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    LOC4344175 protein CHROMATIN REMODELING 5 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4344175, updated on 1-Aug-2024

    Summary

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    Gene symbol
    LOC4344175
    Gene description
    protein CHROMATIN REMODELING 5
    Locus tag
    OSNPB_070660200
    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
    OJ1477_F01.130-1
    Expression
    Ubiquitous expression in roots after flowering (RPKM 36.3), leaves before flowering (RPKM 32.8) and 6 other tissues See more
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    Genomic context

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    See LOC4344175 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (28053382..28067678, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (27825780..27840054, complement)

    Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene uncharacterized protein At5g39865 Neighboring gene DEAD-box ATP-dependent RNA helicase 10-like Neighboring gene uncharacterized LOC9272302 Neighboring gene RNA pseudouridine synthase 6, chloroplastic Neighboring gene putative cis-zeatin O-glucosyltransferase

    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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables histone binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in nucleosome organization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II 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
    protein CHROMATIN REMODELING 5
    Names
    Os07g0660200
    P0496C02.115-1
    chromodomain-helicase-DNA-binding protein-like protein

    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_089041.1 Reference ASM3414082v1 Primary Assembly

      Range
      28053382..28067678 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015791202.3 → XP_015646688.1  protein CHROMATIN REMODELING 5

      UniProtKB/TrEMBL
      B9FUP1
      Conserved Domains (6) summary
      cd00024
      Location:507 → 560
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:617 → 763
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam00176
      Location:600 → 886
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:928 → 1026
      Helicase_C; Helicase conserved C-terminal domain
      pfam13907
      Location:1500 → 1594
      DUF4208; Domain of unknown function (DUF4208)
      cl21498
      Location:1320 → 1384
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    2. XM_066312196.1 → XP_066168293.1  protein CHROMATIN REMODELING 5

      UniProtKB/TrEMBL
      B9FUP1

    3. XM_066312197.1 → XP_066168294.1  protein CHROMATIN REMODELING 5

      UniProtKB/TrEMBL
      B9FUP1
    Nucleotide Protein
    Heading Accession and Version

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