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    LOC4350536 alpha-ketoglutarate-dependent dioxygenase alkB [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4350536, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4350536
    Gene description
    alpha-ketoglutarate-dependent dioxygenase alkB
    Locus tag
    OSNPB_110488500
    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
    Expression
    Ubiquitous expression in leaves before flowering (RPKM 3.9), roots after flowering (RPKM 3.5) and 6 other tissues See more
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    Genomic context

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    See LOC4350536 in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 11 NC_089045.1 (19125827..19129150)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 11 NC_029266.1 (17206812..17210203)

    Chromosome 11 - NC_089045.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136354126 Neighboring gene arabinogalactan O-methyltransferase 2 Neighboring gene uncharacterized LOC4350537 Neighboring gene F-box protein At5g50450

    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. 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 broad specificity oxidative DNA demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ferrous iron binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables oxidative RNA demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in oxidative RNA demethylation 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 nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    alpha-ketoglutarate-dependent dioxygenase alkB
    Names
    Os11g0488500

    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_089045.1 Reference ASM3414082v1 Primary Assembly

      Range
      19125827..19129150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015760245.3 → XP_015615731.1  alpha-ketoglutarate-dependent dioxygenase alkB

      UniProtKB/TrEMBL
      B9FED1
      Conserved Domains (1) summary
      pfam13532
      Location:96 → 364
      2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily
    Nucleotide Protein
    Heading Accession and Version

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