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    LOC4335427 MADS-box transcription factor 25-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4335427, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4335427
    Gene description
    MADS-box transcription factor 25-like
    Locus tag
    OSNPB_040304400
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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
    MADS25; OsMADS25
    Expression
    Restricted expression toward roots before flowering (RPKM 19.9) See more
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    Genomic context

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    See LOC4335427 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 4 NC_089038.1 (13908991..13912165)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 4 NC_029259.1 (13672560..13675934)

    Chromosome 4 - NC_089038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4335425 Neighboring gene phototropin-2-like Neighboring gene chalcone synthase 3-like Neighboring gene small nucleolar RNA R71

    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. Transcription factor OsMADS25 improves rice tolerance to cold stress. Yan LY, et al. Yi Chuan, 2021 Nov 20. PMID 34815210
    2. OsMADS25 regulates root system development via auxin signalling in rice. Zhang G, et al. Plant J, 2018 Sep. PMID 29932274
    3. MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice. Yu C, et al. PLoS One, 2015. PMID 26258667, Free PMC Article
    4. Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. Lee S, et al. Plant Cell Physiol, 2003 Dec. PMID 14701936
    5. 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

    What's a GeneRIF?
    1. Transcription factor OsMADS25 improves rice tolerance to cold stress.
      Title: Transcription factor OsMADS25 improves rice tolerance to cold stress.
    2. regulates root system development via auxin signalling
      Title: OsMADS25 regulates root system development via auxin signalling in rice.
    3. MADS25 is a positive regulator that controls lateral and primary root development in rice via modulation of nitrate accumulation.
      Title: MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice.
    Submit: New GeneRIF Correction

    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 positive regulation of transcription by RNA polymerase II 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
    mADS-box transcription factor 25
    Names
    LOC_Os04g23910
    MADS-box transcription factor 25
    OSJNBa0079M09.14
    transcription factor MADS25

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001419204.1 → NP_001406133.1  mADS-box transcription factor 25

      Status: VALIDATED

      Source sequence(s)
      AK102927
      UniProtKB/Swiss-Prot
      Q0JEA7, Q7XVR2, Q84NC5
      UniProtKB/TrEMBL
      Q01ME4

    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
      13908991..13912165
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q84NC5.2 GenPept UniProtKB/Swiss-Prot:Q84NC5

    Gene LinkOut

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