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    LOC4347003 HMG-Y-related protein A [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4347003, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4347003
    Gene description
    HMG-Y-related protein A
    Locus tag
    OSNPB_090402100
    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 42.8), flower buds (RPKM 39.5) and 6 other tissues See more
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    Genomic context

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    See LOC4347003 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 9 NC_089043.1 (18475676..18476717, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 9 NC_029264.1 (14106172..14107336, complement)

    Chromosome 9 - NC_089043.1Genomic Context describing neighboring genes Neighboring gene plant UBX domain-containing protein 2 Neighboring gene protein XRI1 Neighboring gene putative 1-phosphatidylinositol-3-phosphate 5-kinase FAB1C Neighboring gene uncharacterized LOC107277793

    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 double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables nucleosomal DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in negative regulation of DNA recombination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription 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 nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of nucleosome 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
    HMG-Y-related protein A
    Names
    DNA binding protein PF1
    OSJNBb0014M19.7
    Os09g0402100

    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_089043.1 Reference ASM3414082v1 Primary Assembly

      Range
      18475676..18476717 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015795891.3 → XP_015651377.1  HMG-Y-related protein A

      UniProtKB/TrEMBL
      A0A0P0XMB0, Q43600, Q69MW7
      Conserved Domains (1) summary
      smart00526
      Location:19 → 85
      H15; Domain in histone families 1 and 5
    Nucleotide Protein
    Heading Accession and Version

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