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    emb1138 DEAD box RNA helicase (RH3) [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 832713, updated on 18-Sep-2024

    Summary

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    Official Symbol
    emb1138
    Official Full Name
    DEAD box RNA helicase (RH3)
    Primary source
    TAIR:AT5G26742
    Locus tag
    AT5G26742
    See related
    Araport:AT5G26742
    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
    AtRH3; embryo defective 1138; RH3
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    Genomic context

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    See emb1138 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    11
    Sequence:
    Chromosome: 5; NC_003076.8 (9284557..9289003, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Putative membrane lipoprotein Neighboring gene Putative membrane lipoprotein Neighboring gene Putative membrane lipoprotein Neighboring gene organic solute transporter ostalpha protein (DUF300) Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Defective chloroplast development inhibits maintenance of normal levels of abscisic acid in a mutant of the Arabidopsis RH3 DEAD-box protein during early post-germination growth. Lee KH, et al. Plant J, 2013 Mar. PMID 23227895
    2. Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Asakura Y, et al. Plant Physiol, 2012 Jul. PMID 22576849, Free PMC Article
    3. Identification and dynamics of Arabidopsis adaptor protein-2 complex and its involvement in floral organ development. Yamaoka S, et al. Plant Cell, 2013 Aug. PMID 23975897, Free PMC Article
    4. The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Peltier JB, et al. Mol Cell Proteomics, 2006 Jan. PMID 16207701
    5. Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Elrouby N, et al. Proc Natl Acad Sci U S A, 2010 Oct 5. PMID 20855607, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RH3 is highly expressed in greening tissues of germinating seedlings, and chloroplasts in the rh3-4 mutant have fewer ribosomes, lower amounts of chlorophyll, and poorly developed thylakoids. rh3-4 seedlings displayed ABA-deficient phenotypes.
      Title: Defective chloroplast development inhibits maintenance of normal levels of abscisic acid in a mutant of the Arabidopsis RH3 DEAD-box protein during early post-germination growth.
    2. The function of chloroplast RH3 in maize (Zea mays; ZmRH3) and Arabidopsis (Arabidopsis thaliana; AtRH3) was determined.
      Title: Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001036866.4
    NM_001203473.1
    NM_147920.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding HDA PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Group II intron splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chloroplast organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo development ending in seed dormancy NAS
    Non-traceable Author Statement
    more info
    		  
    involved_in response to salt stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosome biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast envelope HDA PubMed 
    located_in chloroplast stroma HDA PubMed 
    located_in chloroplast stroma IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plastid HDA PubMed 

    General protein information

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    Preferred Names
    DEAD box RNA helicase (RH3)
    NP_001031943.1
    • embryo defective 1138 (emb1138); FUNCTIONS IN: in 6 functions; INVOLVED IN: embryo development ending in seed dormancy; LOCATED IN: chloroplast, membrane; EXPRESSED IN: guard cell, leaf; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), GUCT (InterPro:IPR012562), RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, CCHC-type (InterPro:IPR001878), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: putative mitochondrial RNA helicase 2 (TAIR:AT3G22330.1); Has 62370 Blast hits to 60300 proteins in 3359 species: Archae - 1368; Bacteria - 33087; Metazoa - 7991; Fungi - 5480; Plants - 3250; Viruses - 141; Other Eukaryotes - 11053 (source: NCBI BLink).
    NP_001190402.1
    • embryo defective 1138 (emb1138); FUNCTIONS IN: in 6 functions; INVOLVED IN: embryo development ending in seed dormancy; EXPRESSED IN: guard cell; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), GUCT (InterPro:IPR012562), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, CCHC-type (InterPro:IPR001878), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: putative mitochondrial RNA helicase 2 (TAIR:AT3G22330.1).
    NP_680225.2
    • embryo defective 1138 (emb1138); FUNCTIONS IN: in 6 functions; INVOLVED IN: embryo development ending in seed dormancy; LOCATED IN: chloroplast, chloroplast stroma, membrane; EXPRESSED IN: guard cell, leaf; CONTAINS InterPro DOMAIN/s: RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), GUCT (InterPro:IPR012562), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, CCHC-type (InterPro:IPR001878), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: putative mitochondrial RNA helicase 2 (TAIR:AT3G22330.1); Has 62677 Blast hits to 60420 proteins in 3357 species: Archae - 1370; Bacteria - 33239; Metazoa - 8033; Fungi - 5520; Plants - 3292; Viruses - 108; Other Eukaryotes - 11115 (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_003076.8 Reference assembly

      Range
      9284557..9289003 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001036866.4 → NP_001031943.1  DEAD box RNA helicase (RH3) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031943.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O65255, Q0WMJ9, Q8L7S8, Q8LPE9, Q8RUW1, Q9SB96
      UniProtKB/TrEMBL
      A0A178UT03, A0A5S9Y7X5, A0A7G2FA93
      Conserved Domains (3) summary
      smart00343
      Location:729 → 743
      ZnF_C2HC; zinc finger
      COG0513
      Location:105 → 470
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd12938
      Location:539 → 619
      GUCT_Hera; RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins

    2. NM_001203473.1 → NP_001190402.1  DEAD box RNA helicase (RH3) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190402.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4K180
      Conserved Domains (5) summary
      smart00343
      Location:636 → 650
      ZnF_C2HC; zinc finger
      COG0513
      Location:42 → 377
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd00079
      Location:244 → 360
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cd00268
      Location:26 → 218
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam08152
      Location:444 → 539
      GUCT; GUCT (NUC152) domain

    3. NM_147920.4 → NP_680225.2  DEAD box RNA helicase (RH3) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_680225.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178URN6, A0A7G2FA93
      Conserved Domains (5) summary
      smart00343
      Location:728 → 742
      ZnF_C2HC; zinc finger
      smart00487
      Location:117 → 312
      DEXDc; DEAD-like helicases superfamily
      cd00079
      Location:337 → 453
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cd00268
      Location:107 → 311
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam08152
      Location:537 → 632
      GUCT; GUCT (NUC152) domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8L7S8.2

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