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    LOC9271593 lysine-specific demethylase JMJ17 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9271593, updated on 10-Oct-2024

    Summary

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    Gene symbol
    LOC9271593
    Gene description
    lysine-specific demethylase JMJ17
    Locus tag
    OSNPB_060731500
    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 roots after flowering (RPKM 16.6), leaves before flowering (RPKM 16.2) and 6 other tissues See more
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    Genomic context

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    See LOC9271593 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (32055595..32068444, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (31184913..31197784, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4342154 Neighboring gene tetraspanin-18 Neighboring gene uncharacterized LOC4342158 Neighboring gene transfer RNA proline (anticodon UGG)

    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 IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables histone demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling 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
    part_of chromatin 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
    lysine-specific demethylase JMJ17
    Names
    B1206D04.22
    Os06g0731500
    Os06g0731600
    RB-binding protein-like
    lysine-specific demethylase 5B

    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
      32055595..32068444 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015787548.3 → XP_015643034.1  lysine-specific demethylase JMJ17 isoform X5

      UniProtKB/TrEMBL
      B8B2Y1
      Conserved Domains (8) summary
      cd15543
      Location:291 → 335
      PHD_RSF1; PHD finger found in Remodeling and spacing factor 1 (Rsf-1)
      pfam02373
      Location:462 → 578
      JmjC; JmjC domain, hydroxylase
      pfam02375
      Location:52 → 84
      JmjN; jmjN domain
      pfam02928
      Location:671 → 723
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:1122 → 1441
      PLU-1; PLU-1-like protein
      cl02633
      Location:119 → 218
      ARID; ARID/BRIGHT DNA binding domain
      cl17238
      Location:1484 → 1530
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
      cl22851
      Location:1742 → 1784
      PHD_SF; PHD finger superfamily

    2. XM_066311669.1 → XP_066167766.1  lysine-specific demethylase JMJ17 isoform X2

    3. XM_066311671.1 → XP_066167768.1  lysine-specific demethylase JMJ17 isoform X4

    4. XM_066311668.1 → XP_066167765.1  lysine-specific demethylase JMJ17 isoform X1

    5. XM_066311670.1 → XP_066167767.1  lysine-specific demethylase JMJ17 isoform X3

    Nucleotide Protein
    Heading Accession and Version

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