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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

Gene LinkOut

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