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    LOC4345657 malate dehydrogenase, chloroplastic [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4345657, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC4345657
    Gene description
    malate dehydrogenase, chloroplastic
    Locus tag
    OSNPB_080434300
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Also known as
    P0413H11.6; P0413H11.7
    Expression
    Broad expression in leaves before flowering (RPKM 132.9), roots before flowering (RPKM 127.0) and 5 other tissues See more
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    Genomic context

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    See LOC4345657 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 8 NC_089042.1 (21192202..21195137, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (21054654..21057690, complement)

    Chromosome 8 - NC_089042.1Genomic Context describing neighboring genes Neighboring gene pentatricopeptide repeat-containing protein At3g47530 Neighboring gene extracellular ribonuclease LE Neighboring gene probable glucomannan 4-beta-mannosyltransferase 11 Neighboring gene uncharacterized LOC136351381

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome profiling of various organs at different developmental stages in rice Transcriptome profiling of various organs at different developmental stages in rice
    • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
    • BioProject: PRJNA243371
    • Publication: PMID 26387578
    • Analysis date: Fri Dec 15 20:02:59 2017

    Bibliography

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    Related articles in PubMed

    1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764
    2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables L-malate dehydrogenase (NAD+) activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in malate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in tricarboxylic acid cycle IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    malate dehydrogenase, chloroplastic
    Names
    Os08g0434300
    P0431A03.28
    P0431A03.29
    putative NAD-malate dehydrogenase

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

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

    Reference ASM3414082v1 Primary Assembly

    Genomic

    1. NC_089042.1 Reference ASM3414082v1 Primary Assembly

      Range
      21192202..21195137 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015795179.3 → XP_015650665.1  malate dehydrogenase, chloroplastic

      UniProtKB/TrEMBL
      A2YVI5, Q6YWL3, Q6ZA87
      Conserved Domains (2) summary
      cd01337
      Location:76 → 387
      MDH_glyoxysomal_mitochondrial; Glyoxysomal and mitochondrial malate dehydrogenases
      PLN00106
      Location:63 → 382
      PLN00106; malate dehydrogenase

    2. XM_066303639.1 → XP_066159736.1  malate dehydrogenase, chloroplastic

      UniProtKB/TrEMBL
      Q6YWL3, Q6ZA87
    Nucleotide Protein
    Heading Accession and Version

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