Human Gene SOD3 (ENST00000382120.4_5) from GENCODE V47lift37

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Description: superoxide dismutase 3 (from RefSeq NM_003102.4)
Gencode Transcript: ENST00000382120.4_5
Gencode Gene: ENSG00000109610.6_9
Transcript (Including UTRs)
Position: hg19 chr4:24,797,195-24,802,464 Size: 5,270 Total Exon Count: 2 Strand: +
Coding Region
Position: hg19 chr4:24,801,144-24,801,866 Size: 723 Coding Exon Count: 1

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr4:24,797,195-24,802,464)			mRNA (may differ from genome)		Protein (240 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SODE_HUMAN DESCRIPTION: RecName: Full=Extracellular superoxide dismutase [Cu-Zn]; Short=EC-SOD; EC=1.15.1.1; Flags: Precursor; FUNCTION: Protect the extracellular space from toxic effect of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen. CATALYTIC ACTIVITY: 2 superoxide + 2 H(+) = O(2) + H(2)O(2). COFACTOR: Binds 1 copper ion per subunit (By similarity). COFACTOR: Binds 1 zinc ion per subunit (By similarity). SUBUNIT: Homotetramer. SUBCELLULAR LOCATION: Secreted, extracellular space. Note=99% of EC-SOD is anchored to heparan sulfate proteoglycans in the tissue interstitium, and 1% is located in the vasculature in equilibrium between the plasma and the endothelium. TISSUE SPECIFICITY: Expressed in blood vessels, heart, lung, kidney and placenta. Major SOD isoenzyme in extracellular fluids such as plasma, lymph and synovial fluid. POLYMORPHISM: The variant Gly-231 which is found in about 2.2% of individual displays a 10-fold increased plasma EC-SOD content due to reduced heparin-binding affinity and thus the impairment of its binding ability to endothelial cell surface. SIMILARITY: Belongs to the Cu-Zn superoxide dismutase family. WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/sod3/"; WEB RESOURCE: Name=Wikipedia; Note=Superoxide dismutase entry; URL="http://en.wikipedia.org/wiki/Superoxide_dismutase";

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: SOD3 Diseases sorted by gene-association score: asbestosis (13), diabetic polyneuropathy (9), myocardial stunning (9), optic neuritis (6), diabetic neuropathy (6), amyotrophic lateral sclerosis-parkinsonism/dementia complex (6), heart disease (4)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D002945 Cisplatin D002994 Clofibrate D003300 Copper D004958 Estradiol D004967 Estrogens D004997 Ethinyl Estradiol D010100 Oxygen D010634 Phenobarbital D011374 Progesterone D013749 Tetrachlorodibenzodioxin C018021 cobaltous chloride C059514 resveratrol D015056 1-Methyl-3-isobutylxanthine C011269 2,5-hexanedione C023514 2,6-dinitrotoluene C093973 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one C573693 2-(4-((4-(6-methoxy-3-pyridinyl)-5-(4-(trifluoromethoxy)phenyl)-2-thiazolyl)methoxy)-2-methylphenoxy)acetic acid C031278 2-chloroethyl ethyl sulfide C010643 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid D000082 Acetaminophen D000643 Ammonium Chloride D001149 Arsenates D017632 Asbestos, Serpentine D017638 Asbestos, Crocidolite C051597 Bandrowski's base D001564 Benzo(a)pyrene D002251 Carbon Tetrachloride D002726 Chlorogenic Acid D004390 Chlorpyrifos D003024 Clozapine D003907 Dexamethasone D003976 Diazinon D003993 Dibutyl Phthalate D004041 Dietary Fats D004121 Dimethyl Sulfoxide D004137 Dinitrochlorobenzene D004221 Disulfiram D004237 Diuron D004610 Ellagic Acid D005054 Eugenol D018120 Finasteride D019833 Genistein D005947 Glucose D006034 Glycyrrhetinic Acid D006220 Haloperidol D006581 Hexachlorobenzene D006820 Hyaluronic Acid D006861 Hydrogen Peroxide D007501 Iron D007649 Ketamine D019808 Losartan C523799 MRK 003 C568376 MT19c compound D008627 Mercuric Chloride D008767 Methylmercury Compounds D015735 Mifepristone D010081 Oxazolone D010126 Ozone D010269 Paraquat D010705 Phosgene D010758 Phosphorus D010795 Phthalic Acids D059808 Polyphenols D011285 Pregnenolone Carbonitrile D011692 Puromycin Aminonucleoside D020849 Raloxifene D017382 Reactive Oxygen Species C093642 SB 203580 D012834 Silver D013311 Streptozocin D013481 Superoxides D017392 Thiobarbituric Acid Reactive Substances D014118 Toxins, Biological D014212 Tretinoin D014266 Trientine D014640 Vancomycin D001335 Vehicle Emissions D014750 Vincristine C065179 atorvastatin C039671 ciglitazone C020722 cinnamyl alcohol C007095 cobaltiprotoporphyrin C015763 cumene C017180 decamethrin C045651 epigallocatechin gallate C070081 fulvestrant C080043 hexyl cinnamic aldehyde C036643 isoeugenol C008261 lead acetate C029891 lead chloride C025340 manganese chloride C043243 methyl tert-butyl ether C029938 nickel sulfate C025589 ochratoxin A C485800 osajin C041786 palm oil C084656 paricalcitol C474837 pomiferin C033607 puerarin C529148 rosavin C089730 rosiglitazone C017947 sodium arsenite C061133 tamibarotene C517826 tetrabrominated diphenyl ether 47 C055421 tin mesoporphyrin C015559 trimellitic anhydride

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 464.99 RPKM in Artery - Aorta Total median expression: 3620.89 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-45.30	95	-0.477	Picture	PostScript	Text
3' UTR	-175.60	598	-0.294	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR024134 - SOD_Cu/Zn_/chaperones
IPR018152 - SOD_Cu/Zn_BS
IPR024141 - SOD_Cu/Zn_extracel
IPR001424 - SOD_Cu_Zn_dom

Pfam Domains:
PF00080 - Copper/zinc superoxide dismutase (SODC)

SCOP Domains:
49329 - Cu,Zn superoxide dismutase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2JLP - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P08294


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004784 superoxide dismutase activity GO:0005507 copper ion binding GO:0005515 protein binding GO:0008201 heparin binding GO:0008270 zinc ion binding GO:0016209 antioxidant activity GO:0016491 oxidoreductase activity GO:0046872 metal ion binding Biological Process: GO:0001666 response to hypoxia GO:0006801 superoxide metabolic process GO:0006979 response to oxidative stress GO:0019430 removal of superoxide radicals GO:0034599 cellular response to oxidative stress GO:0046688 response to copper ion GO:0055114 oxidation-reduction process GO:0098869 cellular oxidant detoxification Cellular Component: GO:0005576 extracellular region GO:0005615 extracellular space GO:0005634 nucleus GO:0005737 cytoplasm GO:0005796 Golgi lumen GO:0031012 extracellular matrix GO:0070062 extracellular exosome

Descriptions from all associated GenBank mRNAs


	LF206843 - JP 2014500723-A/14346: Polycomb-Associated Non-Coding RNAs. AK313935 - Homo sapiens cDNA, FLJ94575, highly similar to Homo sapiens superoxide dismutase 3, extracellular (SOD3), mRNA. HM005488 - Homo sapiens clone HTL-T-175 testicular tissue protein Li 175 mRNA, complete cds. LF358497 - JP 2014500723-A/166000: Polycomb-Associated Non-Coding RNAs. JD135063 - Sequence 116087 from Patent EP1572962. BC014418 - Homo sapiens superoxide dismutase 3, extracellular, mRNA (cDNA clone MGC:20077 IMAGE:4644224), complete cds. J02947 - Human extracellular-superoxide dismutase (SOD3) mRNA, complete cds. JD560204 - Sequence 541228 from Patent EP1572962. JD079037 - Sequence 60061 from Patent EP1572962. DQ892086 - Synthetic construct clone IMAGE:100004716; FLH184174.01X; RZPDo839C12144D superoxide dismutase 3, extracellular (SOD3) gene, encodes complete protein. DQ895280 - Synthetic construct Homo sapiens clone IMAGE:100009740; FLH184170.01L; RZPDo839C12143D superoxide dismutase 3, extracellular (SOD3) gene, encodes complete protein. CR541853 - Homo sapiens full open reading frame cDNA clone RZPDo834H0432D for gene SOD3, superoxide dismutase 3, extracellular; complete cds, incl. stopcodon. LF358498 - JP 2014500723-A/166001: Polycomb-Associated Non-Coding RNAs. LF358500 - JP 2014500723-A/166003: Polycomb-Associated Non-Coding RNAs. LF358502 - JP 2014500723-A/166005: Polycomb-Associated Non-Coding RNAs. LF358504 - JP 2014500723-A/166007: Polycomb-Associated Non-Coding RNAs. JD133089 - Sequence 114113 from Patent EP1572962. JD419544 - Sequence 400568 from Patent EP1572962. JD423039 - Sequence 404063 from Patent EP1572962. JD564663 - Sequence 545687 from Patent EP1572962. LF358506 - JP 2014500723-A/166009: Polycomb-Associated Non-Coding RNAs. JD391815 - Sequence 372839 from Patent EP1572962. JD187193 - Sequence 168217 from Patent EP1572962. JD192486 - Sequence 173510 from Patent EP1572962. LF358509 - JP 2014500723-A/166012: Polycomb-Associated Non-Coding RNAs. LF358511 - JP 2014500723-A/166014: Polycomb-Associated Non-Coding RNAs. JD129356 - Sequence 110380 from Patent EP1572962. LF358513 - JP 2014500723-A/166016: Polycomb-Associated Non-Coding RNAs. JD107013 - Sequence 88037 from Patent EP1572962. MA442420 - JP 2018138019-A/14346: Polycomb-Associated Non-Coding RNAs. MA594074 - JP 2018138019-A/166000: Polycomb-Associated Non-Coding RNAs. MA594075 - JP 2018138019-A/166001: Polycomb-Associated Non-Coding RNAs. MA594077 - JP 2018138019-A/166003: Polycomb-Associated Non-Coding RNAs. MA594079 - JP 2018138019-A/166005: Polycomb-Associated Non-Coding RNAs. MA594081 - JP 2018138019-A/166007: Polycomb-Associated Non-Coding RNAs. MA594083 - JP 2018138019-A/166009: Polycomb-Associated Non-Coding RNAs. MA594086 - JP 2018138019-A/166012: Polycomb-Associated Non-Coding RNAs. MA594088 - JP 2018138019-A/166014: Polycomb-Associated Non-Coding RNAs. MA594090 - JP 2018138019-A/166016: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	BioCyc Knowledge Library DETOX1-PWY - superoxide radicals degradation DETOX1-PWY-1 - reactive oxygen species degradation BioCarta from NCI Cancer Genome Anatomy Project h_longevityPathway - The IGF-1 Receptor and Longevity Reactome (by CSHL, EBI, and GO) Protein P08294 (Reactome details) participates in the following event(s): R-HSA-3299682 SOD3 catalyzes 2H+ + 2O2.- => O2 + H2O2 (extracellular) R-HSA-3299685 Detoxification of Reactive Oxygen Species R-HSA-2262752 Cellular responses to stress R-HSA-8953897 Cellular responses to external stimuli

Other Names for This Gene


	Alternate Gene Symbols: ENST00000382120.1, ENST00000382120.2, ENST00000382120.3, NM_003102, P08294, Q5U781, Q6FHA2, SODE_HUMAN, uc318qqw.1, uc318qqw.2 UCSC ID: ENST00000382120.4_5 RefSeq Accession: NM_003102.4 Protein: P08294 (aka SODE_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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