Human Gene SOD2 (ENST00000538183.7_8) from GENCODE V47lift37
  Description: superoxide dismutase 2, transcript variant 1 (from RefSeq NM_000636.4)
Gencode Transcript: ENST00000538183.7_8
Gencode Gene: ENSG00000291237.1_6
Transcript (Including UTRs)
   Position: hg19 chr6:160,090,101-160,114,273 Size: 24,173 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:160,103,525-160,114,199 Size: 10,675 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:160,090,101-160,114,273)mRNA (may differ from genome)Protein (222 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SODM_HUMAN
DESCRIPTION: RecName: Full=Superoxide dismutase [Mn], mitochondrial; EC=1.15.1.1; Flags: Precursor;
FUNCTION: Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
CATALYTIC ACTIVITY: 2 superoxide + 2 H(+) = O(2) + H(2)O(2).
COFACTOR: Binds 1 manganese ion per subunit.
SUBUNIT: Homotetramer.
SUBCELLULAR LOCATION: Mitochondrion matrix.
INDUCTION: Expression is regulated by KRIT1.
PTM: Nitrated under oxidative stress. Nitration coupled with oxidation inhibits the catalytic activity.
DISEASE: Genetic variation in SOD2 is associated with susceptibility to microvascular complications of diabetes type 6 (MVCD6) [MIM:612634]. These are pathological conditions that develop in numerous tissues and organs as a consequence of diabetes mellitus. They include diabetic retinopathy, diabetic nephropathy leading to end-stage renal disease, and diabetic neuropathy. Diabetic retinopathy remains the major cause of new- onset blindness among diabetic adults. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis.
SIMILARITY: Belongs to the iron/manganese superoxide dismutase family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/sod2/";
WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=SOD2";
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.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

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: SOD2
Diseases sorted by gene-association score: microvascular complications of diabetes 6* (594), ischemia (19), diabetic polyneuropathy (16), extrinsic allergic alveolitis (15), lacrimal gland adenoid cystic carcinoma (11), diabetic neuropathy (10), tardive dyskinesia (8), asbestosis (8), aseptic meningitis (7), amyotrophic lateral sclerosis-parkinsonism/dementia complex (7), motor neuron disease (7), esophagitis (6), type 1 diabetes mellitus 10 (5), breast disease (5), prion disease (4), myoclonic epilepsy associated with ragged-red fibers (4), cardiomyopathy (4), dilated cardiomyopathy (2), mitochondrial complex i deficiency (2), mitochondrial disorders (1), parkinson disease, late-onset (1), amyotrophic lateral sclerosis 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 238.45 RPKM in Muscle - Skeletal
Total median expression: 1398.06 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.5074-0.277 Picture PostScript Text
3' UTR -4167.0013424-0.310 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
IPR001189 - Mn/Fe_SOD
IPR019833 - Mn/Fe_SOD_BS
IPR019832 - Mn/Fe_SOD_C
IPR019831 - Mn/Fe_SOD_N

Pfam Domains:
PF00081 - Iron/manganese superoxide dismutases, alpha-hairpin domain
PF02777 - Iron/manganese superoxide dismutases, C-terminal domain

SCOP Domains:
46609 - Fe,Mn superoxide dismutase (SOD), N-terminal domain
54719 - Fe,Mn superoxide dismutase (SOD), C-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1AP5 - X-ray MuPIT 1AP6 - X-ray MuPIT 1EM1 - X-ray MuPIT 1JA8 - X-ray MuPIT 1LUV - X-ray MuPIT 1LUW - X-ray MuPIT 1MSD - X-ray MuPIT 1N0J - X-ray MuPIT 1N0N - X-ray MuPIT 1PL4 - X-ray MuPIT 1PM9 - X-ray MuPIT 1QNM - X-ray MuPIT 1SZX - X-ray MuPIT 1VAR - X-ray MuPIT 1XDC - X-ray MuPIT 1XIL - X-ray MuPIT 1ZSP - X-ray MuPIT 1ZTE - X-ray MuPIT 1ZUQ - X-ray MuPIT 2ADP - X-ray MuPIT 2ADQ - X-ray MuPIT 2GDS - X-ray MuPIT 2P4K - X-ray MuPIT 2QKA - X-ray 2QKC - X-ray MuPIT 3C3S - X-ray MuPIT 3C3T - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P04179
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004784 superoxide dismutase activity
GO:0016491 oxidoreductase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0000303 response to superoxide
GO:0001315 age-dependent response to reactive oxygen species
GO:0001836 release of cytochrome c from mitochondria
GO:0003069 vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006801 superoxide metabolic process
GO:0008217 regulation of blood pressure
GO:0008285 negative regulation of cell proliferation
GO:0019430 removal of superoxide radicals
GO:0030335 positive regulation of cell migration
GO:0032364 oxygen homeostasis
GO:0034599 cellular response to oxidative stress
GO:0035722 interleukin-12-mediated signaling pathway
GO:0043524 negative regulation of neuron apoptotic process
GO:0051289 protein homotetramerization
GO:0055114 oxidation-reduction process
GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1904706 negative regulation of vascular smooth muscle cell proliferation
GO:1905461 positive regulation of vascular associated smooth muscle cell apoptotic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK097395 - Homo sapiens cDNA FLJ40076 fis, clone TESTI2000874, highly similar to Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1).
DQ595177 - Homo sapiens piRNA piR-61289, complete sequence.
DQ590083 - Homo sapiens piRNA piR-57195, complete sequence.
DQ592185 - Homo sapiens piRNA piR-59297, complete sequence.
JD117306 - Sequence 98330 from Patent EP1572962.
JD330133 - Sequence 311157 from Patent EP1572962.
BC001980 - Homo sapiens superoxide dismutase 2, mitochondrial, mRNA (cDNA clone IMAGE:3462291).
BC041951 - Homo sapiens cDNA clone IMAGE:5301545.
BC012423 - Homo sapiens superoxide dismutase 2, mitochondrial, mRNA (cDNA clone MGC:9978 IMAGE:3880111), complete cds.
BC035422 - Homo sapiens superoxide dismutase 2, mitochondrial, mRNA (cDNA clone IMAGE:3880193).
GQ891541 - Homo sapiens clone HEL-S-262 epididymis secretory sperm binding protein mRNA, complete cds.
BC016015 - Homo sapiens cDNA clone IMAGE:4711494, partial cds.
Y00472 - Human mRNA for Mn superoxide dismutase (EC 1.15.1.1.).
JD028317 - Sequence 9341 from Patent EP1572962.
JD365085 - Sequence 346109 from Patent EP1572962.
JD070384 - Sequence 51408 from Patent EP1572962.
JD514162 - Sequence 495186 from Patent EP1572962.
JD514161 - Sequence 495185 from Patent EP1572962.
JD415383 - Sequence 396407 from Patent EP1572962.
M31163 - Human tumor necrosis factor-inducible (TSG-12) mRNA fragment.
JD487382 - Sequence 468406 from Patent EP1572962.
JD212997 - Sequence 194021 from Patent EP1572962.
JD542893 - Sequence 523917 from Patent EP1572962.
JD560935 - Sequence 541959 from Patent EP1572962.
AK304766 - Homo sapiens cDNA FLJ57787 complete cds, moderately similar to Superoxide dismutase (Mn), mitochondrial precursor (EC 1.15.1.1).
X07834 - Human mRNA for manganese superoxide dismutase (EC 1.15.1.1).
AK296809 - Homo sapiens cDNA FLJ57741 complete cds, highly similar to Homo sapiens superoxide dismutase 2, mitochondrial (SOD2), transcript variant 3, mRNA.
JD281717 - Sequence 262741 from Patent EP1572962.
X15132 - Human mRNA for manganese containing superoxide dismutase (EC 1.15.1.1).
X59445 - H.sapiens mRNA for colon carcinoma Manganese Superoxide Dismutase.
X14322 - Human mRNA for mangano-superoxide dismutase (Mn-SOD).
M36693 - Human manganese-containing superoxide dismutase mRNA, complete cds.
Y00985 - Human mRNA for manganese-containing superoxide dismutase.
JD271869 - Sequence 252893 from Patent EP1572962.
A12179 - H.sapiens mRNA for Mn-superoxiddismutase.
A12178 - H.sapiens mRNA for Mn-superoxiddismutase.
AK313082 - Homo sapiens cDNA, FLJ93564, highly similar to Homo sapiens superoxide dismutase 2, mitochondrial (SOD2), mRNA.
BT006967 - Homo sapiens superoxide dismutase 2, mitochondrial mRNA, complete cds.
DQ890587 - Synthetic construct clone IMAGE:100003217; FLH164218.01X; RZPDo839D12162D superoxide dismutase 2, mitochondrial (SOD2) gene, encodes complete protein; nuclear gene for mitochondrial product.
DQ893752 - Synthetic construct Homo sapiens clone IMAGE:100008212; FLH164214.01L; RZPDo839D12161D superoxide dismutase 2, mitochondrial (SOD2) gene, encodes complete protein; nuclear gene for mitochondrial product.
AB528757 - Synthetic construct DNA, clone: pF1KE0171, Homo sapiens SOD2 gene for mitochondrial superoxide dismutase 2, without stop codon, in Flexi system.
AM392836 - Synthetic construct Homo sapiens clone IMAGE:100002132 for hypothetical protein (SOD2 gene).
AY280721 - Homo sapiens cell-line 11.9.14 manganese-containing superoxide dismutase (SOD2) mRNA, partial cds.
AY280718 - Homo sapiens cell-line MCF-12A manganese-containing superoxide dismutase (SOD2) mRNA, partial cds.
AY280719 - Homo sapiens cell-line MCF-7 manganese-containing superoxide dismutase (SOD2) mRNA, partial cds.
AY280720 - Homo sapiens cell-line BT-549 manganese-containing superoxide dismutase (SOD2) mRNA, partial cds.
DQ003134 - Homo sapiens manganese-containing superoxide dismutase (SOD2) mRNA, partial cds; nuclear gene for mitochondrial product.
LQ021074 - Sequence 17 from Patent WO2015144924.
AL050388 - Homo sapiens mRNA; cDNA DKFZp564M2422 (from clone DKFZp564M2422).
BC016934 - Homo sapiens superoxide dismutase 2, mitochondrial, mRNA (cDNA clone MGC:21350 IMAGE:4184203), complete cds.
KJ901754 - Synthetic construct Homo sapiens clone ccsbBroadEn_11148 SOD2 gene, encodes complete protein.

-  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
h_eponfkbPathway - Erythropoietin mediated neuroprotection through NF-kB

Reactome (by CSHL, EBI, and GO)

Protein P04179 (Reactome details) participates in the following event(s):

R-HSA-5688289 SIRT3 deacetylates ACCS2, GLUD, IDH2, SOD2
R-HSA-3299680 SOD2 catalyzes 2H+ + 2O2.- => O2 + H2O2 (mitochondrial matrix)
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models
R-HSA-8950505 Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
R-HSA-2151201 Transcriptional activation of mitochondrial biogenesis
R-HSA-8863678 Neurodegenerative Diseases
R-HSA-9020591 Interleukin-12 signaling
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-1643685 Disease
R-HSA-447115 Interleukin-12 family signaling
R-HSA-3299685 Detoxification of Reactive Oxygen Species
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-449147 Signaling by Interleukins
R-HSA-2262752 Cellular responses to stress
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R7R1, B3KUK2, B4DL20, B4E3K9, E1P5A9, ENST00000538183.1, ENST00000538183.2, ENST00000538183.3, ENST00000538183.4, ENST00000538183.5, ENST00000538183.6, NM_000636, P04179, P78434, Q16792, Q5TCM1, Q96EE6, Q9P2Z3, SODM_HUMAN, uc324qgp.1, uc324qgp.2
UCSC ID: ENST00000538183.7_8
RefSeq Accession: NM_000636.4
Protein: P04179 (aka SODM_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.