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    LIM domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 829839, updated on 18-Sep-2024

    Summary

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    Official Full Name
    LIM domain-containing protein
    Primary source
    TAIR:AT4G36860
    Locus tag
    AT4G36860
    See related
    Araport:AT4G36860
    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
    AP22.33; AP22_33
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    Genomic context

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    Location:
    chromosome: 4
    Exon count:
    12
    Sequence:
    Chromosome: 4; NC_003075.7 (17358343..17362129, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene Galactose oxidase/kelch repeat superfamily protein Neighboring gene PQ-loop repeat family protein / transmembrane family protein Neighboring gene BEL1-like homeodomain 2 Neighboring gene cysteine proteinase1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2. Vanhaeren H, et al. Elife, 2020 Mar 25. PMID 32209225, Free PMC Article
    2. The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis. Peng Y, et al. Plant Cell, 2015 Mar. PMID 25757472, Free PMC Article
    3. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Wanamaker SA, et al. Nat Methods, 2017 Aug. PMID 28650476, Free PMC Article
    4. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Mayer K, et al. Nature, 1999 Dec 16. PMID 10617198

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DA1, DAR1, and DAR2 physically interact with the transcription factors TCP14 and TCP15, which repress endoreduplication.[DAR1]
      Title: The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis.
    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_001342424.1
    NM_001342425.1
    NM_119850.7

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables peptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within regulation of DNA endoreduplication IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of DNA endoreduplication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    LIM domain-containing protein
    NP_195404.6
    • LIM domain-containing protein; FUNCTIONS IN: zinc ion binding; LOCATED IN: plasma membrane; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, LIM-type (InterPro:IPR001781), Ubiquitin interacting motif (InterPro:IPR003903), Protein of unknown function DUF3633 (InterPro:IPR022087); BEST Arabidopsis thaliana protein match is: DA1 (TAIR:AT1G19270.1); Has 6004 Blast hits to 4271 proteins in 323 species: Archae - 7; Bacteria - 228; Metazoa - 4096; Fungi - 190; Plants - 320; Viruses - 67; Other Eukaryotes - 1096 (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_003075.7 Reference assembly

      Range
      17358343..17362129 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_119850.7 → NP_195404.6  LIM domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_195404.6

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O23197, Q8W4F0
      UniProtKB/TrEMBL
      A0A178UYQ5, A0A7G2F3K1
      Conserved Domains (2) summary
      cd09396
      Location:190 → 242
      LIM_DA1; The Lim domain of DA1
      pfam12315
      Location:339 → 549
      DUF3633; Protein of unknown function (DUF3633)

    2. NM_001342424.1 → NP_001328323.1  LIM domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8B4A6, A0A7G2F3K1
      Conserved Domains (2) summary
      cd09396
      Location:190 → 242
      LIM_DA1; The Lim domain of DA1
      pfam12315
      Location:339 → 451
      DA1-like; Protein DA1

    3. NM_001342425.1 → NP_001328324.1  LIM domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8B494, A0A7G2F3K1
      Conserved Domains (2) summary
      cd09396
      Location:214 → 266
      LIM_DA1; The Lim domain of DA1
      pfam12315
      Location:363 → 573
      DA1-like; Protein DA1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8W4F0.3

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