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    LOC4340825 enhancer of mRNA-decapping protein 4 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340825, updated on 13-Jul-2024

    Summary

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    Gene symbol
    LOC4340825
    Gene description
    enhancer of mRNA-decapping protein 4
    Locus tag
    OSNPB_060300800
    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 23.2), flowers (RPKM 23.2) and 6 other tissues See more
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    Genomic context

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    See LOC4340825 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (11399971..11408667)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (11219926..11228545)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4340823 Neighboring gene uncharacterized LOC4340824 Neighboring gene F-box/LRR-repeat/kelch-repeat protein At1g09650 Neighboring gene ERAD-associated E3 ubiquitin-protein ligase HRD1-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 protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in deadenylation-independent decapping of nuclear-transcribed mRNA IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in P-body IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    enhancer of mRNA-decapping protein 4
    Names
    Os06g0300800
    P0501G08.38-1
    P0501G08.38-2
    WD domain, G-beta repeat domain-containing protein
    WD-40 repeat 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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      11399971..11408667
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788091.3 → XP_015643577.1  enhancer of mRNA-decapping protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A0P0WVR0, A0A5S6RBK4, Q0DCQ6, Q5ZA31, Q5ZA32
      Conserved Domains (4) summary
      pfam12868
      Location:37 → 96
      DUF3824; Domain of unknwon function (DUF3824)
      pfam16529
      Location:205 → 513
      Ge1_WD40; WD40 region of Ge1, enhancer of mRNA-decapping protein
      sd00039
      Location:259 → 300
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:248 → 513
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. XM_015788092.3 → XP_015643578.1  enhancer of mRNA-decapping protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A5S6RBK4, Q0DCQ6, Q5ZA31
      Conserved Domains (3) summary
      sd00039
      Location:259 → 300
      7WD40; WD40 repeat [structural motif]
      pfam15822
      Location:42 → 97
      MISS; MAPK-interacting and spindle-stabilizing protein-like
      pfam16529
      Location:205 → 513
      Ge1_WD40; WD40 region of Ge1, enhancer of mRNA-decapping protein
    Nucleotide Protein
    Heading Accession and Version

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