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    EMB25 DEAD/DEAH box helicase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 843343, updated on 18-Sep-2024

    Summary

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    Official Symbol
    EMB25
    Official Full Name
    DEAD/DEAH box helicase
    Primary source
    TAIR:AT1G70070
    Locus tag
    AT1G70070
    See related
    Araport:AT1G70070
    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
    EMBRYO DEFECTIVE 25; F20P5.20; F20P5_20; INCREASED SIZE EXCLUSION LIMIT 2; ISE2; PDE317; PIGMENT DEFECTIVE 317
    Summary
    Allelic to ISE2(increased size exclusion limit of plasmodesmata 2). Mutants maintain dilated plasmodesmata at the embryonic torpedo stage.
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    Genomic context

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    See EMB25 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    6
    Sequence:
    Chromosome: 1; NC_003070.9 (26390016..26394196, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene SIN3-like 4 Neighboring gene Terpenoid cyclases/Protein prenyltransferases superfamily protein Neighboring gene glucosyl transferase family 8

    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. The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. Bobik K, et al. Plant J, 2017 Jul. PMID 28346704
    2. Organelle-nucleus cross-talk regulates plant intercellular communication via plasmodesmata. Burch-Smith TM, et al. Proc Natl Acad Sci U S A, 2011 Dec 20. PMID 22106293, Free PMC Article
    3. INCREASED SIZE EXCLUSION LIMIT 2 encodes a putative DEVH box RNA helicase involved in plasmodesmata function during Arabidopsis embryogenesis. Kobayashi K, et al. Plant Cell, 2007 Jun. PMID 17601829, Free PMC Article
    4. Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata. Burch-Smith TM, et al. Curr Biol, 2010 Jun 8. PMID 20434343, Free PMC Article
    5. Identification of a developmental transition in plasmodesmatal function during embryogenesis in Arabidopsis thaliana. Kim I, et al. Development, 2002 Mar. PMID 11874921

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ISE2 depletion causes splicing defects of chloroplasts transcripts containing group II introns. ISE2 directly binds to chloroplast RNA targets in vivo.
      Title: The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION LIMIT 2 involved in plasmodesmata regulation is required for group II intron splicing.
    2. Data show that silencing of ISE1 and ISE2 phenocopies ise1 and ise2 mutant embryos: when wild-type ISE1 and ISE2 functions are lost, de novo production of plasmodesmata occurs, leading to increased intercellular transport.
      Title: Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata.
    3. Increased size exclusion limit2 (ISE2) function affects plasmodesmata structure and function through the regulation of RNA metabolism and consequent gene expression. [ISE2]
      Title: INCREASED SIZE EXCLUSION LIMIT 2 encodes a putative DEVH box RNA helicase involved in plasmodesmata function during Arabidopsis embryogenesis.
    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_105675.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within Group II intron splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in Group II intron splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within chloroplast rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chloroplast rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cytidine to uridine editing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cytidine to uridine editing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo development ending in seed dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plasmodesmata-mediated intercellular transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plasmodesmata-mediated intercellular transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast stroma HDA PubMed 
    located_in cytoplasmic stress granule 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
    DEAD/DEAH box helicase
    NP_177164.1
    • EMBRYO DEFECTIVE 25 (EMB25); FUNCTIONS IN: RNA helicase activity, ATP-dependent helicase activity; INVOLVED IN: posttranscriptional gene silencing, plasmodesmata-mediated intercellular transport, embryo development ending in seed dormancy; LOCATED IN: stress granule, chloroplast stroma, chloroplast; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 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), 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:AT3G46960.1); Has 21396 Blast hits to 12786 proteins in 1473 species: Archae - 1027; Bacteria - 4600; Metazoa - 5457; Fungi - 2724; Plants - 1158; Viruses - 307; Other Eukaryotes - 6123 (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
      26390016..26394196 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_105675.2 → NP_177164.1  DEAD/DEAH box helicase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_177164.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DFG3, O04538, Q94EZ6
      UniProtKB/TrEMBL
      A0A5S9WR83
      Conserved Domains (5) summary
      smart00490
      Location:497 → 574
      HELICc; helicase superfamily c-terminal domain
      smart00487
      Location:150 → 338
      DEXDc; DEAD-like helicases superfamily
      pfam00270
      Location:157 → 315
      DEAD; DEAD/DEAH box helicase
      pfam08148
      Location:999 → 1166
      DSHCT; DSHCT (NUC185) domain
      pfam15346
      Location:645 → 744
      ARGLU; Arginine and glutamate-rich 1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B9DFG3.2

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