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LOC4328080 transcription factor ILR3 [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4328080, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4328080
Gene description
transcription factor ILR3
Locus tag
OSNPB_020116600
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
OJ1442_E05.19
Expression
Ubiquitous expression in leaves after flowering (RPKM 32.9), roots after flowering (RPKM 32.8) and 6 other tissues See more
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Genomic context

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See LOC4328080 in Genome Data Viewer
Location:
chromosome: 2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (882685..885217, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (875899..878610, complement)

Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene probable metal-nicotianamine transporter YSL8 Neighboring gene dehydrogenase/reductase SDR family member FEY Neighboring gene phytosulfokine receptor 1 Neighboring gene uncharacterized LOC4328082

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. GRASSIUS: a platform for comparative regulatory genomics across the grasses. Yilmaz A, et al. Plant Physiol, 2009 Jan. PMID 18987217, Free PMC Article
  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

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 intracellular iron ion homeostasis IEA
Inferred from Electronic Annotation
more info
 PubMed 
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 ILR3
Names
Os02g0116600
bHLH transcription factor
putative bHLH 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_089036.1 Reference ASM3414082v1 Primary Assembly

    Range
    882685..885217 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015770880.3 → XP_015626366.1  transcription factor ILR3

    UniProtKB/TrEMBL
    A0A0P0VE33, A2X043, Q0E4J4, Q6ZGM4
    Conserved Domains (1) summary
    cd11446
    Location:71 → 146
    bHLH_AtILR3_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins
Nucleotide Protein
Heading Accession and Version

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