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    NERD GW repeat- and PHD finger-containing protein NERD [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 816147, updated on 18-Sep-2024

    Summary

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    Official Symbol
    NERD
    Official Full Name
    GW repeat- and PHD finger-containing protein NERD
    Primary source
    TAIR:AT2G16485
    Locus tag
    AT2G16485
    See related
    Araport:AT2G16485
    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
    F16F14.1; F16F14_1; Needed for RDR2-independent DNA methylation
    Summary
    Encodes NERD (Needed for RDR2-independent DNA methylation), a plant-specific GW repeat- and PHD finger-containing protein involved in siRNA-dependent DNA methylation.
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    Genomic context

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    See NERD in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Sequence:
    Chromosome: 2; NC_003071.7 (7136845..7145424, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene F-box and associated interaction domains-containing protein Neighboring gene coiled-coil 90B-like protein (DUF1640) Neighboring gene XH domain-containing protein Neighboring gene arginine decarboxylase 1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Pontier D, et al. Mol Cell, 2012 Oct 12. PMID 22940247
    2. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Lin X, et al. Nature, 1999 Dec 16. PMID 10617197

    GeneRIFs: Gene References Into Functions

    General gene information

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    NM_127202.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  
    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
    GW repeat- and PHD finger-containing protein NERD
    NP_179241.4
    • nucleic acid binding;zinc ion binding;DNA binding; FUNCTIONS IN: DNA binding, zinc ion binding, nucleic acid binding; INVOLVED IN: histone modification, transcription initiation; LOCATED IN: nucleus; EXPRESSED IN: guard cell, cultured cell; CONTAINS InterPro DOMAIN/s: Zinc finger, CCCH-type (InterPro:IPR000571), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Plus-3 domain, subgroup (InterPro:IPR018144), Zinc finger, PHD-type (InterPro:IPR001965), GYF (InterPro:IPR003169), SWIB/MDM2 domain (InterPro:IPR003121), Plus-3 (InterPro:IPR004343), SWIB domain (InterPro:IPR019835), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: DNA binding;zinc ion binding;nucleic acid binding;nucleic acid binding (TAIR:AT3G51120.1); Has 38357 Blast hits to 25980 proteins in 1833 species: Archae - 670; Bacteria - 4778; Metazoa - 14464; Fungi - 4561; Plants - 3104; Viruses - 298; Other Eukaryotes - 10482 (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_003071.7 Reference assembly

      Range
      7136845..7145424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001335477.1 → NP_001324854.1  GW repeat- and PHD finger-containing protein NERD [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VST4, A0A1P8B1D0

    2. NM_127202.5 → NP_179241.4  GW repeat- and PHD finger-containing protein NERD [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_179241.4

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4IKD7, Q8S8E0, Q9SIV4, Q9SIV5
      UniProtKB/TrEMBL
      A0A178VST4
      Conserved Domains (5) summary
      smart00719
      Location:944 → 1052
      Plus3; Short conserved domain in transcriptional regulators
      smart00444
      Location:1308 → 1363
      GYF; Contains conserved Gly-Tyr-Phe residues
      cd15568
      Location:601 → 646
      PHD5_NSD; PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      pfam00642
      Location:1748 → 1772
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      pfam02201
      Location:809 → 882
      SWIB; SWIB/MDM2 domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SIV5.3

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