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    LOC4340446 putative transcription elongation factor SPT5 homolog 1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340446, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4340446
    Gene description
    putative transcription elongation factor SPT5 homolog 1
    Locus tag
    OSNPB_060208300
    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 roots after flowering (RPKM 55.3), leaves after flowering (RPKM 50.7) and 6 other tissues See more
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    Genomic context

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    See LOC4340446 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (5690576..5697335, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (5523780..5530623, complement)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107277555 Neighboring gene uncharacterized LOC9267282 Neighboring gene probable tyrosine-protein phosphatase DSP2 Neighboring gene lysM domain-containing GPI-anchored protein LYP6-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 mRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables structural constituent of ribosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription elongation 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 
    involved_in transcription elongation by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in transcription elongation-coupled chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in translation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of DSIF complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in ribosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    putative transcription elongation factor SPT5 homolog 1
    Names
    Os06g0208300
    P0664C05.20
    transcription factor
    transcription factor-like

    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
      5690576..5697335 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788355.2 → XP_015643841.1  putative transcription elongation factor SPT5 homolog 1

      UniProtKB/TrEMBL
      B9FS39
      Conserved Domains (5) summary
      cd09888
      Location:200 → 282
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:350 → 933
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:293 → 330
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:999 → 1055
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:122 → 194
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
    Nucleotide Protein
    Heading Accession and Version

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