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    RNA helicase, ATP-dependent, SK12/DOB1 protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 823849, updated on 18-Sep-2024

    Summary

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    Official Full Name
    RNA helicase, ATP-dependent, SK12/DOB1 protein
    Primary source
    TAIR:AT3G46960
    Locus tag
    AT3G46960
    See related
    Araport:AT3G46960
    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
    Summary
    The gene encodes a DExD⁄H box RNA helicase, involved in the regulation of K+ deprivation stress response.
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    Genomic context

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    Location:
    chromosome: 3
    Exon count:
    23
    Sequence:
    Chromosome: 3; NC_003074.8 (17290873..17298222, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene Mitochondrial transcription termination factor family protein Neighboring gene ncRNA Neighboring gene DUTP-PYROPHOSPHATASE-LIKE 1 Neighboring gene alpha-glucan phosphorylase 2 Neighboring gene phosphate transporter 4;3 Neighboring gene DUF740 family protein, putative (DUF740) Neighboring gene ncRNA

    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. A DExD/H box RNA helicase is important for K+ deprivation responses and tolerance in Arabidopsis thaliana. Xu RR, et al. FEBS J, 2011 Jul. PMID 21535471
    2. SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Branscheid A, et al. Nucleic Acids Res, 2015 Dec 15. PMID 26464441, Free PMC Article
    3. SUPERKILLER Complex Components Are Required for the RNA Exosome-Mediated Control of Cuticular Wax Biosynthesis in Arabidopsis Inflorescence Stems. Zhao L, et al. Plant Physiol, 2016 Jun. PMID 27208312, Free PMC Article
    4. Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover. Dorcey E, et al. PLoS Genet, 2012. PMID 22511887, Free PMC Article
    5. The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Carter C, et al. Plant Cell, 2004 Dec. PMID 15539469, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001339289.1
    NM_001339290.1
    NM_114563.7

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA fragment catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of wax biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within potassium ion transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to potassium ion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Ski complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plant-type vacuole HDA PubMed 

    General protein information

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    Preferred Names
    RNA helicase, ATP-dependent, SK12/DOB1 protein
    NP_190280.5
    • RNA helicase, ATP-dependent, SK12/DOB1 protein; FUNCTIONS IN: hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: vacuole; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DSH, C-terminal (InterPro:IPR012961), DEAD-like helicase, N-terminal (InterPro:IPR014001), RNA helicase, ATP-dependent, SK12/DOB1 (InterPro:IPR016438), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: RNA helicase, ATP-dependent, SK12/DOB1 protein (TAIR:AT1G59760.1); Has 10417 Blast hits to 7271 proteins in 1110 species: Archae - 777; Bacteria - 3025; Metazoa - 1455; Fungi - 1476; Plants - 602; Viruses - 48; Other Eukaryotes - 3034 (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
      17290873..17298222 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_114563.7 → NP_190280.5  RNA helicase, ATP-dependent, SK12/DOB1 protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190280.5

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4JAA5, Q9SD77, Q9STG8
      UniProtKB/TrEMBL
      A0A178VQ85, A0A5S9XJ64, A0A654FFD5
      Conserved Domains (5) summary
      smart00490
      Location:711 → 791
      HELICc; helicase superfamily c-terminal domain
      COG4581
      Location:264 → 1343
      Dob10; Superfamily II RNA helicase [Replication, recombination and repair]
      pfam00270
      Location:365 → 509
      DEAD; DEAD/DEAH box helicase
      pfam08148
      Location:1169 → 1337
      DSHCT; DSHCT (NUC185) domain
      pfam13234
      Location:848 → 1142
      rRNA_proc-arch; rRNA-processing arch domain

    2. NM_001339290.1 → NP_001325878.1  RNA helicase, ATP-dependent, SK12/DOB1 protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VQ85, A0A1I9LMJ9, A0A5S9XJ64, A0A654FFD5

    3. NM_001339289.1 → NP_001325879.1  RNA helicase, ATP-dependent, SK12/DOB1 protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VQ85, A0A1I9LMK0, A0A5S9XJ64, A0A654FFD5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4JAA5.1

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