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    CHR38 chromatin remodeling 38 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 823287, updated on 18-Sep-2024

    Summary

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    Official Symbol
    CHR38
    Official Full Name
    chromatin remodeling 38
    Primary source
    TAIR:AT3G42670
    Locus tag
    AT3G42670
    See related
    Araport:AT3G42670
    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
    chromatin remodeling 38; CLASSY 1; CLASSY1; CLSY; CLSY1
    Summary
    Encodes a nuclear localized SNF domain containing protein involved in RNA silencing. Mutants were identified in a screen for defects in the spread of RNA silencing. CLSY1 may affect production of dsRNA from the locus to be silenced.
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    Genomic context

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    See CHR38 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    6
    Sequence:
    Chromosome: 3; NC_003074.8 (14755798..14760629, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene pseudo Neighboring gene transducin family protein / WD-40 repeat family protein Neighboring gene pseudo Neighboring gene pseudo

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Smith LM, et al. Plant Cell, 2007 May. PMID 17526749, Free PMC Article
    2. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Zhou M, et al. Nat Genet, 2018 Jun. PMID 29736015, Free PMC Article
    3. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Zhang H, et al. Proc Natl Acad Sci U S A, 2013 May 14. PMID 23637343, Free PMC Article
    4. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. Law JA, et al. PLoS Genet, 2011 Jul. PMID 21811420, Free PMC Article
    5. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat M, et al. Nature, 2000 Dec 14. PMID 11130713

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data show that SHH1(AT1G15215), RDR2, CLASSY1, and RDM4 were co-purified with NRPD1(At1g63020), the largest subunit of Pol-IV.
      Title: SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.
    2. A SNF2 domain-containing protein (CLASSY1) that acts together with RDR2 and NRPD1a in the spread of transgene silencing and in the production of endogenous 24-nucleotide short interfering RNAs (siRNAs), is identified.[CLSY1]
      Title: An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells 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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    NM_001339088.1
    NM_114134.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in gene silencing by siRNA-directed DNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within transcription by RNA polymerase IV IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus 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
    chromatin remodeling 38
    NP_189853.1
    • chromatin remodeling 38 (CHR38); FUNCTIONS IN: helicase activity, DNA binding, ATP binding, nucleic acid binding; INVOLVED IN: gene silencing by RNA; LOCATED IN: nucleolus; EXPRESSED IN: 13 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: chromatin remodeling 42 (TAIR:AT5G20420.1); Has 13835 Blast hits to 12445 proteins in 1668 species: Archae - 89; Bacteria - 4181; Metazoa - 3164; Fungi - 3150; Plants - 1308; Viruses - 62; Other Eukaryotes - 1881 (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_003074.8 Reference assembly

      Range
      14755798..14760629 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001339087.1 → NP_001327910.1  chromatin remodeling 38 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9M297
      UniProtKB/TrEMBL
      A0A178VEK9, A0A5S9XIY7
      Conserved Domains (3) summary
      cd18793
      Location:1050 → 1186
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18007
      Location:674 → 939
      DEXHc_ATRX-like; DEXH-box helicase domain of ATRX-like proteins
      pfam16719
      Location:24 → 120
      SAWADEE; SAWADEE domain

    2. NM_001339086.1 → NP_001327912.1  chromatin remodeling 38 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9M297
      UniProtKB/TrEMBL
      A0A178VEK9, A0A5S9XIY7
      Conserved Domains (3) summary
      cd18793
      Location:1050 → 1186
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18007
      Location:674 → 939
      DEXHc_ATRX-like; DEXH-box helicase domain of ATRX-like proteins
      pfam16719
      Location:24 → 120
      SAWADEE; SAWADEE domain

    3. NM_114134.2 → NP_189853.1  chromatin remodeling 38 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_189853.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9M297
      UniProtKB/TrEMBL
      A0A178VEK9, A0A5S9XIY7
      Conserved Domains (3) summary
      cd18793
      Location:1050 → 1186
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18007
      Location:674 → 939
      DEXHc_ATRX-like; DEXH-box helicase domain of ATRX-like proteins
      pfam16719
      Location:24 → 120
      SAWADEE; SAWADEE domain

    4. NM_001339088.1 → NP_001327911.1  chromatin remodeling 38 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1I9LTS2, A0A5S9XIY7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9M297.1

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