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SOD2 superoxide dismutase 2 [ Homo sapiens (human) ]

Gene ID: 6648, updated on 5-Jan-2020

Summary

Official Symbol
SOD2provided by HGNC
Official Full Name
superoxide dismutase 2provided by HGNC
Primary source
HGNC:HGNC:11180
See related
Ensembl:ENSG00000112096 Ensembl:ENSG00000285441 MIM:147460
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IPOB; IPO-B; MNSOD; MVCD6; GClnc1; Mn-SOD
Summary
This gene is a member of the iron/manganese superoxide dismutase family. It encodes a mitochondrial protein that forms a homotetramer and binds one manganese ion per subunit. This protein binds to the superoxide byproducts of oxidative phosphorylation and converts them to hydrogen peroxide and diatomic oxygen. Mutations in this gene have been associated with idiopathic cardiomyopathy (IDC), premature aging, sporadic motor neuron disease, and cancer. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 1. [provided by RefSeq, Apr 2016]
Expression
Ubiquitous expression in appendix (RPKM 186.4), bone marrow (RPKM 85.8) and 23 other tissues See more
Orthologs

Genomic context

See SOD2 in Genome Data Viewer
Location:
6q25.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (159669069..159762281, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (160100148..160114353, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 69 Neighboring gene uncharacterized LOC105378085 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 pseudogene 1 Neighboring gene RNA, U4atac small nuclear 18, pseudogene Neighboring gene WT1 associated protein Neighboring gene SOD2 overlapping transcript 1 Neighboring gene acetyl-CoA acetyltransferase 2 Neighboring gene small nucleolar RNA, H/ACA box 20 Neighboring gene small nucleolar RNA, H/ACA box 29 Neighboring gene t-complex 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Microvascular complications of diabetes 6
MedGen: C2675128 OMIM: 612634 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env Free radical scavengers such as superoxide dismutase (SOD), dimethylthiourea (DMTU) and catalase attenuate morphine and gp160-induced human monocyte apoptosis PubMed
Tat tat HIV-1 Tat upregulates NQO1, CAT, SOD1, SOD2, and HMOX1 (HO1) mRNA levels in SH-SY5Y cells PubMed
tat Microarray analysis indicates HIV-1 Tat-induced upregulation of mitochondrial superoxide dismutase 2 (SOD2; Mn-SOD) in primary human brain microvascular endothelial cells PubMed
tat Cell-permeable SOD inhibits the activation of MAP kinases including ERK, JNK and p38 and the upregulation of ICAM-1 and VCAM-1 by HIV-1 Tat PubMed
tat Treatment of astrocytes with cell-permeable superoxide dismutase (SOD) leads to a decrease in Tat-induced ROS generation and NF-kappaB activation PubMed
tat HIV-1 Tat inhibits Tip60 histone-acetyltransferase activity and abolishes Tip60-dependent transcriptional activity of the Mn-SOD promoter, resulting in downregulation of Mn-SOD PubMed
tat HIV-1 Tat downregulates SOD2 expression by interacting with Sp1 and Sp3 to increase the Sp3-containing complexes on the basal SOD2 promoter PubMed
tat The membrane transduction efficiencies and biological activities of the SOD protein are enhanced by fusing with the Tat protein transduction domain (PTD) at both termini PubMed
tat HIV-1 Tat reduces the expression of MnSOD in several cell types PubMed
tat HIV-1 Tat downregulates the expression of Mn-SOD, an effect that potentiates TNF-induced NF-kappa B activation and that requires the C-terminus (amino acids 72-86) of Tat PubMed
Vif vif HIV-1 Vif upregulates the expression of superoxide dismutase 2 (SOD2, mitochondrial) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
manganese ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
manganese ion binding IDA
Inferred from Direct Assay
more info
PubMed 
manganese ion binding TAS
Traceable Author Statement
more info
PubMed 
metal ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
superoxide dismutase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
superoxide dismutase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure ISS
Inferred from Sequence or Structural Similarity
more info
 
age-dependent response to reactive oxygen species IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to oxidative stress TAS
Traceable Author Statement
more info
 
interleukin-12-mediated signaling pathway TAS
Traceable Author Statement
more info
 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of neuron apoptotic process IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of vascular smooth muscle cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
oxygen homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of vascular associated smooth muscle cell apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of vascular smooth muscle cell differentiation involved in phenotypic switching IDA
Inferred from Direct Assay
more info
PubMed 
protein homotetramerization IPI
Inferred from Physical Interaction
more info
PubMed 
regulation of blood pressure ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
release of cytochrome c from mitochondria ISS
Inferred from Sequence or Structural Similarity
more info
 
removal of superoxide radicals IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to superoxide IMP
Inferred from Mutant Phenotype
more info
PubMed 
superoxide metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
mitochondrial matrix IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial matrix TAS
Traceable Author Statement
more info
PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
superoxide dismutase [Mn], mitochondrial
Names
Mn superoxide dismutase
epididymis secretory sperm binding protein
gastric cancer-associated lncRNA 1
indophenoloxidase B
manganese-containing superoxide dismutase
mangano-superoxide dismutase
superoxide dismutase 2, mitochondrial
NP_000627.2
NP_001019636.1
NP_001019637.1
NP_001309743.1
NP_001309744.1
NP_001309745.1
NP_001309746.1
NP_001309748.1
NP_001309749.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008729.3 RefSeqGene

    Range
    74289..88466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000636.4NP_000627.2  superoxide dismutase [Mn], mitochondrial isoform A precursor

    See identical proteins and their annotated locations for NP_000627.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (A). Both variants 1 and 2 encode the same isoform (A).
    Source sequence(s)
    AA126703, AK313082, AL135914, DA318772, X07834
    Consensus CDS
    CCDS5265.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000446252.1, ENST00000538183.7
    Conserved Domains (1) summary
    COG0605
    Location:23222
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
  2. NM_001024465.3NP_001019636.1  superoxide dismutase [Mn], mitochondrial isoform A precursor

    See identical proteins and their annotated locations for NP_001019636.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) splices out a region of the 3' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (A).
    Source sequence(s)
    AA126703, AL135914, BC001980, BC012423, DA318772
    Consensus CDS
    CCDS5265.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000356022.4, ENST00000367055.8
    Conserved Domains (1) summary
    COG0605
    Location:23222
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
  3. NM_001024466.3NP_001019637.1  superoxide dismutase [Mn], mitochondrial isoform B

    See identical proteins and their annotated locations for NP_001019637.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, and splices out a region of the 3' UTR, compared to variant 1. The encoded isoform (B) is shorter than isoform A. Both variants 3 and 4 encode the same isoform (B).
    Source sequence(s)
    AA126703, AL135914, BM724413, DA318772
    Consensus CDS
    CCDS34564.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000356021.2, ENST00000367054.6
    Conserved Domains (3) summary
    COG0605
    Location:23183
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
    pfam00081
    Location:2583
    Sod_Fe_N; Iron/manganese superoxide dismutases, alpha-hairpin domain
    pfam02777
    Location:75177
    Sod_Fe_C; Iron/manganese superoxide dismutases, C-terminal domain
  4. NM_001322814.2NP_001309743.1  superoxide dismutase [Mn], mitochondrial isoform B

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (B) that is shorter than isoform A. Both variants 3 and 4 encode the same isoform (B).
    Source sequence(s)
    AA126703, AK296809, AL135914
    Consensus CDS
    CCDS34564.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000337127.4, ENST00000337404.8
    Conserved Domains (3) summary
    COG0605
    Location:23183
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
    pfam00081
    Location:2583
    Sod_Fe_N; Iron/manganese superoxide dismutases, alpha-hairpin domain
    pfam02777
    Location:75177
    Sod_Fe_C; Iron/manganese superoxide dismutases, C-terminal domain
  5. NM_001322815.2NP_001309744.1  superoxide dismutase [Mn], mitochondrial isoform C precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (C) that is shorter than isoform A.
    Source sequence(s)
    AA126703, AK304766, AL135914
    Consensus CDS
    CCDS83143.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000404804.2, ENST00000444946.6
    Conserved Domains (3) summary
    PLN02471
    Location:1157
    PLN02471; superoxide dismutase [Mn]
    pfam00081
    Location:25106
    Sod_Fe_N; Iron/manganese superoxide dismutases, alpha-hairpin domain
    pfam02777
    Location:113156
    Sod_Fe_C; Iron/manganese superoxide dismutases, C-terminal domain
  6. NM_001322816.1NP_001309745.1  superoxide dismutase [Mn], mitochondrial isoform D

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks three 3' exons but contains an alternate 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (D) has a distinct C-terminus and is shorter than isoform A.
    Source sequence(s)
    AL050388, AV658055, BC016934, BU164685, CD367203, DA041701, DA318772
    Consensus CDS
    CCDS83142.1
    UniProtKB/TrEMBL
    G5E9P6, Q96AM7, Q9UG59
    Related
    ENSP00000406713.2, ENST00000452684.2
    Conserved Domains (1) summary
    pfam00081
    Location:2576
    Sod_Fe_N; Iron/manganese superoxide dismutases, alpha-hairpin domain
  7. NM_001322817.2NP_001309746.1  superoxide dismutase [Mn], mitochondrial isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains alternate 5' and 3' exon structure, and it thus differs in both UTRs and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (E) is shorter at the N-terminus, compared to isoform A. Variants 7, 8 and 9 all encode the same isoform (E).
    Source sequence(s)
    AA126703, AK097395, AL135914
    Consensus CDS
    CCDS83141.1
    UniProtKB/Swiss-Prot
    P04179
    Related
    ENSP00000442920.1, ENST00000546087.5
    Conserved Domains (1) summary
    COG0605
    Location:1176
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
  8. NM_001322819.2NP_001309748.1  superoxide dismutase [Mn], mitochondrial isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (E) is shorter at the N-terminus, compared to isoform A. Variants 7, 8 and 9 all encode the same isoform (E).
    Source sequence(s)
    AL135914
    Consensus CDS
    CCDS83141.1
    UniProtKB/Swiss-Prot
    P04179
    Conserved Domains (1) summary
    COG0605
    Location:1176
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]
  9. NM_001322820.2NP_001309749.1  superoxide dismutase [Mn], mitochondrial isoform E

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (E) is shorter at the N-terminus, compared to isoform A. Variants 7, 8 and 9 all encode the same isoform (E).
    Source sequence(s)
    AA126703, AL135914, DA094180, X07834
    Consensus CDS
    CCDS83141.1
    UniProtKB/Swiss-Prot
    P04179
    Conserved Domains (1) summary
    COG0605
    Location:1176
    SodA; Superoxide dismutase [Inorganic ion transport and metabolism]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    159669069..159762281 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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