FB2025_01 , released February 20, 2025
Gene: Dmel\Fum1
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General Information
Symbol
Dmel\Fum1
Species
D. melanogaster
Name
Fumarase 1
Annotation Symbol
CG4094
Feature Type
protein_coding_gene
FlyBase ID
FBgn0286222
Gene Model Status
Current
Stock Availability
14 publicly available
Enzyme Name (EC)
fumarate hydratase (4.2.1.2)
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

l(1)G0255, Fum, l(1)G0290, lethal (1) G0255, Fumarate hydratase

Key Links
Genomic Location
Cytogenetic map
6C5-6C5
Sequence location
Recombination map
1-18
RefSeq locus
NC_004354 REGION:6678424..6681845
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables fumarate hydratase activity
inferred from electronic annotation with InterPro:IPR005677
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000154499
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:P08417
(Gene Ontology Curators, 2002-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in fumarate metabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000154499
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:P08417
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR005677
(InterPro Project Members, 2004-)
involved_in malate metabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000154499
(GO Reference Genome Project, 2011-)
involved_in tricarboxylic acid cycle
inferred from sequence or structural similarity with UniProtKB:P08417
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR018951
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000154499
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in mitochondrion
inferred from high throughput direct assay
(Tan et al., 2009, Alonso et al., 2005)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in mitochondrial matrix
inferred from sequence or structural similarity with UniProtKB:P08417
(Gene Ontology Curators, 2002-)
is_active_in mitochondrion
inferred from biological aspect of ancestor with PANTHER:PTN000154501
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
fumarate hydratase activity
(S)-malate = fumarate + H2O (4.2.1.2)
RHEA 12460:
Summaries
Gene Group (FlyBase)
FUMARATE HYDRATASES -
Fumarate hydratases are tricarboxylic-acid cycle enzymes that catalyze the reversible interconversion of fumarate and malate. (Adapted from FBrf0030365).
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
Fum: Fumarase
The structural gene for fumarase [FUM; L-malate hydro-lyase (EC 4.2.1.2)]. Enzyme level observed depends on genetic background (Laurie-Ahlberg, Maroni, Bewley, Lucchesi, and Wier, 1980, Proc. Nat. Acad. Sci. USA 77: 1073-77). Enzyme levels higher in females than in males in midlarval, pupal, and pharate-adult stages; female levels drop and are surpassed by male levels in older adults (Whitney and Lucchesi, 1972, Insect Biochem. 2: 367-70). Head and thorax have higher activities than abdomen (Pipkin, Chakrabarthy, and Bremner, 1977, J. Hered. 68: 245-52). Activity equally distributed between mitochondrial and cytoplasmic fractions (Pipkin et al.).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Fum1 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 Q9W3X6)

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

Gene model reviewed during 5.52

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

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Fum1-RA
FBtr0070953
NM_132111
1740
495
Fum1-RB
FBtr0070954
NM_167081
1668
467
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
Fum1-PA
FBpp0070914
53.6
495
8.67
Q9W3X6
NP_572339
AAF46186
Fum1-PB
FBpp0070915
50.5
467
7.62
Q8IRQ5
NP_727108
AAN09177
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\Fum1 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).

-1.16

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 5 of adulthood & male -- day 7 of adulthood & male
spermatozoon
(Dorus et al., 2006)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in mitochondrion
inferred from high throughput direct assay
(Tan et al., 2009, Alonso et al., 2005)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Fum1 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
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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 ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Fum1
Transgenic constructs containing regulatory region of Fum1
Aberrations (Deficiencies and Duplications) ( 3 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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\FH
14 of 14
Yes
Yes
Hsap\ADSL
1 of 14
No
No
Hsap\ASL
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\Fh
14 of 14
Yes
Yes
Rnor\Adsl
1 of 14
No
No
Rnor\Asl
1 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Fh1
13 of 14
Yes
Yes
Mmus\Adsl
1 of 14
No
No
Mmus\Asl
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\fh
7 of 13
Yes
Yes
Xtro\map1lc3c
5 of 13
No
Yes
Xtro\asl
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\fh
14 of 14
Yes
Yes
Drer\adsl
1 of 14
No
No
Drer\asl
1 of 14
No
No
Drer\LOC100535417
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\fum-1
13 of 14
Yes
Yes
Cele\adsl-1
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP001884
12 of 12
Yes
Yes
Agam\AgaP_AGAP002378
1 of 12
No
No
Agam\AgaP_AGAP008141
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (5)
Atha\FUM1
13 of 13
Yes
Yes
Atha\FUM2
13 of 13
Yes
Yes
Atha\AT1G36280
1 of 13
No
No
Atha\AT4G18440
1 of 13
No
No
Atha\AT5G10920
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\FUM1
13 of 13
Yes
Yes
Scer\ADE13
1 of 13
No
No
Scer\ARG4
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (5)
Spom\fum1
12 of 12
Yes
Yes
Spom\ade8
1 of 12
No
No
Spom\arg7
1 of 12
No
No
Spom\SPBC8E4.05c
1 of 12
No
No
Spom\SPBC1539.03c
1 of 12
No
No
Escherichia coli (enterobacterium) (4)
Ecol\fumC
11 of 11
Yes
Yes
Ecol\aspA
3 of 11
No
Yes
Ecol\argH
1 of 11
No
No
Ecol\purB
1 of 11
No
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Fum1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (5)
Fum2
11 of 13
Fum3
11 of 13
Fum4
11 of 13
Adsl
2 of 13
Argl
2 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
    FH; fumarate hydratase
    model of  fumarase deficiency
    IEA
    (FlyBase, 2019-)
    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?
    FH; fumarate hydratase
    14 of 14
    136850
    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
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Fum1 - Cs1
    experimental knowledge based
    (Guruharsha et al., 2011)
    Fum1 - Mdh2
    experimental knowledge based
    (Guruharsha et al., 2011)
    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
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    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.
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-18
    Cytogenetic map
    6C5-6C5
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    6C5-6C5
    Limits computationally determined from genome sequence between P{EP}Ctr1AEP1364&P{EP}EP1445 and P{EP}C3GEP1613
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    6C1-6C7
    (determined by in situ hybridisation) 6C4--8 (determined by in situ hybridisation)
    (Peter et al., 2002)
    6C1-6C7
    (determined by in situ hybridisation)
    (Schäfer et al., 1999.8.12)
    6C4-6C8
    (determined by in situ hybridisation)
    (Schäfer et al., 1999.6.15)
    Experimentally Determined Recombination Data
    Location

    1-18

    (FlyBase, 2016)

    1-18.6

    (Comeron et al., 2012)

    1-

    (Choudhary et al., 1992)

    1-[14]

    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (14)
    Genomic Clones (12)
     

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

    cDNA Clones (271)
     

    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
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          The effect of dietary sucrose and ethanol on Fum activity in the third larval instar has been studied.

          (Geer et al., 1983)

          The structural gene for fumarase (FUM; L-malate hydro-lyase). Enzyme level observed depends on genetic background (Laurie-Ahlberg, Maroni, Bewley, Lucchesi and Wier, 1980). Enzyme levels higher in females than in males in midlarval, pupal and pharate-adult stages; female levels drop and are surpassed by male levels in older adults (Whitney and Lucchesi, 1972). Head and thorax have higher activities than abdomen (Pipkin, Chakrabarthy and Bremner, 1977). Activity equally distributed between mitochondrial and cytoplasmic fractions (Pipkin et al., 1977).

          Relationship to Other Genes
          Source for database merge of

          Source for merge of: l(1)G0255 l(1)G0290 CG4094

          (Peter et al., 2002)

          Source for merge of: Fum l(1)G0255

          (Marygold, 2018.3.2)
          Additional comments

          "l(1)G0255" may correspond to "Fum" based on map position and relevant GO annotations.

          (Gelbart, 2009.2.13)

          "Fum" is likely to correspond to "l(1)G0255" and/or "CG4095" based on map position and relevant GO annotations.

          (Gelbart, 2009.2.13)

          "l(1)G0254" may affect "CG4094".

          (Peter et al., 2002)
          Nomenclature History
          Source for database identify of

          Source for identity of: Fum1 l(1)G0255

          (Marygold, 2018.3.2)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (14)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 46 )
          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.
          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.
          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)
          Linkouts
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          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 (76)