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    LOC4335808 transcription factor E2FA [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4335808, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4335808
    Gene description
    transcription factor E2FA
    Locus tag
    OSNPB_040416100
    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 before flowering (RPKM 14.7), leaves before flowering (RPKM 11.9) and 6 other tissues See more
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    Genomic context

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    See LOC4335808 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 4 NC_089038.1 (20934096..20939293, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (20550009..20555299, complement)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene non-specific lipid-transfer protein 4.1 Neighboring gene uncharacterized LOC4335807 Neighboring gene 2-Cys peroxiredoxin BAS1, chloroplastic-like Neighboring gene uncharacterized LOC136356274

    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. E2F sites that can interact with E2F proteins cloned from rice are required for meristematic tissue-specific expression of rice and tobacco proliferating cell nuclear antigen promoters. Kosugi S, et al. Plant J, 2002 Jan. PMID 12060226
    2. 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
    3. 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
    4. 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription factor E2FA
    Names
    Os04g0416100

    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
      20934096..20939293 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015781623.3 → XP_015637109.1  transcription factor E2FA isoform X4

      UniProtKB/TrEMBL
      Q7XTF3
      Conserved Domains (2) summary
      cd14660
      Location:216 → 323
      E2F_DD; Dimerization domain of E2F transcription factors
      pfam02319
      Location:141 → 206
      E2F_TDP; E2F/DP family winged-helix DNA-binding domain

    2. XM_015781621.3 → XP_015637107.1  transcription factor E2FA isoform X2

      UniProtKB/TrEMBL
      Q7XTF3
      Conserved Domains (2) summary
      cd14660
      Location:214 → 321
      E2F_DD; Dimerization domain of E2F transcription factors
      pfam02319
      Location:141 → 204
      E2F_TDP; E2F/DP family winged-helix DNA-binding domain

    3. XM_026024855.2 → XP_025880640.1  transcription factor E2FA isoform X1

      UniProtKB/TrEMBL
      Q7XTF3
      Conserved Domains (2) summary
      cd14660
      Location:216 → 323
      E2F_DD; Dimerization domain of E2F transcription factors
      pfam02319
      Location:141 → 206
      E2F_TDP; E2F/DP family winged-helix DNA-binding domain

    4. XM_015781622.3 → XP_015637108.1  transcription factor E2FA isoform X3

      UniProtKB/TrEMBL
      Q7XTF3
      Conserved Domains (2) summary
      cd14660
      Location:216 → 323
      E2F_DD; Dimerization domain of E2F transcription factors
      pfam02319
      Location:141 → 206
      E2F_TDP; E2F/DP family winged-helix DNA-binding domain
    Nucleotide Protein
    Heading Accession and Version

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