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    LOC4334324 transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4334324, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4334324
    Gene description
    transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like
    Locus tag
    OSNPB_030782500
    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
    Broad expression in roots after flowering (RPKM 20.4), flower buds (RPKM 12.2) and 5 other tissues See more
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    Genomic context

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    Location:
    chromosome: 3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (32431874..32435842)

    Chromosome 3 - NC_029258.1Genomic Context describing neighboring genes Neighboring gene formin-2 Neighboring gene vegetative cell wall protein gp1 Neighboring gene transfer RNA valine (anticodon AAC) Neighboring gene transfer RNA valine (anticodon AAC)

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029258.1 Chromosome 3 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 DNA-binding transcription factor activity 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 DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like
    Names
    Os03g0782500
    transcription factor PIF5

    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_029258.1 Reference IRGSP-1.0 Primary Assembly

      Range
      32431874..32435842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015777837.2 → XP_015633323.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X3

    2. XM_015777833.2 → XP_015633319.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X1

      UniProtKB/TrEMBL
      B8AKW2
      Conserved Domains (1) summary
      cd00083
      Location:380 → 439
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

    3. XM_015777836.2 → XP_015633322.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X2

      UniProtKB/TrEMBL
      B8AKW2
      Conserved Domains (1) summary
      cd11445
      Location:336 → 399
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    4. XM_015777838.1 → XP_015633324.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X4

      UniProtKB/Swiss-Prot
      Q10CH5
      UniProtKB/TrEMBL
      Q10CH6
      Conserved Domains (1) summary
      cd11445
      Location:231 → 294
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    5. XM_015777839.1 → XP_015633325.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X5

      UniProtKB/Swiss-Prot
      Q10CH5
      Conserved Domains (1) summary
      cd11445
      Location:229 → 292
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    RNA

    1. XR_001544881.2 RNA Sequence

    2. XR_001544882.2 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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