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    LOC9270554 transcription elongation factor SPT6-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 9270554, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC9270554
    Gene description
    transcription elongation factor SPT6-like
    Locus tag
    OSNPB_050494800
    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 51.8), flower buds (RPKM 48.2) and 6 other tissues See more
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    Genomic context

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    See LOC9270554 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (24301338..24309854)

    Chromosome 5 - NC_029260.1Genomic Context describing neighboring genes Neighboring gene EID1-like F-box protein 3 Neighboring gene uncharacterized LOC107278338 Neighboring gene probable E3 ubiquitin-protein ligase RHC1A Neighboring gene zinc finger protein 830 Neighboring gene basic leucine zipper 23

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029260.1 Chromosome 5 Reference IRGSP-1.0 Primary Assembly

    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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 histone binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables nucleosome binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in nucleosome organization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in positive regulation of transcription elongation 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 
    Component Evidence Code Pubs
    part_of transcription elongation factor complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription elongation factor SPT6-like
    Names
    Os05g0494800
    Os05g0494900
    transcription elongation factor SPT6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference IRGSP-1.0 Primary Assembly

    Genomic

    1. NC_029260.1 Reference IRGSP-1.0 Primary Assembly

      Range
      24301338..24309854
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015783221.2 → XP_015638707.1  transcription elongation factor SPT6-like

      UniProtKB/TrEMBL
      A2Y633, B9FKX6
      Conserved Domains (3) summary
      COG2183
      Location:334 → 1209
      Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
      pfam14632
      Location:90 → 130
      SPT6_acidic; Acidic N-terminal SPT6
      pfam14633
      Location:1234 → 1439
      SH2_2; SH2 domain
    Nucleotide Protein
    Heading Accession and Version

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