A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Gene Dmel\mt:ND3

General Information
SymbolDmel\mt:ND3SpeciesD. melanogaster
Namemitochondrial NADH-ubiquinone oxidoreductase chain 3Annotation symbolCG34076
Feature typeprotein_coding_geneFlyBase IDFBgn0013681
Gene Model StatusCurrent Stock availability None publicly available
Also Known AsND3
Genomic Location
Chromosome (arm)dmel_mitochondrion_genomeRecombination map
Cytogenetic mapSequence locationdmel_mitochondrion_genome:5,608..5,961 [+]

Genomic Maps

GBrowse View Help
Beta
detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene mitochondrial NADH-ubiquinone oxidoreductase chain 3 is referred to in FlyBase by the symbol Dmel\mt:ND3 (CG34076, FBgn0013681). It is a protein_coding_gene from Drosophila melanogaster. It is reported to have molecular function: NADH dehydrogenase (ubiquinone) activity. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: oxidation-reduction process. One allele is reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: NADH:ubiquinone/plastoquinone oxidoreductase, chain 3. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of no expression detected. Peak expression observed within 00-06 and 18-24 hour embryonic stages, during early larval stages, during early pupal stages. Summary of FlyAtlas Anatomical Expression Data: No FlyAtlas data available because no Affy2 ProbeSet aligns to an exon of mt:ND3. Comments on Affy2 ProbeSet: No relevant information because no Affy2 ProbeSet aligns to an exon of mt:ND3. Gene sequence location is dmel_mitochondrion_genome:5608..5961.
User Contributed Data
hide 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.
atom feed
FB2013_03
FB2013_02
All updates Click here to see a list of all updates to this record from FB2010_08 and on.
hide 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
hide Gene Model & Products
Please see the GBrowse view of Dmel\mt:ND3 for information on other features GBrowse View Help
To submit a correction to a gene model please use the Contact FlyBase form
detailed view FBtr0100863 FBtr0100864 FBtr0100865 FBtr0100866 FBtr0100867 FBtr0100868 FBtr0100869 FBtr0100870 FBtr0100871 FBtr0100872 FBtr0100873 FBtr0100874 FBtr0100875 FBtr0100876 FBtr0100877 FBpp0100177 FBpp0100178 FBpp0100179 FBpp0100180 FBpp0100181 FBpp0100182
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
mt:ND3-RA
FBtr0100870
 
  354
  117
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
mt:ND3-PA  
FBpp0100181  
13.6  
117  
8.49  
 
  NP_008283
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 (IPR000440)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AF200828
AAF77232
 
AF200829
AAF77244
 
AJ400907
CAB91057
 
J01404
AAB59244
 
M37275
AAA69709
 
U37541
AAC47817
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
hide 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
hide External Data
Linkouts
Crossreferences
hide Expression Data
hideTranscript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
hide Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term
Evidence
References
hide Expression Deduced from Reporters
hide High-Throughput Expression Data
Associated Tools
Reference
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
hide FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
hide modENCODE Anatomy RNA-Seq
hide modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (Graveley et al., 2011)
hide modENCODE Cell Lines RNA-Seq
hide modENCODE Treatments RNA-Seq
hide Expression Clusters
hide External Data & Images
Linkouts
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
•
hide Alleles & Phenotypes
hide Summary of Allele Phenotypes
Phenotype manifest in
Allele
hide Classical Alleles ( 0 )
For All Classical Alleles Show

Allele of mt:ND3ClassMutagenStocksKnown lesion
hide Alleles Carried on Transgenic Constructs ( 1 )
For All Alleles Carried on Transgenic Constructs Show

Allele of mt:ND3ClassMutagenStocksKnown lesion
mt:ND3KK1159300 Yes
hide Aneuploid Aberrations
hide Transgenic Constructs & Insertions
Transgenic Constructs
Type of construct
Name
Expression data
UAS construct
P{KK115930}
NA
Insertions
Type of insertions
Name
Expression data
hide Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
hide Terms Based on Experimental Evidence ( 0 terms )
hide Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term
Evidence
References
NADH dehydrogenase (ubiquinone) activity
inferred from electronic annotation with InterPro:IPR000440
(FlyBase Curators et al., 2004-)
non-traceable author statement
(FlyBase, 1992-, Swiss-Prot Project Members, 1990.11.1)
Biological Process
CV term
Evidence
References
oxidation-reduction process
inferred from electronic annotation with InterPro:IPR000440
(FlyBase Curators et al., 2004-)
Cellular Component
CV term
Evidence
References
mitochondrial respiratory chain complex I
non-traceable author statement
(FlyBase, 1992-)
mitochondrion
non-traceable author statement
(FlyBase, 1992-)
hide Sequence Ontology: Class of Gene
mt_gene
 
protein_coding_gene
 
hide Interactions & Pathways
hide Summary of Physical Interactions
hide Summary of Genetic Interactions
Interacts with
Please look at the allele data for full details of the genetic interactions
mt:ND3 allele
Gene
References
hide External Data
Linkouts
DroID - A comprehensive database of gene and protein interactions.
•
InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.
•
hide Orthologs
hide OrthoDB Orthologs (2) - 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
No orthologs identified
Dipteran inclusive ortholog search
No orthologs identified
Insect inclusive ortholog search
EOG6S7HNJ
Arthropod inclusive ortholog search
No orthologs identified
Metazoa inclusive ortholog search
No orthologs identified
Orthologs in Drosophila Species (None identified)
No orthologies identified
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
hideOrthologs in non-Dipteran Insects (EOG6S7HNJ)
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Nasonia vitripennis
Parasitic wasp 
Nvit\Nasvi2EG034571
 
Camponotus floridanus
Florida carpenter ant 
Cflo\CFLO12169
 
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
hide Human Orthologs (0)
Gene
OMIM
HGNC
hideAAA Orthologs (0) based on analysis using Dmel annotation version 4.3
No orthologs identified
hide Stocks & Reagents
hide Stocks Listed in FlyBase ( 0 )
hide Genomic Clones ( 0 )
hide 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
hide RNAi & Array Information
Linkouts
DRSC - Results from RNAi screens.
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
hide Antibody Information
hide Other Information
hide Discoverer
hide Etymology
hide Identification
hide Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
hide Other Comments
New annotation (CG34076) in release 4.3 of the genome annotation.
(FlyBase Genome Annotators, 2005)
hide External Crossreferences & Linkouts
Sequence Crossreferences
DDBJ / EMBL / GenBank
•
Entrez Gene - A searchable database of RefSeq genes.
•
UniProtKB/Swiss-Prot
•
Other Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 (IPR000440)
Linkouts
DroID - A comprehensive database of gene and protein interactions.
•
DRSC - Results from RNAi screens.
•
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
•
FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.
•
modMine - Data generated by the modENCODE project.
•
hide Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym
CG34076
(FlyBase Genome Annotators, 2005, Keleman et al., 2009.8.5)
mt:ND3
 
nad3
(Stewart and Beckenbach, 2009)
NADH3
(Weinreich and Rand, 2000)
ND3
(Azou and Bregliano, 2001, Nachman, 1998, Rand and Kann, 1996, Calleja et al., 1993, Seligmann, 2012, Roberti et al., 2006, Ballard, 2000)
URF3
 
Name Synonym
mitochondrial NADH-ubiquinone oxidoreductase chain 3
 
Secondary FlyBase IDs
  • FBgn0002867
hide References ( 18 )
Research paper
Seligmann, 2012, J. Theor. Biol. 298: 51--76
An overlapping genetic code for frameshifted overlapping genes in Drosophila mitochondria: Antisense antitermination tRNAs UAR insert serine. [FBrf0217548]
Stewart and Beckenbach, 2009, Gene 445(1-2): 49--57
Characterization of mature mitochondrial transcripts in Drosophila, and the implications for the tRNA punctuation model in arthropods. [FBrf0208404]
Roberti et al., 2006, Biochim. Biophys. Acta 1757(9-10): 1199--1206
MTERF3, the most conserved member of the mTERF-family, is a modular factor involved in mitochondrial protein synthesis. [FBrf0194696]
Azou and Bregliano, 2001, Heredity 86(1): 110--116
I-R system of hybrid dysgenesis in Drosophila melanogaster: analysis of the mitochondrial DNA in reactive strains exhibiting different potentials for I factor transposition. [FBrf0135828]
Ballard, 2000, J. Mol. Evol. 51(1): 48--63
Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. [FBrf0128384]
Weinreich and Rand, 2000, Genetics 156(1): 385--399
Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. [FBrf0132137]
Nachman, 1998, Genetica 102/103: 61--69
Deleterious mutations in animal mitochondrial DNA. [FBrf0104636]
Moriyama and Powell, 1997, J. Mol. Evol. 45(4): 378--391
Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. [FBrf0098855]
Rand and Kann, 1996, Mol. Biol. Evol. 13(6): 735--748
Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. [FBrf0089791]
Calleja et al., 1993, J. Biol. Chem. 268(25): 18891--18897
Mitochondrial DNA remains intact during Drosophila aging, but the levels of mitochondrial transcripts are significantly reduced. [FBrf0064388]
Karlovsky and Fartmann, 1992, J. Mol. Evol. 34(3): 254--258
Genetic code and phylogenetic origin of oomycetous mitochondria. [FBrf0056634]
Garesse, 1988, Genetics 118: 649--663
Drosophila melanogaster mitochondrial DNA: Gene organization and evolutionary considerations. [FBrf0048236]
Personal communication to FlyBase
Keleman et al., 2009.8.5, RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center
RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0208510]
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]
Abstract
Rand and Kann, 1996, A. Dros. Res. Conf. 37: 308
Are departures from neutrality strand-specific in Drosophila mitochondrial DNA? [FBrf0085792]
FlyBase analysis
FlyBase Genome Annotators, 2005, Changes affecting gene model number or type in release 4.3 of the annotated D.melanogaster genome.
Changes affecting gene model number or type in release 4.3 of the annotated D.melanogaster genome. [FBrf0188580]
FlyBase, 1992-, FlyBase curation.
FlyBase curation. [FBrf0105495]
Protein sequence record
Swiss-Prot Project Members, 1990.11.1, UniProtKB: P18930
NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 3 (EC 1.6.5.3). [FBrf0123696]