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    LOC4325898 homeobox-DDT domain protein RLT2 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4325898, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4325898
    Gene description
    homeobox-DDT domain protein RLT2
    Locus tag
    OSNPB_010672201
    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
    P0007F06.9; OJ1125_C04.27
    Expression
    Ubiquitous expression in flowers (RPKM 11.5), flower buds (RPKM 11.3) and 6 other tissues See more
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    Genomic context

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    See LOC4325898 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (28169296..28186095)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (27581370..27598835)

    Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene NAC domain-containing protein 73 Neighboring gene pentatricopeptide repeat-containing protein At5g46100 Neighboring gene protein DEHYDRATION-INDUCED 19 homolog 3-like Neighboring gene callose synthase 12 Neighboring gene small nucleolar RNA J33

    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. GRASSIUS: a platform for comparative regulatory genomics across the grasses. Yilmaz A, et al. Plant Physiol, 2009 Jan. PMID 18987217, Free PMC Article
    2. 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 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 

    General protein information

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    Preferred Names
    homeobox-DDT domain protein RLT2
    Names
    DDT transcription factor
    Os01g0672201
    Os01g0672300
    P0007F06.10
    homeobox protein
    homeobox transcription factor-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_089035.1 Reference ASM3414082v1 Primary Assembly

      Range
      28169296..28186095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015760926.3 → XP_015616412.1  homeobox-DDT domain protein RLT2 isoform X1

      UniProtKB/TrEMBL
      B8A788
      Conserved Domains (6) summary
      pfam00046
      Location:49 → 103
      Homeobox; Homeobox domain
      pfam02791
      Location:632 → 687
      DDT; DDT domain
      pfam05066
      Location:807 → 875
      HARE-HTH; HB1, ASXL, restriction endonuclease HTH domain
      pfam13868
      Location:439 → 588
      TPH; Trichohyalin-plectin-homology domain
      pfam15612
      Location:1027 → 1072
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:1207 → 1281
      WSD; Williams-Beuren syndrome DDT (WSD), D-TOX E motif

    2. XM_015760935.3 → XP_015616421.1  homeobox-DDT domain protein RLT2 isoform X2

      UniProtKB/TrEMBL
      B8A788
      Conserved Domains (5) summary
      pfam02791
      Location:344 → 399
      DDT; DDT domain
      pfam05066
      Location:519 → 587
      HARE-HTH; HB1, ASXL, restriction endonuclease HTH domain
      pfam13868
      Location:151 → 300
      TPH; Trichohyalin-plectin-homology domain
      pfam15612
      Location:739 → 784
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:919 → 993
      WSD; Williams-Beuren syndrome DDT (WSD), D-TOX E motif
    Nucleotide Protein
    Heading Accession and Version

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