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    LOC4328076 transcription factor IIIA [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4328076, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4328076
    Gene description
    transcription factor IIIA
    Locus tag
    OSNPB_020116000
    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 after flowering (RPKM 28.1), flower buds (RPKM 22.9) and 6 other tissues See more
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    Genomic context

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    See LOC4328076 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (860530..866610, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (853788..859895, complement)

    Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene catalase isozyme A-like Neighboring gene heat shock 70 kDa protein BIP1-like Neighboring gene uncharacterized LOC136355181 Neighboring gene probable metal-nicotianamine transporter YSL7

    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 5S rDNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus 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
    pentatricopeptide repeat-containing protein At5g56310; transcription factor IIIA
    Names
    Os02g0116000
    Os02g0116100
    pentatricopeptide repeat-containing protein At2g22410, mitochondrial
    zinc finger protein 729

    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_089036.1 Reference ASM3414082v1 Primary Assembly

      Range
      860530..866610 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015771369.3 → XP_015626855.1  transcription factor IIIA isoform X1

      UniProtKB/TrEMBL
      A2X037, A3A2F3
      Conserved Domains (3) summary
      COG5048
      Location:70 → 244
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:72 → 92
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:259 → 279
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. XM_066307468.1 → XP_066163565.1  pentatricopeptide repeat-containing protein At5g56310 isoform X4

    3. XM_026023135.2 → XP_025878920.1  transcription factor IIIA isoform X3

      UniProtKB/TrEMBL
      B7EQH7, Q0E4J8
      Conserved Domains (1) summary
      sd00019
      Location:141 → 161
      ZF_C2H2; C2H2 Zn finger [structural motif]

    4. XM_026023133.2 → XP_025878918.1  transcription factor IIIA isoform X2

      UniProtKB/TrEMBL
      Q0E4J8
      Conserved Domains (3) summary
      COG5048
      Location:1 → 150
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:9 → 28
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:165 → 185
      ZF_C2H2; C2H2 Zn finger [structural motif]
    Nucleotide Protein
    Heading Accession and Version

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