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    LOC4344415 B3 domain-containing protein IDEF1-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4344415, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4344415
    Gene description
    B3 domain-containing protein IDEF1-like
    Locus tag
    OSNPB_080101000
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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
    IDEF1; OsJ_25718
    Expression
    Ubiquitous expression in leaves before flowering (RPKM 35.7), flowers (RPKM 32.1) and 6 other tissues See more
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    Genomic context

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    Location:
    chromosome: 8
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (63619..67675, complement)

    Chromosome 8 - NC_029263.1Genomic Context describing neighboring genes Neighboring gene branchpoint-bridging protein Neighboring gene uncharacterized LOC4344413 Neighboring gene high mobility group B protein 7 Neighboring gene protein odr-4 homolog

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029263.1 Chromosome 8 Reference IRGSP-1.0 Primary Assembly

    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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. CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa. Tan S, et al. Sci Rep, 2016 May 3. PMID 27137867, Free PMC Article
    2. The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants. Kobayashi T, et al. Proc Natl Acad Sci U S A, 2007 Nov 27. PMID 18025467, Free PMC Article
    3. 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

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    B3 domain-containing protein IDEF1
    Names
    B1147B12.12
    LOC_Os08g01090
    Protein IRON DEFICIENCY-RESPONSIVE ELEMENT FACTOR 1
    transcription factor IDEF1
    transcription factor viviparous 1-like

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001422366.1 → NP_001409295.1  B3 domain-containing protein IDEF1

      Status: VALIDATED

      Source sequence(s)
      AK107456, BR000654, CF309657, CI302633
      UniProtKB/Swiss-Prot
      A0A0P0XAM4, A9JTY5, Q6Z1Z3

    RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference IRGSP-1.0 Primary Assembly

    Genomic

    1. NC_029263.1 Reference IRGSP-1.0 Primary Assembly

      Range
      63619..67675 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015792673.2 → XP_015648159.1  B3 domain-containing protein IDEF1 isoform X1

      UniProtKB/Swiss-Prot
      Q6Z1Z3
      Conserved Domains (1) summary
      cd10017
      Location:252 → 350
      B3_DNA; Plant-specific B3-DNA binding domain

    2. XM_015792676.2 → XP_015648162.1  B3 domain-containing protein IDEF1 isoform X2

      Conserved Domains (1) summary
      cl15242
      Location:252 → 308
      BfiI_C_EcoRII_N_B3; DNA binding domains of BfiI, EcoRII and plant B3 proteins
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6Z1Z3.1 GenPept UniProtKB/Swiss-Prot:Q6Z1Z3

    Gene LinkOut

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