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    LOC4338934 protein TRANSPARENT TESTA 1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338934, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4338934
    Gene description
    protein TRANSPARENT TESTA 1
    Locus tag
    OSNPB_050444200
    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
    Biased expression in roots before flowering (RPKM 99.8) and leaves before flowering (RPKM 5.0) See more
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    Genomic context

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    Location:
    chromosome: 5
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (21848274..21850666)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (21737251..21739738)

    Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene cell division protein FtsZ homolog 2-2, chloroplastic Neighboring gene transcription factor TGAL5-like Neighboring gene uncharacterized LOC4338935 Neighboring gene uncharacterized LOC136356583 Neighboring gene uncharacterized LOC107275954 Neighboring gene uncharacterized LOC107281153

    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

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in anatomical structure development IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein TRANSPARENT TESTA 1
    Names
    Os05g0444200

    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_089039.1 Reference ASM3414082v1 Primary Assembly

      Range
      21848274..21850666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015785256.3 → XP_015640742.1  protein TRANSPARENT TESTA 1

      UniProtKB/TrEMBL
      A0A0P0WN03, A0A482G4B5, A2Y564, Q0DHT0, Q6F2N5
      Conserved Domains (1) summary
      sd00017
      Location:300 → 316
      ZF_C2H2; C2H2 Zn finger [structural motif]
    Nucleotide Protein
    Heading Accession and Version

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