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    SHH1 SAWADEE HOMEODOMAIN protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 838088, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SHH1
    Official Full Name
    SAWADEE HOMEODOMAIN protein
    Primary source
    TAIR:AT1G15215
    Locus tag
    AT1G15215
    See related
    Araport:AT1G15215
    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
    DNA-binding transcription factor 1; DTF1; SAWADEE homeodomain homolog 1
    Summary
    Encodes SHH1, a homeodomain protein required for DNA methylation. It is an atypical RNA-directed DNA methylation component, and functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways.
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    Genomic context

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    See SHH1 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    9
    Sequence:
    Chromosome: 1; NC_003070.9 (5238044..5240051)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene protein-protein interaction regulator family protein Neighboring gene pleiotropic drug resistance 7 Neighboring gene cytochrome c biogenesis protein family Neighboring gene uncharacterized protein Neighboring gene phox (PX) domain-containing protein Neighboring gene Zinc-binding ribosomal protein family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Law JA, et al. Nature, 2013 Jun 20. PMID 23636332, Free PMC Article
    2. An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing. Liu J, et al. Cell Res, 2011 Dec. PMID 22064704, 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 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. [DTF1]
      Title: DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
    2. central role for methylated H3K9 binding in SHH1 function; key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RNA-directed DNA methylation targets.
      Title: Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
    3. 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.
    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_001035971.2
    NM_001332154.1
    NM_001332155.1
    NM_179335.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    SAWADEE HOMEODOMAIN protein
    NP_001031048.1
    • BEST Arabidopsis thaliana protein match is: sequence-specific DNA binding transcription factors;sequence-specific DNA binding (TAIR:AT3G18380.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_001319007.1
    • BEST Arabidopsis thaliana protein match is: sequence-specific DNA binding transcription factors;sequence-specific DNA binding (TAIR:AT3G18380.1); Has 89 Blast hits to 86 proteins in 16 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 89; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
    NP_849666.2
    • BEST Arabidopsis thaliana protein match is: sequence-specific DNA binding transcription factors;sequence-specific DNA binding (TAIR:AT3G18380.1); Has 89 Blast hits to 86 proteins in 16 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 89; Viruses - 0; Other Eukaryotes - 0 (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_003070.9 Reference assembly

      Range
      5238044..5240051
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_179335.3 → NP_849666.2  SAWADEE HOMEODOMAIN protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_849666.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MRU8, Q2V4N1, Q8GYR2, Q9XI47
      UniProtKB/TrEMBL
      A0A5S9UIQ3, A0A654EKT9
      Conserved Domains (1) summary
      pfam16719
      Location:125 → 253
      SAWADEE; SAWADEE domain

    2. NM_001332155.1 → NP_001321872.1  SAWADEE HOMEODOMAIN protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178W211, A0A1P8AS73, A0A384LAK3, A0A5S9UIQ3
      Conserved Domains (1) summary
      pfam16719
      Location:125 → 241
      SAWADEE; SAWADEE domain

    3. NM_001332154.1 → NP_001319007.1  SAWADEE HOMEODOMAIN protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178W1M1, A0A2H1ZEB1, A0A384KV25

    4. NM_001035971.2 → NP_001031048.1  SAWADEE HOMEODOMAIN protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031048.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9UIQ3
      Conserved Domains (1) summary
      pfam16719
      Location:125 → 241
      SAWADEE; SAWADEE domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9XI47.1

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