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    D2hgdh D-2-hydroxyglutarate dehydrogenase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301624, updated on 9-Dec-2024

    Summary

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    Official Symbol
    D2hgdhprovided by RGD
    Official Full Name
    D-2-hydroxyglutarate dehydrogenaseprovided by RGD
    Primary source
    RGD:1307976
    See related
    EnsemblRapid:ENSRNOG00000019012 AllianceGenome:RGD:1307976
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307976
    Summary
    Enables (R)-2-hydroxyglutarate dehydrogenase activity. Involved in response to cobalt ion; response to manganese ion; and response to zinc ion. Located 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]
    Expression
    Biased expression in Kidney (RPKM 106.6), Adrenal (RPKM 98.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See D2hgdh in Genome Data Viewer
    Location:
    9q36
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (101796287..101815727)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (94350555..94368384)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (100956570..100974393)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene deoxythymidylate kinase Neighboring gene inhibitor of growth family, member 5 Neighboring gene galactose-3-O-sulfotransferase 2 Neighboring gene neuraminidase 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Identification of a dehydrogenase acting on D-2-hydroxyglutarate. Achouri Y, et al. Biochem J, 2004 Jul 1. PMID 15070399, Free PMC Article
    2. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, et al. Nature, 2004 Apr 1. PMID 15057822
    3. 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
    4. 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 RGD

    Function Evidence Code Pubs
    enables (R)-2-hydroxyglutarate dehydrogenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables (R)-2-hydroxyglutarate dehydrogenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables (R)-2-hydroxyglutarate dehydrogenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables FAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in malate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in malate metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in malate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT involved_in response to calcium ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to cobalt ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in response to magnesium ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to manganese ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to zinc ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    D-2-hydroxyglutarate dehydrogenase, mitochondrial
    NP_001100396.2
    XP_006245582.1
    XP_006245583.1
    XP_006245584.1

    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_001106926.2 → NP_001100396.2  D-2-hydroxyglutarate dehydrogenase, mitochondrial

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      P84850
      UniProtKB/TrEMBL
      A6JR40, B2GV75
      Conserved Domains (1) summary
      COG0277
      Location:90 → 532
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      101796287..101815727
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006245520.4 → XP_006245582.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A8L2R544, A6JR40
      Related
      ENSRNOP00000071036.2, ENSRNOT00000078222.3
      Conserved Domains (3) summary
      COG0277
      Location:108 → 550
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:133 → 270
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:307 → 547
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain

    2. XM_006245522.5 → XP_006245584.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X2

      See identical proteins and their annotated locations for XP_006245584.1

      UniProtKB/Swiss-Prot
      P84850
      UniProtKB/TrEMBL
      A6JR40, B2GV75
      Conserved Domains (1) summary
      COG0277
      Location:90 → 532
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]

    3. XM_006245521.5 → XP_006245583.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X2

      See identical proteins and their annotated locations for XP_006245583.1

      UniProtKB/Swiss-Prot
      P84850
      UniProtKB/TrEMBL
      A6JR40, B2GV75
      Conserved Domains (1) summary
      COG0277
      Location:90 → 532
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]

    RNA

    1. XR_005488880.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P84850.1 GenPept UniProtKB/Swiss-Prot:P84850

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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