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    RCF3 RNA-binding KH domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 835386, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RCF3
    Official Full Name
    RNA-binding KH domain-containing protein
    Primary source
    TAIR:AT5G53060
    Locus tag
    AT5G53060
    See related
    Araport:AT5G53060
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    MNB8.12; MNB8_12; regulator of CBF gene expression 3; SHI1; SHINY 1
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    Genomic context

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    See RCF3 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    9
    Sequence:
    Chromosome: 5; NC_003076.8 (21514896..21520421)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene alpha/beta-Hydrolases superfamily protein Neighboring gene miscRNA Neighboring gene Ribosomal protein L9/RNase H1 Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein Neighboring gene NAD(P)-binding Rossmann-fold superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis. Guan Q, et al. Mol Plant, 2013 Mar. PMID 23087326
    2. HOS5-a negative regulator of osmotic stress-induced gene expression in Arabidopsis thaliana. Xiong L, et al. Plant J, 1999 Sep. PMID 10504578
    3. The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress. Thatcher LF, et al. PLoS One, 2015. PMID 25985302, Free PMC Article
    4. Regulation of abiotic stress signalling by Arabidopsis C-terminal domain phosphatase-like 1 requires interaction with a k-homology domain-containing protein. Jeong IS, et al. PLoS One, 2013. PMID 24303021, Free PMC Article
    5. The arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression. Jiang J, et al. PLoS Genet, 2013. PMID 23874224, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.
      Title: KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1.
    2. HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5)affects the biogenesis of a subset of miRNA.
      Title: The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.
    3. a KH domain-containing putative RNA-binding protein RCF3 is an important upstream regulator for heat stress-responsive gene expression and thermotolerance in Arabidopsis [RCF3]
      Title: A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis.
    4. In fry2 mutants, HOS5 failed to be localized in nuclear speckles but was found mainly in the nucleoplasm. hos5 mutants were impaired in mRNA export and accumulated a significant amount of mRNA in the nuclei, particularly under salt stress conditions. [HOS5]
      Title: A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.
    5. K-homology domain-containing protein named SHINY1 (SHI1) interacts with CPL1 to modulate gene expression. [SHI1] [SHINY1]
      Title: The arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001203597.1
    NM_001345032.1
    NM_124685.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables primary miRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within heat acclimation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within jasmonic acid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within primary miRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of defense response to fungus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to osmotic stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear dicing body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding KH domain-containing protein
    NP_001190526.1
    • RNA-binding KH domain-containing protein; FUNCTIONS IN: RNA binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: K Homology, type 1, subgroup (InterPro:IPR018111), K Homology (InterPro:IPR004087), K Homology, type 1 (InterPro:IPR004088); BEST Arabidopsis thaliana protein match is: RNA-binding KH domain-containing protein (TAIR:AT5G15270.1).
    NP_200118.3
    • RNA-binding KH domain-containing protein; FUNCTIONS IN: RNA binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: K Homology, type 1, subgroup (InterPro:IPR018111), K Homology (InterPro:IPR004087), K Homology, type 1 (InterPro:IPR004088); BEST Arabidopsis thaliana protein match is: RNA-binding KH domain-containing protein (TAIR:AT5G15270.1); Has 2883 Blast hits to 1912 proteins in 183 species: Archae - 0; Bacteria - 2; Metazoa - 1739; Fungi - 239; Plants - 817; Viruses - 2; Other Eukaryotes - 84 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      21514896..21520421
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_124685.4 → NP_200118.3  RNA-binding KH domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200118.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8W4B1, Q9LVU6
      UniProtKB/TrEMBL
      A0A178UIE3, A0A5S9YDN8, A0A654GAE7
      Conserved Domains (3) summary
      cd22459
      Location:67 → 140
      KH-I_PEPPER_rpt1_like; first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins
      cd22460
      Location:178 → 250
      KH-I_PEPPER_rpt2_like; second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins
      cd22463
      Location:576 → 644
      KH-I_RCF3_like_rpt5; fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein

    2. NM_001345032.1 → NP_001330551.1  RNA-binding KH domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8BB62, A0A5S9YDN8, A0A654GAE7

    3. NM_001203597.1 → NP_001190526.1  RNA-binding KH domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190526.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4KIZ8
      Conserved Domains (1) summary
      cd02396
      Location:69 → 143
      PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8W4B1.1

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