FB2024_02 , released April 23, 2024
Gene: Dmel\mt:ND4
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General Information
Symbol
Dmel\mt:ND4
Species
D. melanogaster
Name
mitochondrial NADH-ubiquinone oxidoreductase chain 4
Annotation Symbol
CG34085
Feature Type
protein_coding_gene
FlyBase ID
FBgn0262952
Gene Model Status
Current
Stock Availability
2 publicly available
Enzyme Name (EC)
NADH:ubiquinone reductase (H(+)-translocating) (7.1.1.2)
Gene Summary
Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). (UniProt, P18931)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

ND4, dND4, BEST:CK00534 , nad4

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
RefSeq locus
NC_024511 REGION:8207..9545
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
Function
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables NADH dehydrogenase (ubiquinone) activity
inferred from electronic annotation with InterPro:IPR003918
(InterPro Project Members, 2004-)
contributes_to NADH dehydrogenase activity
inferred from biological aspect of ancestor with PANTHER:PTN000511780
(GO Reference Genome Project, 2011-)
enables ubiquinone binding
inferred from biological aspect of ancestor with PANTHER:PTN000511780
(GO Reference Genome Project, 2011-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in aerobic respiration
inferred from biological aspect of ancestor with PANTHER:PTN000511780
(GO Reference Genome Project, 2011-)
involved_in ATP synthesis coupled electron transport
inferred from electronic annotation with InterPro:IPR003918
(InterPro Project Members, 2004-)
involved_in electron transport coupled proton transport
inferred from biological aspect of ancestor with PANTHER:PTN000511780
(GO Reference Genome Project, 2011-)
involved_in mitochondrial electron transport, NADH to ubiquinone
inferred by curator from GO:0005747
(Agip et al., 2023)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of mitochondrial respiratory chain complex I
inferred from direct assay
(Agip et al., 2023)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of mitochondrial respiratory chain complex I
inferred from sequence or structural similarity with UniProtKB:P03905
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN001865568
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the complex I subunit 4 family. (P18931)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
NADH dehydrogenase activity
RHEA 11356: NADH dehydrogenase (ubiquinone) activity
a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) (7.1.1.2)
RHEA 29091:
Summaries
Gene Group (FlyBase)
MITOCHONDRIAL COMPLEX I - CORE SUBUNITS -
Mitochondrial Complex I is the first and largest holoenzyme of the mitochondrial electron transport chain. It oxidizes NADH from the tricarboxylic acid cycle and β oxidation of fatty acids, reduces ubiquinone and transports protons across the inner membrane, contributing to the proton-motive force. It is also involved in the cellular production of reactive oxygen species. Fourteen distinct subunits form the catalytic centers of the enzyme as they are directly involved in transferring electrons from NADH to ubiquinone, or for generation of the membrane potential - they are referred to as the 'core' or 'central' subunits and are conserved from the ancestral enzyme in bacteria to mammals. Seven core subunits are encoded by mtDNA, while the others are encoded the nuclear genome. (Adapted from PMID:23527692 and FBrf0244962.)
MITOCHONDRIAL COMPLEX I - TESTIS-SPECIFIC VARIANT -
Mitochondrial Complex I is the first and largest holoenzyme of the mitochondrial electron transport chain. It oxidizes NADH from the tricarboxylic acid cycle and _ oxidation of fatty acids, reduces ubiquinone and transports protons across the inner membrane, contributing to the proton-motive force. It is also involved in the cellular production of reactive oxygen species. Fourteen distinct subunits form the catalytic centers of the enzyme as they are directly involved in transferring electrons from NADH to ubiquinone, or for generation of the membrane potential. (Adapted from PMID:23527692 and FBrf0244962.)
MITOCHONDRIAL COMPLEX I -
Mitochondrial Complex I is the first and largest holoenzyme of the mitochondrial electron transport chain. It oxidizes NADH from the tricarboxylic acid cycle and _ oxidation of fatty acids, reduces ubiquinone and transports protons across the inner membrane, contributing to the proton-motive force. It is also involved in the cellular production of reactive oxygen species. Fourteen distinct subunits form the catalytic centers of the enzyme as they are directly involved in transferring electrons from NADH to ubiquinone, or for generation of the membrane potential. (Adapted from PMID:23527692 and FBrf0244962.)
Protein Function (UniProtKB)
Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity).
(UniProt, P18931)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\mt:ND4 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 P18931)

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
PDB - An information portal to biological macromolecular structures
Comments on Gene Model
Sequence Ontology: Class of Gene
mt_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
mt:ND4-RB
FBtr0433500
1339
446
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
mt:ND4-PB
FBpp0390632
51.4
446
8.69
A0A075E721
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
PDB - An information portal to biological macromolecular structures
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\mt:ND4 using the Feature Mapper tool.

External Data
Crossreferences
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).

NA

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
• membrane
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of mitochondrial respiratory chain complex I
inferred from direct assay
(Agip et al., 2023)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mt:ND4 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of mt:ND4
Transgenic constructs containing regulatory region of mt:ND4
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
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.
    Phenotype manifest in
    Allele
    Orthologs
    Downloads
    Download All DIOPT Orthologs
    Human Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Homo sapiens (Human) (3)
    Hsap\ND4
    12 of 14
    Yes
    Yes
    Hsap\ND2
    1 of 14
    No
    No
    Hsap\ND5
    1 of 14
    No
    No
    Model Organism Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Rattus norvegicus (Norway rat) (3)
    Rnor\ND4
    12 of 14
    Yes
    Yes
    Rnor\ND2
    1 of 14
    No
    No
    Rnor\ND5
    1 of 14
    No
    No
    Mus musculus (laboratory mouse) (3)
    Mmus\ND4
    11 of 14
    Yes
    Yes
    Mmus\ND2
    1 of 14
    No
    No
    Mmus\ND5
    1 of 14
    No
    No
    Xenopus tropicalis (Western clawed frog) (1)
    Xtro\ND4
    10 of 13
    Yes
    Yes
    Danio rerio (Zebrafish) (2)
    Drer\ND4
    12 of 14
    Yes
    Yes
    Drer\ND5
    1 of 14
    No
    No
    Caenorhabditis elegans (Nematode, roundworm) (2)
    Cele\ND4
    11 of 14
    Yes
    Yes
    Cele\ND5
    1 of 14
    No
    No
    Anopheles gambiae (African malaria mosquito) (3)
    Agam\ND4
    9 of 12
    Yes
    Yes
    Agam\AgaP_AGAP012727
    6 of 12
    No
    Yes
    Agam\ND5
    1 of 12
    No
    No
    Arabidopsis thaliana (thale-cress) (6)
    Atha\ndhD
    8 of 13
    Yes
    Yes
    Atha\AT2G07633
    1 of 13
    No
    Yes
    Atha\AT2G07689
    1 of 13
    No
    No
    Atha\nad4
    1 of 13
    No
    Yes
    Atha\ndhB
    1 of 13
    No
    No
    Atha\ndhF
    1 of 13
    No
    No
    Saccharomyces cerevisiae (Brewer's yeast) (0)
    Schizosaccharomyces pombe (Fission yeast) (0)
    Escherichia coli (enterobacterium) (7)
    Ecol\nuoM
    8 of 11
    Yes
    Yes
    Ecol\hycC
    1 of 11
    No
    Yes
    Ecol\hyfB
    1 of 11
    No
    Yes
    Ecol\hyfD
    1 of 11
    No
    Yes
    Ecol\hyfF
    1 of 11
    No
    No
    Ecol\nuoL
    1 of 11
    No
    No
    Ecol\nuoN
    1 of 11
    No
    No
    Other Organism Orthologs (via OrthoDB)
    Data provided directly from OrthoDB:mt:ND4. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    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 ( 0 )
      Human Ortholog
      Disease
      Evidence
      References
      Modifiers Based on Experimental Evidence ( 0 )
      Allele
      Disease
      Interaction
      References
      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?
      MT-ND4; mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4
      12 of 14
      516003
          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
          Interactions Browser
          Summary of Genetic Interactions
          esyN Network Diagram
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          External Data
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          Pathways
          Signaling Pathways (FlyBase)
          Metabolic Pathways
          FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
          KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
          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)
          mitochondrion_genome
          Recombination map
          Cytogenetic map
          Sequence location
          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
          Stocks and Reagents
          Stocks (2)
          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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

            cDNA clones, fully sequenced
            BDGP DGC clones
              Other clones
                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.

                  cDNA Clones, End Sequenced (ESTs)
                  BDGP DGC clones
                    Other clones
                      RNAi and Array Information
                      Linkouts
                      Antibody Information
                      Laboratory Generated Antibodies
                       

                      polyclonal

                      (Murari et al., 2020)
                      Commercially Available Antibodies
                       
                      Cell Line Information
                      Publicly Available Cell Lines
                       
                        Other Stable Cell Lines
                         
                          Other Comments

                          New annotation (CG34085) in release 4.3 of the genome annotation.

                          (FlyBase Genome Annotators, 2005)

                          During oogenesis RNA from mt:srRNA, mt:lrRNA, mt:ND2, mt:CoI, mt:CoII, mt:CoIII, mt:ND4, mt:ND5 and mt:Cyt-b shows fluctuations in RNA density after stage 9 in follicle and nurse cells.There is a correlation between the mtRNA level and the cell volume and/or the nuclear DNA content suggesting a global extra-mitochondrial, transcriptional control mechanism.

                          (Tourmente et al., 1990)
                          Relationship to Other Genes
                          Source for database merge of

                          Source for merge of: mt:ND4 BEST:CK00534

                          (FlyBase, 1996-)
                          Additional comments
                          Nomenclature History
                          Source for database identify of
                          Nomenclature comments
                          Etymology
                          Synonyms and Secondary IDs (11)
                          Datasets (0)
                          Study focus (0)
                          Experimental Role
                          Project
                          Project Type
                          Title
                          Study result (0)
                          Result
                          Result Type
                          Title
                          External Crossreferences and Linkouts ( 39 )
                          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.
                          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.
                          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.
                          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                          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.
                          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                          InterPro - A database of protein families, domains and functional sites
                          KEGG Genes - Molecular building blocks of life in the genomic space.
                          MARRVEL_MODEL - MARRVEL (model organism gene)
                          PDB - An information portal to biological macromolecular structures
                          Linkouts
                          DroID - A comprehensive database of gene and protein interactions.
                          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                          FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
                          KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
                          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.
                          Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
                          References (74)