FB2021_01, released Feb 18, 2021

Gene: Dmel\D2hgdh

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General Information
Symbol
Dmel\D2hgdh
Species
D. melanogaster
Name
D-2-hydroxyglutaric acid dehydrogenase
Annotation Symbol
CG3835
Feature Type
protein_coding_gene
FlyBase ID
FBgn0023507
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Snapshot
D-2-hydroxyglutaric acid dehydrogenase (D2hgdh) encodes an enzyme involved in oxidation-reduction metabolism. [Date last reviewed: 2019-09-19]
Other Summaries
Also Known As

EG:87B1.3

Key Links
Genomic Location
Cytogenetic map
2D4-2D4
Sequence location
X:2,141,489..2,144,937 [+]
Recombination map

1-0.6

RefSeq locus
NC_004354 REGION:2141489..2144937
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables (R)-2-hydroxyglutarate dehydrogenase activity
inferred from mutant phenotype
(Reitman et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables FAD binding
inferred from electronic annotation with InterPro:IPR016166
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in organic acid metabolic process
inferred from mutant phenotype
(Reitman et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in oxidation-reduction process
inferred from electronic annotation with InterPro:IPR006094
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in mitochondrion
inferred from biological aspect of ancestor with PANTHER:PTN000202300
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
OTHER CH-OH OXIDOREDUCTASES -
The Other CH-OH oxidoreductases, is a collection of oxidoreductases that do not fit into any of the other major CH-OH oxidoreductases.
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\D2hgdh 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
Comments on Gene Model

Gene model reviewed during 5.44

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
D2hgdh-RA
FBtr0070383
NM_130626
1987
533
D2hgdh-RB
FBtr0070381
NM_166929
1862
533
D2hgdh-RC
FBtr0070382
NM_166930
1966
533
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
RefSeq ID
GenBank
D2hgdh-PA
FBpp0070367
58.4
533
6.93
NP_569982
AAF45729
D2hgdh-PB
FBpp0070365
58.4
533
6.93
NP_726794
AAF45731
D2hgdh-PC
FBpp0070366
58.4
533
6.93
NP_726795
AAF45730
Polypeptides with Identical Sequences

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

533 aa isoforms: D2hgdh-PA, D2hgdh-PB, D2hgdh-PC
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
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\D2hgdh using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
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
anlage in statu nascendi
(Fisher et al., 2012)
central brain anlage in statu nascendi
(Fisher et al., 2012)
dorsal ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)
organism | gap expression pattern
(Fisher et al., 2012)
ventral ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)
antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
embryonic stage 7 -- 8
dorsal ectoderm
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic/larval midgut
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\D2hgdh in GBrowse 2
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
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 D2hgdh
Transgenic constructs containing regulatory region of D2hgdh
Aberrations (Deficiencies and Duplications) ( 3 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\D2HGDH
14 of 15
Yes
Yes
Hsap\LDHD
3 of 15
No
Yes
Hsap\AGPS
1 of 15
No
No
Hsap\DHCR24
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\D2hgdh
12 of 15
Yes
Yes
Mmus\Ldhd
3 of 15
No
Yes
Mmus\Agps
1 of 15
No
No
Mmus\Dhcr24
1 of 15
No
Yes
Mmus\Gm7889
1 of 15
No
Yes
Mmus\Gulo
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (5)
Rnor\D2hgdh
12 of 13
Yes
Yes
Rnor\Ldhd
2 of 13
No
Yes
Rnor\Agps
1 of 13
No
No
Rnor\Dhcr24
1 of 13
No
Yes
Rnor\Gulo
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\d2hgdh
3 of 12
Yes
Yes
Xtro\agps
1 of 12
No
No
Xtro\dhcr24
1 of 12
No
Yes
Danio rerio (Zebrafish) (4)
Drer\d2hgdh
13 of 15
Yes
Yes
Drer\ldhd
2 of 15
No
Yes
Drer\agps
1 of 15
No
No
Drer\dhcr24
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\F54D5.12
13 of 15
Yes
Yes
Cele\ads-1
1 of 15
No
No
Cele\F32D8.12
1 of 15
No
Yes
Cele\F52H2.6
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\D2HGDH
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (4)
Scer\DLD2
13 of 15
Yes
Yes
Scer\DLD3
9 of 15
No
Yes
Scer\DLD1
2 of 15
No
Yes
Scer\ALO1
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPBC713.03
11 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190614 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00005254
Drosophila simulans
Dsim\GD16587
Drosophila sechellia
Dsec\GM19199
Drosophila erecta
Dere\GG12909
Drosophila yakuba
Dyak\GE16237
Drosophila ananassae
Dana\GF21462
Drosophila pseudoobscura pseudoobscura
Dpse\GA17719
Drosophila persimilis
Dper\GL14161
Drosophila willistoni
Dwil\GK10230
Drosophila virilis
Dvir\GJ16929
Drosophila mojavensis
Dmoj\GI11068
Drosophila grimshawi
Dgri\GH24571
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504HI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17020793
Glossina morsitans
Tsetse fly
Gmor\GMOY001298
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_02314
Mayetiola destructor
Hessian fly
Mdes\Mdes002083
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL005921
Anopheles darlingi
American malaria mosquito
Adar\ADAC008065
Anopheles gambiae
Malaria mosquito
Agam\AGAP004195
Anopheles gambiae
Malaria mosquito
Agam\AGAP004189
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ001318
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W078Y )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA009966
Danaus plexippus
Monarch butterfly
Dple\DPOGS202444-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL016404
Apis florea
Little honeybee
Aflo\2208576148
Apis mellifera
Western honey bee
Amel\GB47474
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP22203
Bombus terrestris
Buff-tailed bumblebee
Bter\15212235
Linepithema humile
Argentine ant
Lhum\LH11715
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0029bb
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG021446
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06074
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02085
Tribolium castaneum
Red flour beetle
Tcas\TC030784
Tribolium castaneum
Red flour beetle
Tcas\TC002688
Pediculus humanus
Human body louse
Phum\PHUM396380
Rhodnius prolixus
Kissing bug
Rpro\RPRC004650
Rhodnius prolixus
Kissing bug
Rpro\RPRC004645
Cimex lectularius
Bed bug
Clec\CLEC004643
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI001841
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI089105
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI000361
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_07355
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0741 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR013275
Ixodes scapularis
Black-legged tick
Isca\ISCW005219
Stegodyphus mimosarum
African social velvet spider
Smim\KFM81984.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur17g01530
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_307847
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0AXU )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-D2hgdh
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000012479
Gallus gallus
Domestic chicken
Ggal\D2HGDH
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Agps
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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
    D2HGDH; D-2-hydroxyglutarate dehydrogenase
    model of  D-2-hydroxyglutaric aciduria 1
    IEA
    (FlyBase, 2019-)
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 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?
    D2HGDH; D-2-hydroxyglutarate dehydrogenase
    14 of 15
    609186
    LDHD; lactate dehydrogenase D
    3 of 15
    607490
      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:
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser
      View in Interactions Browser
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      D2hgdh - Hsp60A
      experimental knowledge based
      (Guruharsha et al., 2011)
      D2hgdh - Nrd1
      anti tag coimmunoprecipitation, Identification by mass spectrometry
      (Yoon et al., 2017)
      D2hgdh - Rab18
      pull down, peptide massfingerprinting
      (Gillingham et al., 2014, Gillingham et al., 2014)
      D2hgdh - cry
      experimental knowledge based
      (Guruharsha et al., 2011)
      Summary of Genetic Interactions
      esyN Network Diagram
      esyN Network Key:
      Suppression
      Enhancement
      View in Interactions Browser
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Idh
      suppressible
      D2hgdh
      (Reitman et al., 2015)
      External Data
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map

      1-0.6

      Cytogenetic map
      2D4-2D4
      Sequence location
      X:2,141,489..2,144,937 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      2D4-2D4
      Limits computationally determined from genome sequence between P{EP}ActnEP1193&P{EP}CG4322EP1631 and P{EP}EP1460&P{EP}CG2924EP1596
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      1-0.6

      (FlyBase, 2016)

      1-0.2

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (6)
      Genomic Clones (5)
       

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

      cDNA Clones (92)
       

      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
      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
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of

      Source for identity of: D2hgdh CG3835

      (Reitman et al., 2015)
      Source for database merge of
      Additional comments
      Other Comments
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 49 )
      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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DPiM - Drosophila Protein interaction map
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (6)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (55)