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LOC4339778 RNA polymerase sigma factor sigC [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4339778, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4339778
Gene description
RNA polymerase sigma factor sigC
Locus tag
OSNPB_050589200
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
Biased expression in leaves before flowering (RPKM 317.7), roots after flowering (RPKM 278.8) and 3 other tissues See more
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Genomic context

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See LOC4339778 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (29527466..29531589)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (29341246..29345422)

Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4339776 Neighboring gene transfer RNA valine (anticodon UAC) Neighboring gene transfer RNA valine (anticodon AAC) Neighboring gene transcription factor MYBS3-like

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 DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription initiation IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
RNA polymerase sigma factor sigC
Names
Os05g0589200

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_089039.1 Reference ASM3414082v1 Primary Assembly

    Range
    29527466..29531589
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015782153.3 → XP_015637639.1  RNA polymerase sigma factor sigC

    UniProtKB/TrEMBL
    B8AX92
    Conserved Domains (4) summary
    cd06171
    Location:485 → 543
    Sigma70_r4; Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or ...
    TIGR02393
    Location:330 → 554
    RpoD_Cterm; RNA polymerase sigma factor RpoD, C-terminal domain
    pfam04539
    Location:404 → 479
    Sigma70_r3; Sigma-70 region 3
    pfam04542
    Location:330 → 384
    Sigma70_r2; Sigma-70 region 2
Nucleotide Protein
Heading Accession and Version

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