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

    Gene ID: 4334324, updated on 17-Jul-2024

    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
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    Genomic context

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    See LOC4334324 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (33403477..33407339)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (32431874..32435842)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4334322 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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    Go to nucleotide: Graphics FASTA GenBank

    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
    2. 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
    3. 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

    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 

    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: 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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      33403477..33407339
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015777833.3 → 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, ...

    2. XM_015777836.3 → 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

    3. XM_015777838.2 → XP_015633324.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X3

      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

    4. XM_015777839.2 → XP_015633325.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X4

      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_010740237.1 RNA Sequence

    2. XR_001544882.3 RNA Sequence

    3. XR_001544881.3 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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