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    LOC4342861 alanine--tRNA ligase [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4342861, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4342861
    Gene description
    alanine--tRNA ligase
    Locus tag
    OSNPB_070258100
    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
    OJ1057_E05.124; OJ1354_H07.104
    Expression
    Ubiquitous expression in leaves before flowering (RPKM 30.4), flower buds (RPKM 30.1) and 6 other tissues See more
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    Genomic context

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    See LOC4342861 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (9011267..9025036, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (8929991..8937554, complement)

    Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107281586 Neighboring gene uncharacterized LOC4342860 Neighboring gene uncharacterized LOC136357354 Neighboring gene metal transporter Nramp1-like

    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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables K48-linked deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables alanine-tRNA ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables aminoacyl-tRNA editing activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables cysteine-type carboxypeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in alanyl-tRNA aminoacylation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in protein K48-linked deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell periphery IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in chloroplast IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in cytosol 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
    alanine--tRNA ligase; uncharacterized protein LOC4342861
    Names
    Os07g0258100
    proline-rich protein-like

    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_089041.1 Reference ASM3414082v1 Primary Assembly

      Range
      9011267..9025036 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_066312575.1 → XP_066168672.1  alanine--tRNA ligase isoform X2

    2. XM_015791215.3 → XP_015646701.1  uncharacterized protein LOC4342861 isoform X1

      Conserved Domains (1) summary
      pfam14551
      Location:299 → 357
      MCM_N; MCM N-terminal domain
    Nucleotide Protein
    Heading Accession and Version

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