• Home
• Tools
  • Tools Overview
  • Query Tools

    
    • QuickSearch
    • QueryBuilder
    • TermLink
    • CytoSearch
    • RNA-Seq Search
    • Interactions Browser
    • ImageBrowse
    • Find A Person
    • Google™ FlyBase
  • Genomic/Map Tools

    
    • BLAST
    • GBrowse
    • GBrowse 2 Beta
    • CytoSearch
    • Feature Mapper
    • Aberrations Maps
    • Chromosome Maps
    • Coordinates Converter
  • Retrieve/Convert

    
    • Batch Download
    • Coordinates Converter
    • ID Converter
  • Data Submission

    
    • Fast-Track Your Paper
    • Submit Personal Comm
    • Add A New Person
    • Update Person Info
  • People

    
    • Find A Person
    • Add A New Person
    • Update Person Info
• Files
  • Files Overview
  • Current release
  • Archived releases
  • Map Conversion
  • FTP site:
  • Releases (FTP)
  • Genomes (FTP)
• Species
  • Phylogeny
  • Sequenced Species
  • Synteny Table
  • Color Illustrations
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All Resources
  • Model Organisms
  • Stock Collections
  • Vectors & Constructs
  • Other links:
  • BDGP
  • DGRC
  • DIS by issue
  • FlyExpress
  • Interactive Fly
  • modENCODE
  • Textpresso for Fly
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • FlyBase Guides
  • Video Tutorials
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Contact FlyBase
• Archives
  • Prior Release
  • Other Archives
  • Coordinate Converter

Gene Dvir\Sod

General Information
Symbol	Dvir\Sod	Species	D. virilis
Name	Superoxide dismutase	Annotation symbol	GJ11304
Feature type	protein_coding_gene	FlyBase ID	FBgn0013096
Gene Model Status	Current	Stock availability	None publicly available
Also Known As	sod
Genomic Location
Chromosome (arm)	scaffold_13049	Recombination map
Cytogenetic map		Sequence location	scaffold_13049:23,153,197..23,154,211 [-]
Genomic Maps	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Superoxide dismutase is referred to in FlyBase by the symbol Dvir\Sod (GJ11304, FBgn0013096). It is a protein_coding_gene from Drosophila virilis. An electronic pipeline based on InterPro domains suggests that it has the molecular function: metal ion binding; superoxide dismutase activity. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: oxidation-reduction process; superoxide metabolic process. No alleles are reported. It has one annotated transcript and one annotated polypeptide. Protein features are: Superoxide dismutase (Cu/Zn) / chaperones; Superoxide dismutase, copper/zinc binding domain; Superoxide dismutase, copper/zinc, binding site. Gene sequence location is scaffold_13049:23153197..23154211.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dvir\Sod for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Dvir\Sod-RA FBtr0227229  XM_002048496   462   153
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Dvir\Sod-PA   FBpp0225721   15.8   153   6.29     XP_002048532   EDW70874
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Superoxide dismutase, copper/zinc, binding site (IPR018152) Superoxide dismutase, copper/zinc binding domain (IPR001424) Superoxide dismutase (Cu/Zn) / chaperones (IPR024134)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name CH940647 EDW70874   X13831 CAA32060
UniProtKB/Swiss-Prot	P10791
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
modENCODE Anatomy RNA-Seq
modENCODE Development RNA-Seq
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Dvir\Sod Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Dvir\Sod Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term Evidence References
metal ion binding inferred from electronic annotation with InterPro:IPR001424 (FlyBase Curators et al., 2004-) superoxide dismutase activity inferred from electronic annotation with InterPro:IPR018152 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
oxidation-reduction process inferred from electronic annotation with InterPro:IPR001424, InterPro:IPR018152, InterPro:IPR024134 (FlyBase Curators et al., 2004-) superoxide metabolic process inferred from electronic annotation with InterPro:IPR001424, InterPro:IPR024134 (FlyBase Curators et al., 2004-)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	gene   nuclear_gene (Drosophila 12 Genomes Consortium, 2008) protein_coding_gene (Drosophila 12 Genomes Consortium, 2008)
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Dvir\Sod allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (1) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6549K5 Dipteran inclusive ortholog search EOG6H9XVT Insect inclusive ortholog search EOG6XSJMG Arthropod inclusive ortholog search EOG67SQWX Metazoa inclusive ortholog search EOG6677FZ
Ortholog(s) in Drosophila melanogaster (EOG6549K5)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Sod Y
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (1) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila melanogaster Dmel\Sod
Stocks & Reagents
Stocks Listed in FlyBase ( 0 )
Genomic Clones ( 0 )
cDNA Clones ( 0 )
	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 GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	The Dwil\Sod gene region has been cloned and sequenced, and compared with the comparable region from D.virilis, D.melanogaster and D.simulans. (Kwiatowski et al., 1994) Camo\Sod has been cloned, sequenced and compared with the Sod genes from a number of Drosophila species, including D.virilis. (Kwiatowski et al., 1992) Phylogenetic trees for 25 Cu-Zn superoxide dismutases (including D.melanogaster Sod and Dvir\Sod) and 31 Mn/Fe superoxide dismutases (including D.melanogaster Sod2) have been constructed and the evolutionary rate of change for the two groups of proteins has been compared. (Smith and Doolittle, 1992) Dvir\Sod has been cloned and sequenced. (Kwiatowski and Ayala, 1989)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • XM_002048496 RefSeq (Proteins) • XP_002048532 DDBJ / EMBL / GenBank • CAA32060 EDW70874 X13831 Entrez Gene - A searchable database of RefSeq genes. • 6624514 UniProtKB/Swiss-Prot • P10791
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Superoxide dismutase, copper/zinc, binding site (IPR018152) Superoxide dismutase, copper/zinc binding domain (IPR001424) Superoxide dismutase (Cu/Zn) / chaperones (IPR024134)
Linkouts
	FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0013096
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	Cu,Zn Sod (Kwiatowski et al., 1994) Cu-Zn SOD (Smith and Doolittle, 1992) dvir_GLEANR_11352 (Drosophila 12 Genomes Consortium, 2008) Dvir\Sod (Drosophila 12 Genomes Consortium, 2008) sod (McVean and Vieira, 1999, Joshi and Nguyen, 1995) Sod (Drosophila 12 Genomes Consortium, 2008)
Name Synonym	Superoxide dismutase
Secondary FlyBase IDs
References ( 19 )
Research paper	Drosophila 12 Genomes Consortium et al., 2007, Nature 450(7167): 203--218 Evolution of genes and genomes on the Drosophila phylogeny. [FBrf0200326] Avedisov et al., 2001, Mol. Biol. Evol. 18(11): 2110--2118 Rapid Evolution of a Cyclin A Inhibitor Gene, roughex, in Drosophila. [FBrf0139753] Dunn et al., 2001, Genetics 157(1): 295--305 Substitution rates in Drosophila nuclear genes. Implications for translational selection. [FBrf0132336] Tarrio et al., 2001, Mol. Biol. Evol. 18(8): 1464--1473 Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. [FBrf0137314] Rodriguez-Trelles et al., 2000, Mol. Biol. Evol. 17(11): 1710--1717 Evidence for a high ancestral GC content in Drosophila. [FBrf0131391] McVean and Vieira, 1999, J. Mol. Evol. 49(1): 63--75 The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing. [FBrf0108927] Tatarenkov et al., 1999, J. Mol. Evol. 48(4): 445--462 On the evolution of dopa decarboxylase (Ddc) and Drosophila systematics. [FBrf0108025] Moriyama and Powell, 1997, J. Mol. Evol. 45(5): 514--523 Codon usage bias and tRNA abundance in Drosophila. [FBrf0098854] Joshi and Nguyen, 1995, Nucleic Acids Res. 23(4): 541--549 5' untranslated leader sequences of eukaryotic mRNAs encoding heat shock induced proteins. [FBrf0080602] Kwiatowski et al., 1994, J. Mol. Evol. 38(5): 443--454 Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene. [FBrf0073675] Kwiatowski et al., 1994, Gene 147(2): 295--296 Characterization of a Cu/Zn superoxide dismutase-encoding gene region in Drosophila willistoni. [FBrf0076483] Kwiatowski et al., 1992, Insect Mol. Biol. 1(1): 3--13 Structure and sequence of the Cu, Zn superoxide dismutase gene of Chymomyza amoena: phylogeny of the genus and codon-use evolution. [FBrf0063605] Smith and Doolittle, 1992, J. Mol. Evol. 34: 175--184 A comparison of evolutionary rates of the two major kinds of superoxide dismutase. [FBrf0056633] Kwiatowski et al., 1991, Free Radical Res. Commun. 12-13: 363--370 The rate of Cu, Zn superoxide-dismutase evolution. [FBrf0091326] Kwiatowski and Ayala, 1989, Nucleic Acids Res. 17: 2133 Drosophila virilis Cu-Zn superoxide dismutase gene sequence. [FBrf0050697] Kwiatowski et al., 1989, Nucleic Acids Res. 17: 1264 Drosophila melanogaster Cu, Zn superoxide dismutase gene sequence. [FBrf0050695]
Personal communication to FlyBase	Drosophila 12 Genomes Consortium, 2008, personal communication to FlyBase Symbols and class of gene information for the GLEANR consensus sequences of the 11 sequenced non-melanogaster Drosophila species (Drosophila ananassae, erecta, grimshawi, mojavensis, persimilis, pseudoobscura, sechellia, simulans, willistoni, virilis and yakuba). [FBrf0202436] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
FlyBase analysis	FlyBase, 2008, Newly sequenced Drosophila genomes: associations of GLEANR gene predictions (Releases 1.0) with previously known genes in FlyBase. Newly sequenced Drosophila genomes: associations of GLEANR gene predictions (Releases 1.0) with previously known genes in FlyBase. [FBrf0202439]