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    LOC9267065 chromatin structure-remodeling complex protein SYD [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9267065, updated on 1-Aug-2024

    Summary

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    Gene symbol
    LOC9267065
    Gene description
    chromatin structure-remodeling complex protein SYD
    Locus tag
    OSNPB_060255200
    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 before flowering (RPKM 32.3), roots after flowering (RPKM 29.0) and 6 other tissues See more
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    Genomic context

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    See LOC9267065 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (8212438..8236283)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (8043571..8067365)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene 1-aminocyclopropane-1-carboxylate oxidase homolog 4 Neighboring gene 1-aminocyclopropane-1-carboxylate oxidase homolog 4 Neighboring gene nudix hydrolase 21, chloroplastic Neighboring gene protein CHROMATIN REMODELING 35

    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. The N-terminal ATPase AT-hook-containing region of the Arabidopsis chromatin-remodeling protein SPLAYED is sufficient for biological activity. Su Y, et al. Plant J, 2006 May. PMID 16640604
    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 ATP binding 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 histone binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    chromatin structure-remodeling complex protein SYD
    Names
    Os06g0255200
    Os06g0255300
    P0592E11.17-1
    P0592E11.17-2
    P0592E11.18
    SYD chromatin remodeling ATPase
    chromatin remodeling protein-like
    putative STH1 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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      8212438..8236283
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015786969.3 → XP_015642455.1  chromatin structure-remodeling complex protein SYD isoform X1

      UniProtKB/TrEMBL
      B9FSK5
      Conserved Domains (7) summary
      pfam09528
      Location:3091 → 3527
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      smart00951
      Location:490 → 515
      QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
      cd00046
      Location:1065 → 1206
      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:1048 → 1339
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1363 → 1478
      Helicase_C; Helicase conserved C-terminal domain
      pfam07529
      Location:877 → 947
      HSA; HSA
      pfam14619
      Location:1572 → 1665
      SnAC; Snf2-ATP coupling, chromatin remodelling complex

    2. XM_015786972.3 → XP_015642458.1  chromatin structure-remodeling complex protein SYD isoform X2

      UniProtKB/TrEMBL
      B9FSK5
      Conserved Domains (8) summary
      smart00951
      Location:461 → 486
      QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
      PLN03142
      Location:878 → 1477
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      COG0419
      Location:742 → 955
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      COG5271
      Location:3645 → 4168
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      pfam05109
      Location:1671 → 2074
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam09606
      Location:214 → 453
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam14619
      Location:1544 → 1636
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
      NF033913
      Location:4186 → 4360
      fibronec_FbpA; LPXTG-anchored fibronectin-binding protein FbpA

    3. XM_015786968.3 → XP_015642454.1  chromatin structure-remodeling complex protein SYD isoform X1

      UniProtKB/TrEMBL
      B9FSK5
      Conserved Domains (7) summary
      pfam09528
      Location:3091 → 3527
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      smart00951
      Location:490 → 515
      QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
      cd00046
      Location:1065 → 1206
      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:1048 → 1339
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1363 → 1478
      Helicase_C; Helicase conserved C-terminal domain
      pfam07529
      Location:877 → 947
      HSA; HSA
      pfam14619
      Location:1572 → 1665
      SnAC; Snf2-ATP coupling, chromatin remodelling complex

    4. XM_015786970.3 → XP_015642456.1  chromatin structure-remodeling complex protein SYD isoform X1

      UniProtKB/TrEMBL
      B9FSK5
      Conserved Domains (7) summary
      pfam09528
      Location:3091 → 3527
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      smart00951
      Location:490 → 515
      QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
      cd00046
      Location:1065 → 1206
      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:1048 → 1339
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1363 → 1478
      Helicase_C; Helicase conserved C-terminal domain
      pfam07529
      Location:877 → 947
      HSA; HSA
      pfam14619
      Location:1572 → 1665
      SnAC; Snf2-ATP coupling, chromatin remodelling complex

    5. XM_066311898.1 → XP_066167995.1  chromatin structure-remodeling complex protein SYD isoform X2

      UniProtKB/TrEMBL
      B9FSK5
    Nucleotide Protein
    Heading Accession and Version

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