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    LOC9267457 tRNA:m(4)X modification enzyme TRM13-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9267457, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC9267457
    Gene description
    tRNA:m(4)X modification enzyme TRM13-like
    Locus tag
    OSNPB_030833200
    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 flower buds (RPKM 3.9), leaves before flowering (RPKM 3.4) and 6 other tissues See more
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    Genomic context

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    See LOC9267457 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (35977369..35980417)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (35004535..35007690)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4334682 Neighboring gene short-chain dehydrogenase reductase 5 Neighboring gene squamosa promoter-binding-like protein 6 Neighboring gene uncharacterized LOC136355739 Neighboring gene uncharacterized LOC4334687

    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. The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. Wang Y, et al. J Exp Bot, 2017 Mar 1. PMID 28369540, Free PMC Article
    2. 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
    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

    What's a GeneRIF?
    1. OsTRM13, encoding a rice tRNA nucleoside methyltransferase, is an important regulator of salt stress tolerance in rice.
      Title: The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables tRNA 2'-O-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in tRNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tRNA:m(4)X modification enzyme TRM13-like
    Names
    Os03g0833200
    tRNA:m(4)X modification enzyme TRM13 homolog

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      35977369..35980417
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015773378.3 → XP_015628864.1  tRNA:m(4)X modification enzyme TRM13-like

      UniProtKB/TrEMBL
      B8AMR9
      Conserved Domains (3) summary
      pfam05206
      Location:181 → 458
      TRM13; Methyltransferase TRM13
      pfam05253
      Location:63 → 86
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:20 → 48
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
    Nucleotide Protein
    Heading Accession and Version

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