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    LOC4336722 DNA-directed RNA polymerase IV subunit 1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4336722, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4336722
    Gene description
    DNA-directed RNA polymerase IV subunit 1
    Locus tag
    OSNPB_040572600
    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
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    Genomic context

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    See LOC4336722 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 4 NC_089038.1 (29339420..29353042)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (28833236..28846888)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene dehydration-responsive element-binding protein 1E-like Neighboring gene uncharacterized LOC107276184 Neighboring gene zinc finger CCCH domain-containing protein 17-like Neighboring gene uncharacterized LOC136356355

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    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
    2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    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 RNA polymerase II activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II, core complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA-directed RNA polymerase IV subunit 1
    Names
    Os04g0572600

    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_089038.1 Reference ASM3414082v1 Primary Assembly

      Range
      29339420..29353042
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015781553.3 → XP_015637039.1  DNA-directed RNA polymerase IV subunit 1 isoform X2

      UniProtKB/TrEMBL
      Q01JX0
      Conserved Domains (3) summary
      cd02737
      Location:902 → 1280
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      cd10506
      Location:23 → 873
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1366 → 1438
      DUF3223; Protein of unknown function (DUF3223)

    2. XM_015781554.3 → XP_015637040.1  DNA-directed RNA polymerase IV subunit 1 isoform X3

      UniProtKB/TrEMBL
      Q01JX0
      Conserved Domains (4) summary
      cd02737
      Location:901 → 1279
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      PRK14977
      Location:11 → 1271
      PRK14977; bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
      cd10506
      Location:23 → 872
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1365 → 1436
      DUF3223; Protein of unknown function (DUF3223)

    3. XM_015781552.2 → XP_015637038.1  DNA-directed RNA polymerase IV subunit 1 isoform X1

      UniProtKB/TrEMBL
      Q01JX0
      Conserved Domains (4) summary
      cd02737
      Location:908 → 1286
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      PRK14977
      Location:17 → 1278
      PRK14977; bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
      cd10506
      Location:29 → 879
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1372 → 1443
      DUF3223; Protein of unknown function (DUF3223)

    4. XM_015781557.3 → XP_015637043.1  DNA-directed RNA polymerase IV subunit 1 isoform X4

      UniProtKB/TrEMBL
      Q01JX0
      Conserved Domains (4) summary
      cd02737
      Location:686 → 1064
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      smart00663
      Location:18 → 307
      RPOLA_N; RNA polymerase I subunit A N-terminus
      cd10506
      Location:1 → 657
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1150 → 1221
      DUF3223; Protein of unknown function (DUF3223)
    Nucleotide Protein
    Heading Accession and Version

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