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LOC4342383 transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4342383, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4342383
Gene description
transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like
Locus tag
OSNPB_070143200
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
Also known as
PIF4; OJ1343_B12.103; OJ1351_C05.131
Expression
Broad expression in leaves before flowering (RPKM 15.2), leaves after flowering (RPKM 13.0) and 6 other tissues See more
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Genomic context

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See LOC4342383 in Genome Data Viewer
Location:
chromosome: 7
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (2218259..2221980)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (2206894..2210724)

Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene uncharacterized oxidoreductase At1g06690, chloroplastic Neighboring gene uncharacterized oxidoreductase At1g06690, chloroplastic Neighboring gene uncharacterized LOC107276945 Neighboring gene transfer RNA methionine (anticodon CAU)

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
  • 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 protein dimerization activity 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
Os07g0143200
rice phytochrome-interacting factor 4
transcription factor BHLH9-like protein

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_089041.1 Reference ASM3414082v1 Primary Assembly

    Range
    2218259..2221980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015792559.3 → XP_015648045.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X1

    UniProtKB/TrEMBL
    Q8GRJ1
    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

  2. XM_015792558.3 → XP_015648044.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X1

    UniProtKB/TrEMBL
    Q8GRJ1
    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

  3. XM_015792557.3 → XP_015648043.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X1

    UniProtKB/TrEMBL
    Q8GRJ1
    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

  4. XM_015792560.3 → XP_015648046.1  transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X2

    UniProtKB/TrEMBL
    K4F270, Q8GRJ1
    Conserved Domains (1) summary
    cd11445
    Location:225 → 288
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins
Nucleotide Protein
Heading Accession and Version

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