FlyBase Gene Report: Dmel\Sod3

General Information

Symbol

Dmel\Sod3

Species

D. melanogaster

Name

Superoxide dismutase 3

Annotation Symbol

CG9027

Feature Type

protein_coding_gene

FlyBase ID

FBgn0033631

Gene Model Status

Current

Stock Availability

4 publicly available

Enzyme Name (EC)

superoxide dismutase (1.15.1.1)

Gene Summary

Superoxide dismutase 3 (Sod3) encodes an extra-cellular Cu Zn superoxide dismutase that can be produced as secreted and membrane bound forms. It converts oxygen free radicals to hydrogen peroxide and is involved in free radical defense and redox balance. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

47F7-47F8

Sequence location

2R:11,380,347..11,384,114 [-]

Recombination map

2-64

RefSeq locus

NT_033778 REGION:11380347..11384114

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (8 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables superoxide dismutase activity

inferred from mutant phenotype

(Blackney et al., 2014)

inferred from direct assay

(Jung et al., 2011)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables copper ion binding

inferred from biological aspect of ancestor with PANTHER:PTN000000113

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR024134

(InterPro Project Members, 2004-)

enables superoxide dismutase activity

inferred from biological aspect of ancestor with PANTHER:PTN000000113

(GO Reference Genome Project, 2011-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in removal of superoxide radicals

inferred from mutant phenotype

(Blackney et al., 2014)

involved_in response to oxidative stress

inferred from mutant phenotype

(Jung et al., 2011)

involved_in UV protection

inferred from direct assay

(Jung et al., 2011)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in removal of superoxide radicals

inferred from biological aspect of ancestor with PANTHER:PTN000000113

(GO Reference Genome Project, 2011-)

involved_in superoxide metabolic process

inferred from electronic annotation with InterPro:IPR001424, InterPro:IPR036423

(InterPro Project Members, 2004-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in extracellular space

inferred from direct assay

(Jung et al., 2011)

located_in plasma membrane

inferred from high throughput direct assay

(Tan et al., 2009)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

SUPEROXIDE DISMUTASES

Protein Family (UniProt)

Belongs to the Cu-Zn superoxide dismutase family. (Q7JR71)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

superoxide dismutase activity

2 H(+) + 2 superoxide = H2O2 + O2 (1.15.1.1)

RHEA 20696:

Summaries

Gene Snapshot

Gene Group (FlyBase)

SUPEROXIDE DISMUTASES -: Superoxide dismutase enzymes catalyze the breakdown of superoxide into hydrogen peroxide and water and are therefore central regulators of reactive oxygen species levels. (Adapted from FBrf0184132.)

Protein Function (UniProtKB)

Protects the extracellular space from the toxic effects of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen.

(UniProt, Q7JR71)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Sod3 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q7JR71)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.49

Gene model reviewed during 6.05

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Sod3-RA

FBtr0089938

NM_165829

896

181

Sod3-RB

FBtr0089939

NM_136838

1040

181

Sod3-RD

FBtr0110897

NM_001043071

1095

217

Sod3-RE

FBtr0339489

NM_001038850

1228

243

Sod3-RF

FBtr0433531

NM_001316415

1772

181

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Sod3-PA

FBpp0088877

19.2

181

6.50

FBpp0088878

19.2

181

6.50

FBpp0110197

23.1

217

5.96

FBpp0308571

26.4

243

6.65

FBpp0390663

19.2

181

6.50

Q7JR71

NP_001303344

ALI30174

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

181 aa isoforms: Sod3-PA, Sod3-PB, Sod3-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Sod3 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Sod3_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.26

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

(Blackney et al., 2014)

adult stage | female

(Blackney et al., 2014)

Additional Descriptive Data

Isoform-specific expression is reported as well as differences in levels between males and females.

(Blackney et al., 2014)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in extracellular space

inferred from direct assay

(Jung et al., 2011)

located_in plasma membrane

inferred from high throughput direct assay

(Tan et al., 2009)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Sod3 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Sod3

View exonic expression by tissue for Dmel\Sod3

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0033631

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

36232/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0033631

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033631

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0033631

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0033631

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Sod3

Transgenic constructs containing regulatory region of Sod3

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel6060

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

partially lethal, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Sod3^GD4801

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Sod3^GD3774

viable, with Scer\GAL4^Mef2.PR

Sod3^GD4801

viable, with Scer\GAL4^pnr-MD237

Sod3^GD4801

viable, with Scer\GAL4^tin.CΔ4

Sod3^GD4801

Other Phenotypes

Allele

abnormal body color, with Scer\GAL4^pnr-MD237

Sod3^GD4801

abnormal oxidative stress response

abnormal oxidative stress response, with Scer\GAL4^da.G32

Sod3^GD4801

short lived

Sod3^G3462

short lived, with Scer\GAL4^da.G32

Sod3^GD4801

some die during pupal stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Sod3^GD4801

wild-type

Phenotype manifest in

Allele

mesothoracic tergum, with Scer\GAL4^pnr-MD237

Sod3^GD4801

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (3)

Hsap\SOD1

8 of 14

Yes

Hsap\SOD3

4 of 14

Yes

Hsap\CCS

3 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Sod1

8 of 14

Yes

Rnor\Sod3

4 of 14

Yes

Rnor\Ccs

3 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Sod1

8 of 14

Yes

Mmus\Ccs

3 of 14

Mmus\Sod3

3 of 14

Yes

Xenopus tropicalis (Western clawed frog) (4)

Xtro\sod1

6 of 13

Yes

Xtro\sod3

3 of 13

Yes

Xtro\ccs

2 of 13

Xtro\tnip2

1 of 13

Yes

Danio rerio (Zebrafish) (5)

Drer\sod1

8 of 14

Yes

Drer\sod3a

4 of 14

Yes

Drer\sod3b

4 of 14

Yes

Drer\ccs

2 of 14

Drer\LOC110439923

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\sod-5

9 of 14

Yes

Cele\sod-1

8 of 14

Cele\sod-4

8 of 14

Yes

Cele\T01D3.3

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\CUSOD2

11 of 12

Yes

6 of 12

3 of 12

3 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (6)

Atha\CSD2

9 of 13

Yes

8 of 13

8 of 13

2 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\SOD1

8 of 13

Yes

Scer\CCS1

2 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\sod1

7 of 12

Yes

Spom\ccs1

3 of 12

Escherichia coli (enterobacterium) (1)

Ecol\sodC

11 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Sod3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (4)

Sod1

10 of 13

Ccs

7 of 13

Sodq

4 of 13

Rsod

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

SOD1; superoxide dismutase 1

model of amyotrophic lateral sclerosis type 1

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

Sod3^GD4801

ameliorates Alzheimer's disease

modeled by Hsap\APP^{Arctic.Aβ42.UAS.cJa.Tag:SS(nec)}

(Favrin et al., 2013)

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

SOD1; superoxide dismutase 1

8 of 14

147450

amyotrophic lateral sclerosis type 1

SOD3; superoxide dismutase 3

4 of 14

185490

CCS; copper chaperone for superoxide dismutase

3 of 14

603864

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

62020

DroID - A comprehensive database of gene and protein interactions.

FBgn0033631

MIST (protein-protein) - An integrated Molecular Interaction Database

36232

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-64

Cytogenetic map

47F7-47F8

Sequence location

2R:11,380,347..11,384,114 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

47F7-47F8

Limits computationally determined from genome sequence between P{lacW}Tapδ^k17005&P{lacW}k05103 and P{lacW}l(2)k13403^k13403&P{lacW}Egm^k14708

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-64

(FlyBase, 2016)

2-64.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

14138

y¹ w^67c23; P{SUPor-P}Sod3^KG06029

NIG-Fly

2RG-0458

y² VhaAC39-1^cho-1 v¹; P{U6-Sod3.NIG.sgRNA}attP40/CyO

VDRC

v8760

w¹¹¹⁸; P{GD3774}v8760

v37793

w¹¹¹⁸; P{GD4801}v37793

Genomic Clones (18)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (43)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

MIP19391

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0033631

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0033631

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: CG9027 CG13200

(FlyBase Genome Annotators, 2006)

Additional comments

Annotations CG9027 and CG13200 merged as CG9027 in release 5.1 of the genome annotation.

(FlyBase Genome Annotators, 2006)

Nomenclature History

Source for database identify of

Source for identity of: Sod3 CG9027

(Jung et al., 2011)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG13200

(Schertel et al., 2013, Bjorklund et al., 2006, Giot et al., 2003)

CG9027

(National Institute of Genetics Fly Stocks, 2022-, Pegoraro et al., 2022, Widmer et al., 2018, Blackney et al., 2014, Favrin et al., 2013, Butchar et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Kong et al., 2010, Tan et al., 2009, Adryan et al., 2007, Ostrin et al., 2006, Jordan et al., 2005, Landis and Tower, 2005, Stanyon et al., 2004, Giot et al., 2003)

CT25938

(Ceriani et al., 2002)

Dmel/CG9027

(Jung et al., 2011)

SOD3

(Hewitt and Degnan, 2022, Parker et al., 2004)

Sod3

(Hoffman et al., 2023, Liu et al., 2022, Ge et al., 2021, Pang et al., 2021, Fujisawa et al., 2020, Jeon et al., 2020, Liu et al., 2020, Li et al., 2018, Widmer et al., 2018, Kurmangaliyev et al., 2015, Bischof and FlyORF project members, 2014.6.20, Blackney et al., 2014, Luck et al., 2014, Favrin et al., 2013, Landis and Tower, 2005)

dSOD3

(Wu and Storey, 2016)

dSod3

(Jung et al., 2011)

sod-3

(Chen et al., 2021)

Name Synonyms

Superoxide dismutase 3

Secondary FlyBase IDs

FBan0013200
FBgn0033630

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 63 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

36232

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q7JR71

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q7JR71

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

A1Z8K9

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q7JR71

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0033631

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

36232/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0033631

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0033631

FlyMine - An integrated database for Drosophila genomics

FBgn0033631

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG9027

MARRVEL_MODEL - MARRVEL (model organism gene)

36232

Linkouts

BioGRID - A database of protein and genetic interactions.

62020

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0033631

DroID - A comprehensive database of gene and protein interactions.

FBgn0033631

DRSC - Results frm RNAi screens

FBgn0033631

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Sod3_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033631

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0033631

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

Flygut - An atlas of the Drosophila adult midgut

FBgn0033631

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0033631

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

MIST (protein-protein) - An integrated Molecular Interaction Database

36232

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (66)

The following external sites may use different assemblies or annotations than FlyBase.

-0.26

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