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

    Gene ID: 828706, updated on 7-Sep-2023

    Summary

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    Gene symbol
    PEP
    Gene description
    RNA-binding KH domain-containing protein
    Primary source
    Araport:AT4G26000
    Locus tag
    AT4G26000
    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
    F20B18.110; F20B18_110; PEPPER
    Summary
    Encodes a novel Arabidopsis gene encoding a polypeptide with K-homology (KH) RNA-binding modules, which acts on vegetative growth and pistil development. Genetic studies suggest that PEP interacts with element(s) of the CLAVATA signaling pathway.
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    Genomic context

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    Location:
    chromosome: 4
    Exon count:
    6
    Sequence:
    Chromosome: 4; NC_003075.7 (13197069..13199841)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene phosphatidylserine decarboxylase 3 Neighboring gene peroxidase superfamily protein Neighboring gene CCT motif family protein Neighboring gene Peroxidase superfamily protein Neighboring gene 4/1 protein short form protein Neighboring gene C2H2-like zinc finger protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium development in Arabidopsis. Ripoll JJ, et al. Dev Biol, 2006 Jan 15. PMID 16356489
    2. Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C. Ripoll JJ, et al. Dev Biol, 2009 Sep 15. PMID 19576878
    3. K-homology nuclear ribonucleoproteins regulate floral organ identity and determinacy in arabidopsis. Rodríguez-Cazorla E, et al. PLoS Genet, 2015 Feb. PMID 25658099, Free PMC Article
    4. Toward an interaction map of the two-component signaling pathway of Arabidopsis thaliana. Dortay H, et al. J Proteome Res, 2008 Sep. PMID 18642946
    5. Evidence for network evolution in an Arabidopsis interactome map. Arabidopsis Interactome Mapping Consortium. Science, 2011 Jul 29. PMID 21798944, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our data better delineates the roles of PEP in plant development and, for the first time, links FLK to a morphogenetic process
      Title: K-homology nuclear ribonucleoproteins regulate floral organ identity and determinacy in arabidopsis.
    2. PEP is a new factor for FLC upregulation, underscoring the importance of RNA-binding activities during developmental timing of flowering
      Title: Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C.
    3. PEPPER (PEP), encodes a polypeptide with K-homology (KH) RNA-binding modules, which acts on vegetative growth and pistil development.[PEPPER] [PEP]
      Title: PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium development in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_118733.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gynoecium development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of long-day photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of short-day photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within shoot system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus 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_194330.1
    • PEPPER (PEP); FUNCTIONS IN: RNA binding, nucleic acid binding; INVOLVED IN: shoot development, gynoecium development; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 14 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:AT3G04610.1); Has 2804 Blast hits to 2065 proteins in 185 species: Archae - 0; Bacteria - 0; Metazoa - 1818; Fungi - 225; Plants - 670; Viruses - 0; Other Eukaryotes - 91 (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_003075.7 Reference assembly

      Range
      13197069..13199841
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_118733.4 → NP_194330.1  RNA-binding KH domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_194330.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9SZH4
      UniProtKB/TrEMBL
      A0A178UZE9, A0A5S9XVX2, A0A654FSV6
      Conserved Domains (2) summary
      cd02396
      Location:75 → 144
      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 ...
      pfam00013
      Location:343 → 405
      KH_1; KH domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SZH4.1

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