U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LOC4343902 DNA-directed RNA polymerases II, IV and V subunit 9A [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4343902, updated on 12-Jul-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC4343902
    Gene description
    DNA-directed RNA polymerases II, IV and V subunit 9A
    Locus tag
    OSNPB_070615800
    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 flower buds (RPKM 26.1), flowers (RPKM 24.7) and 6 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC4343902 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (25594315..25596954, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (25369214..25371933, complement)

    Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene oligouridylate-binding protein 1 Neighboring gene uncharacterized LOC4343901 Neighboring gene protein FAR1-RELATED SEQUENCE 5 Neighboring gene probable GPI-anchored adhesin-like protein PGA55

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. 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
    2. 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

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA-directed 5'-3' RNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables zinc ion binding 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 
    involved_in maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in transcription initiation at RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in transcription-coupled nucleotide-excision repair 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

    Go to the top of the page Help
    Preferred Names
    DNA-directed RNA polymerases II, IV and V subunit 9A
    Names
    B1056G08.105
    Os07g0615800
    P0616D06.132
    putative RNA Polymerase II subunit 14.5 kD

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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
      25594315..25596954 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015791869.3 → XP_015647355.1  DNA-directed RNA polymerases II, IV and V subunit 9A isoform X2

      UniProtKB/TrEMBL
      Q0D4N8
      Conserved Domains (3) summary
      smart00661
      Location:7 → 49
      RPOL9; RNA polymerase subunit 9
      COG1594
      Location:5 → 115
      RPB9; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
      cd10508
      Location:65 → 114
      Zn-ribbon_RPB9; C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II

    2. XM_015791868.3 → XP_015647354.1  DNA-directed RNA polymerases II, IV and V subunit 9A isoform X1

      UniProtKB/TrEMBL
      Q0D4N8, Q7EZ81, Q8GSD5
      Conserved Domains (2) summary
      COG1594
      Location:5 → 116
      RPB9; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
      cd10508
      Location:66 → 115
      Zn-ribbon_RPB9; C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials