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    RGD3 ROOT GROWTH DEFECTIVE 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 824595, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RGD3
    Official Full Name
    ROOT GROWTH DEFECTIVE 3
    Primary source
    TAIR:AT3G54280
    Locus tag
    AT3G54280
    See related
    Araport:AT3G54280
    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
    ATBTAF1; BTAF1; CHA16; CHR16; ROOT GROWTH DEFECTIVE 3
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    Genomic context

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    See RGD3 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    30
    Sequence:
    Chromosome: 3; NC_003074.8 (20091852..20104257)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene sucrose-6F-phosphate phosphohydrolase family protein Neighboring gene ncRNA Neighboring gene hemerythrin HHE cation-binding domain protein Neighboring gene vesicle-associated membrane protein 727

    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. Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis. Tamaki H, et al. Plant J, 2009 Mar. PMID 19054368
    2. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat M, et al. Nature, 2000 Dec 14. PMID 11130713

    GeneRIFs: Gene References Into Functions

    General gene information

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    NM_001203156.1
    NM_115288.8

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables TBP-class protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of shoot apical meristem development 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
    ROOT GROWTH DEFECTIVE 3
    NP_001190085.1
    • ROOT GROWTH DEFECTIVE 3 (RGD3); FUNCTIONS IN: helicase activity, binding, DNA binding, nucleic acid binding, ATP binding; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Armadillo-like helical (InterPro:IPR011989), DEAD-like helicase, N-terminal (InterPro:IPR014001), Armadillo-type fold (InterPro:IPR016024), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: Homeotic gene regulator (TAIR:AT3G06010.1).
    NP_190996.3
    • ROOT GROWTH DEFECTIVE 3 (RGD3); FUNCTIONS IN: binding, helicase activity, DNA binding, nucleic acid binding, ATP binding; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Armadillo-like helical (InterPro:IPR011989), DEAD-like helicase, N-terminal (InterPro:IPR014001), Armadillo-type fold (InterPro:IPR016024), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: Homeotic gene regulator (TAIR:AT3G06010.1); Has 18805 Blast hits to 15736 proteins in 1976 species: Archae - 119; Bacteria - 5461; Metazoa - 3891; Fungi - 4072; Plants - 1633; Viruses - 163; Other Eukaryotes - 3466 (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
      20091852..20104257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_115288.8 → NP_190996.3  ROOT GROWTH DEFECTIVE 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190996.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B5BT18, Q9M378
      UniProtKB/TrEMBL
      A0A178VE23
      Conserved Domains (6) summary
      cd00046
      Location:1471 → 1615
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:1791 → 1935
      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 ...
      pfam00176
      Location:1454 → 1767
      SNF2_N; SNF2 family N-terminal domain
      pfam12054
      Location:782 → 1239
      DUF3535; Domain of unknown function (DUF3535)
      pfam13513
      Location:561 → 606
      HEAT_EZ; HEAT-like repeat
      sd00044
      Location:9 → 34
      HEAT; HEAT repeat [structural motif]

    2. NM_001203156.1 → NP_001190085.1  ROOT GROWTH DEFECTIVE 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190085.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VE23, F4JCU6
      Conserved Domains (6) summary
      cd00046
      Location:1502 → 1646
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:1822 → 1966
      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 ...
      pfam00176
      Location:1485 → 1798
      SNF2_N; SNF2 family N-terminal domain
      pfam12054
      Location:813 → 1270
      DUF3535; Domain of unknown function (DUF3535)
      pfam13513
      Location:592 → 637
      HEAT_EZ; HEAT-like repeat
      sd00044
      Location:9 → 34
      HEAT; HEAT repeat [structural motif]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B5BT18.1

    Gene LinkOut

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