; extracellular superoxide dismutase [Cu-Zn]; Superoxide dimutase 3; superoxide dismutase 3, extracellular; superoxide dismutase B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Sod3m1Mcwi  
Genetic Models: SS-Sod3m1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21458,610,104 - 58,615,845 (-)NCBI
Rnor_6.0 Ensembl1460,958,592 - 60,964,324 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01460,958,583 - 60,971,143 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01461,071,304 - 61,083,776 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41463,381,447 - 63,387,180 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11463,383,838 - 63,389,571 (-)NCBI
Celera1457,707,717 - 57,713,440 (-)NCBICelera
Cytogenetic Map14q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(E)-cinnamyl alcohol  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,5-hexanedione  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (EXP)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
Actein  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
alpha-hexylcinnamaldehyde  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
atorvastatin calcium  (EXP)
Bandrowski's base  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
butylated hydroxyanisole  (EXP)
calcitriol  (ISO)
carbendazim  (EXP)
chlorogenic acid  (ISO)
chlorpyrifos  (EXP)
cholic acid  (ISO)
ciglitazone  (EXP)
cinnamyl alcohol  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP,ISO)
clozapine  (EXP)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cumene  (ISO)
D-glucose  (EXP)
DDT  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dimethyl sulfoxide  (EXP)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
donepezil hydrochloride  (EXP)
doxorubicin  (ISO)
ellagic acid  (ISO)
ethanol  (ISO)
eugenol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
formaldehyde  (ISO)
fulvestrant  (EXP)
genistein  (ISO)
glucose  (EXP)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
GW 4064  (ISO)
GW 501516  (ISO)
haloperidol  (EXP)
hexachlorobenzene  (EXP)
hyaluronic acid  (ISO)
hydrogen peroxide  (ISO)
isoeugenol  (ISO)
ketamine  (EXP)
L-ascorbic acid  (EXP,ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
losartan  (ISO)
lutein  (ISO)
mercury dichloride  (EXP)
methotrexate  (ISO)
methyl tert-butyl ether  (EXP)
methylmercury chloride  (EXP)
mifepristone  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (EXP)
nickel sulfate  (ISO)
nimesulide  (EXP)
ochratoxin A  (ISO)
Osajin  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
paricalcitol  (ISO)
permethrin  (EXP)
peroxynitrous acid  (ISO)
phenobarbital  (EXP,ISO)
phosgene  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
Pomiferin  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
probucol  (EXP)
progesterone  (EXP,ISO)
puerarin  (ISO)
Pyridostigmine bromide  (EXP)
quercetin  (ISO)
raloxifene  (EXP)
resveratrol  (EXP,ISO)
Rosavin  (ISO)
rotenone  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
streptozocin  (EXP,ISO)
sulfasalazine  (ISO)
sunitinib  (ISO)
superoxide  (ISO)
tamibarotene  (ISO)
tetrachloromethane  (ISO)
thymoquinone  (EXP)
trans-isoeugenol  (ISO)
triclosan  (ISO)
trimellitic anhydride  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Adachi T, etal., J Endocrinol. 2004 Jun;181(3):413-7.
2. Auten RL, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Jan;290(1):L32-40. Epub 2005 Aug 12.
3. Beyer AM, etal., Am J Physiol Heart Circ Physiol. 2014 Feb;306(3):H339-47. doi: 10.1152/ajpheart.00619.2012. Epub 2013 Dec 6.
4. Bowler RP, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Apr;282(4):L719-26.
5. Bowler RP, etal., J Biol Chem 2002 May 10;277(19):16505-11.
6. Carlsson LM, etal., Proc Natl Acad Sci U S A 1996 May 28;93(11):5219-22.
7. Cheng YK, etal., Laryngoscope. 2006 Mar;116(3):417-22.
8. Chu Y, etal., Circ Res. 2003 Mar 7;92(4):461-8. Epub 2003 Jan 23.
9. Ciechanowski K, etal., Diabetologia. 2003 Jul;46(7):1026-7. Epub 2003 Jun 27.
10. Constantino L, etal., Intensive Care Med Exp. 2014 Dec;2(1):17. doi: 10.1186/2197-425X-2-17. Epub 2014 May 23.
11. Freiberger J, etal., Undersea Hyperb Med. 2004 Summer;31(2):227-32.
12. Fujita H, etal., J Am Soc Nephrol. 2009 Jun;20(6):1303-13. Epub 2009 May 21.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. GOA data from the GO Consortium
15. Gongora MC, etal., Hypertension. 2006 Sep;48(3):473-81. Epub 2006 Jul 24.
16. Horiuchi M, etal., Arterioscler Thromb Vasc Biol. 2004 Jan;24(1):106-11. Epub 2003 Oct 30.
17. Iida S, etal., Am J Physiol Heart Circ Physiol. 2005 Aug;289(2):H525-32.
18. Iida S, etal., Am J Physiol Heart Circ Physiol. 2006 Aug;291(2):H914-20.
19. Johnson WT, etal., J Nutr Biochem. 2005 Nov;16(11):682-92. Epub 2005 Aug 2.
20. Juul K, etal., Am J Respir Crit Care Med. 2006 Apr 15;173(8):858-64. Epub 2006 Jan 6.
21. Kimura F, etal., Diabetes Care. 2003 Apr;26(4):1246-50.
22. Kinnula VL, etal., Histopathology. 2006 Jul;49(1):66-74.
23. Landmesser U, etal., Circulation. 2000 May 16;101(19):2264-70.
24. MGD data from the GO Consortium
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Park JW, etal., Am J Physiol Heart Circ Physiol. 2005 Jul;289(1):H181-7. Epub 2005 Mar 18.
27. Pechenino AS and Brown TR, Prostate. 2006 Apr 1;66(5):522-35.
28. Perry AC, etal., Biochem J 1993 Jul 1;293 ( Pt 1):21-5.
29. RGD automated data pipeline
30. RGD automated import pipeline for gene-chemical interactions
31. Sheng H, etal., Exp Neurol. 2000 Jun;163(2):392-8.
32. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
33. Tamai M, etal., Diabetes Res Clin Pract. 2006 Feb;71(2):140-5. Epub 2005 Jun 28.
34. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
35. Wheeler MD, etal., Hum Gene Ther. 2001 Dec 10;12(18):2167-77.
36. Willems J, etal., J Biol Chem 1993 Nov 25;268(33):24614-21.
37. Zelko IN and Folz RJ, Endocrinology. 2005 Jan;146(1):332-40. Epub 2004 Sep 16.
38. Zhang C, etal., Wei Sheng Yan Jiu. 2012 Jul;41(4):555-61.
39. Zotova EV, etal., Mol Biol (Mosk). 2003 May-Jun;37(3):404-8.
Additional References at PubMed
PMID:9699963   PMID:15016652   PMID:15489334   PMID:15528465   PMID:16371425   PMID:17196988   PMID:19198181   PMID:19495415   PMID:20033309   PMID:20551380   PMID:21736484   PMID:21909393  
PMID:22540739   PMID:23376485   PMID:23533145   PMID:24006456   PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Sod3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21458,610,104 - 58,615,845 (-)NCBI
Rnor_6.0 Ensembl1460,958,592 - 60,964,324 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01460,958,583 - 60,971,143 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01461,071,304 - 61,083,776 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41463,381,447 - 63,387,180 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11463,383,838 - 63,389,571 (-)NCBI
Celera1457,707,717 - 57,713,440 (-)NCBICelera
Cytogenetic Map14q11NCBI
SOD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl424,789,912 - 24,800,842 (+)EnsemblGRCh38hg38GRCh38
GRCh38424,795,478 - 24,800,845 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37424,797,195 - 24,802,464 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36424,406,183 - 24,411,565 (+)NCBINCBI36hg18NCBI36
Build 34424,472,323 - 24,478,733NCBI
Celera425,246,551 - 25,251,936 (+)NCBI
Cytogenetic Map4p15.2NCBI
HuRef424,139,594 - 24,144,972 (+)NCBIHuRef
CHM1_1424,796,442 - 24,801,824 (+)NCBICHM1_1
Sod3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39552,521,146 - 52,527,080 (+)NCBIGRCm39mm39
GRCm39 Ensembl552,521,133 - 52,528,760 (+)Ensembl
GRCm38552,363,804 - 52,369,738 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl552,363,791 - 52,371,418 (+)EnsemblGRCm38mm10GRCm38
MGSCv37552,755,043 - 52,760,977 (+)NCBIGRCm37mm9NCBIm37
MGSCv36552,652,052 - 52,657,986 (+)NCBImm8
Celera549,732,370 - 49,738,292 (+)NCBICelera
Cytogenetic Map5C1NCBI
cM Map527.92NCBI
Sod3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955480257,716 - 263,149 (-)NCBIChiLan1.0ChiLan1.0
SOD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1424,480,912 - 24,486,382 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl424,485,059 - 24,485,781 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0419,195,941 - 19,201,298 (+)NCBIMhudiblu_PPA_v0panPan3
SOD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1385,382,698 - 85,387,144 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl385,382,484 - 85,387,455 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha387,896,595 - 87,901,009 (-)NCBI
ROS_Cfam_1.0386,357,866 - 86,362,385 (-)NCBI
UMICH_Zoey_3.1385,490,694 - 85,495,210 (-)NCBI
UNSW_CanFamBas_1.0385,596,388 - 85,600,748 (-)NCBI
UU_Cfam_GSD_1.0385,980,631 - 85,986,057 (-)NCBI
SOD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl818,796,636 - 18,802,154 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1818,796,633 - 18,802,156 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2819,293,239 - 19,293,972 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SOD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12725,554,474 - 25,559,873 (-)NCBI
ChlSab1.1 Ensembl2725,555,082 - 25,555,804 (-)Ensembl
Sod3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247557,535,044 - 7,541,298 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat


Genetic Models
This gene Sod3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:287
Count of miRNA genes:163
Interacting mature miRNAs:180
Transcripts:ENSRNOT00000005155
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 21 31 19 5 19 8 11 20 31 33 11 8
Low 22 26 22 14 22 54 4 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005155   ⟹   ENSRNOP00000005155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1460,958,592 - 60,964,324 (-)Ensembl
RefSeq Acc Id: NM_012880   ⟹   NP_037012
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,610,104 - 58,615,845 (-)NCBI
Rnor_6.01460,958,591 - 60,964,324 (-)NCBI
Rnor_5.01461,071,304 - 61,083,776 (-)NCBI
RGSC_v3.41463,381,447 - 63,387,180 (-)RGD
Celera1457,707,717 - 57,713,440 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251030   ⟹   XP_006251092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01460,958,583 - 60,971,143 (-)NCBI
Rnor_5.01461,071,304 - 61,083,776 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037012   ⟸   NM_012880
- Peptide Label: precursor
- UniProtKB: Q08420 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251092   ⟸   XM_006251030
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000005155   ⟸   ENSRNOT00000005155

Transcriptome

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

Promoters
RGD ID:13699337
Promoter ID:EPDNEW_R9862
Type:initiation region
Name:Sod3_1
Description:superoxide dismutase 3
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_6.01460,964,292 - 60,964,352EPDNEW

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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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:3733 AgrOrtholog
Ensembl Genes ENSRNOG00000003869 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000005155 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005155 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.200 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5598594 IMAGE-MGC_LOAD
InterPro EC-SOD UniProtKB/Swiss-Prot
  SOD-like_Cu/Zn_dom_sf UniProtKB/Swiss-Prot
  SOD_Cu/Zn_/chaperone UniProtKB/Swiss-Prot
  SOD_Cu/Zn_BS UniProtKB/Swiss-Prot
  SOD_Cu_Zn_dom UniProtKB/Swiss-Prot
KEGG Report rno:25352 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72515 IMAGE-MGC_LOAD
NCBI Gene 25352 ENTREZGENE
PANTHER PTHR10003 UniProtKB/Swiss-Prot
  PTHR10003:SF77 UniProtKB/Swiss-Prot
Pfam Sod_Cu UniProtKB/Swiss-Prot
PhenoGen Sod3 PhenoGen
PRINTS CUZNDISMTASE UniProtKB/Swiss-Prot
PROSITE SOD_CU_ZN_1 UniProtKB/Swiss-Prot
  SOD_CU_ZN_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49329 UniProtKB/Swiss-Prot
TIGR TC218284
UniProt Q08420 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q64667 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-24 Sod3  superoxide dismutase 3  Sod3  superoxide dismutase 3, extracellular  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Sod3  superoxide dismutase 3, extracellular    superoxide dismutase 3  Name updated 1299863 APPROVED
2003-04-09 Sod3  superoxide dismutase 3    Superoxide dismutase 3  Name updated 629478 APPROVED
2001-12-21 Sod3  Superoxide dismutase 3      Name updated 69729 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in epididymis 730184
gene_homology presence of Asp28 is associated with dimerization of the rat protein rather than tetramer formation observed in mice and human homologs, which contain Val28 730025
gene_mutations_overexpression D28V mutant forms a tetramer and has high affinity for heparin sulfate 730025
gene_physical_interaction binds to heparin 730119
gene_process may be involved in preserving spermatozoa fertility by preventing lipid peroxidation 730184
gene_protein forms a dimer; a copper-zinc containing glycoprotein 730025