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    d2hgdh D-2-hydroxyglutarate dehydrogenase [ Danio rerio (zebrafish) ]

    Gene ID: 565889, updated on 9-Dec-2024

    Summary

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    Official Symbol
    d2hgdhprovided by ZNC
    Official Full Name
    D-2-hydroxyglutarate dehydrogenaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070112-482
    See related
    Ensembl:ENSDARG00000060210 AllianceGenome:ZFIN:ZDB-GENE-070112-482
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:158661
    Summary
    Predicted to enable (R)-2-hydroxyglutarate dehydrogenase activity and zinc ion binding activity. Predicted to be involved in malate metabolic process. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in D-2-hydroxyglutaric aciduria 1. Orthologous to human D2HGDH (D-2-hydroxyglutarate dehydrogenase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See d2hgdh in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (41546175..41562875, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (41695488..41713561, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene otolith matrix protein Neighboring gene activin A receptor, type 1 like Neighboring gene zinc finger protein 622 Neighboring gene zgc:110158

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Sabharwal A, et al. Genes (Basel), 2022 Jul 23. PMID 35893052, Free PMC Article
    2. Building the vertebrate codex using the gene breaking protein trap library. Ichino N, et al. Elife, 2020 Aug 11. PMID 32779569, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables (R)-2-hydroxyglutarate dehydrogenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables (R)-2-hydroxyglutarate dehydrogenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables FAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables flavin adenine dinucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in malate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    D-2-hydroxyglutarate dehydrogenase, mitochondrial
    NP_001074066.1
    XP_005168474.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001080597.1 → NP_001074066.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_001074066.1

      Status: PROVISIONAL

      Source sequence(s)
      BC129361
      UniProtKB/Swiss-Prot
      A1L258
      Related
      ENSDARP00000079032.4, ENSDART00000084597.5
      Conserved Domains (3) summary
      COG0277
      Location:81 → 529
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:112 → 249
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:286 → 526
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007113.7 Reference GRCz11 Primary Assembly

      Range
      41546175..41562875 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005168417.5 → XP_005168474.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A8M2BGD0, F1R1R3
      Conserved Domains (3) summary
      COG0277
      Location:81 → 529
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:112 → 249
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:286 → 526
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1L258.1 GenPept UniProtKB/Swiss-Prot:A1L258

    Gene LinkOut

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