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    SOM Zinc finger C-x8-C-x5-C-x3-H type family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 839408, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SOM
    Official Full Name
    Zinc finger C-x8-C-x5-C-x3-H type family protein
    Primary source
    TAIR:AT1G03790
    Locus tag
    AT1G03790
    See related
    Araport:AT1G03790
    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
    AtTZF4; F21M11.30; F21M11_30; SOMNUS; Tandem CCCH Zinc Finger protein 4; TZF4
    Summary
    Encodes SOMNUS (SOM), a nucleus-localized CCCH-type zinc finger protein. SOM negatively regulates light-dependent seed germination downstream of PIL5 (AT2G20180).
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    Genomic context

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    See SOM in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    1
    Sequence:
    Chromosome: 1; NC_003070.9 (954290..956144)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene switch 2 Neighboring gene Prefoldin chaperone subunit family protein Neighboring gene RING 1B Neighboring gene targeting protein for XKLP2 Neighboring gene ERF domain protein 10 Neighboring gene Nucleic acid-binding, OB-fold-like 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. SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5. Kim DH, et al. Plant Cell, 2008 May. PMID 18487351, Free PMC Article
    2. AFP2 as the novel regulator breaks high-temperature-induced seeds secondary dormancy through ABI5 and SOM in Arabidopsis thaliana. Chang G, et al. Biochem Biophys Res Commun, 2018 Jun 18. PMID 29723526
    3. The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination. Bogamuwa S, et al. Plant Cell Environ, 2013 Aug. PMID 23421766
    4. ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds. Park J, et al. Plant Cell, 2011 Apr. PMID 21467583, Free PMC Article
    5. Plant Tandem CCCH Zinc Finger Proteins Interact with ABA, Drought, and Stress Response Regulators in Processing-Bodies and Stress Granules. Bogamuwa S, et al. PLoS One, 2016. PMID 26978070, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SOM is reported to negatively regulate seeds germination by altering GA/ABA metabolism, here we found that AFP2 and ABI5 altered SOM transcription. Data demonstrate that AFP2 is a novel regulator to control high temperature-induced secondary seed dormancy through ABI5 and SOM.
      Title: AFP2 as the novel regulator breaks high-temperature-induced seeds secondary dormancy through ABI5 and SOM in Arabidopsis thaliana.
    2. ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
      Title: ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis.
    3. AtTZF4, 5 and 6 affect seed germination by controlling genes critical for abscisic acid (ABA) and gibberellic acid (GA) response.
      Title: The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination.
    4. ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter.
      Title: ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds.
    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_100258.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription TAS
    Traceable Author Statement
    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 

    General protein information

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    Preferred Names
    Zinc finger C-x8-C-x5-C-x3-H type family protein
    NP_171875.1
    • SOMNUS (SOM); CONTAINS InterPro DOMAIN/s: Zinc finger, CCCH-type (InterPro:IPR000571); BEST Arabidopsis thaliana protein match is: Zinc finger C-x8-C-x5-C-x3-H type family protein (TAIR:AT5G44260.1); Has 3270 Blast hits to 1059 proteins in 150 species: Archae - 0; Bacteria - 0; Metazoa - 444; Fungi - 30; Plants - 421; Viruses - 3; Other Eukaryotes - 2372 (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
      954290..956144
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_100258.3 → NP_171875.1  Zinc finger C-x8-C-x5-C-x3-H type family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_171875.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8GZ44, Q9ZWA1
      UniProtKB/TrEMBL
      A0A178W4T9, A0A5S9SFQ6, A0A7G2DQF9
      Conserved Domains (1) summary
      pfam00642
      Location:123 → 149
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ZWA1.1

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