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    LIMD1 LIM domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 8994, updated on 17-Jun-2024

    Summary

    Official Symbol
    LIMD1provided by HGNC
    Official Full Name
    LIM domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:6612
    See related
    Ensembl:ENSG00000144791 MIM:604543; AllianceGenome:HGNC:6612
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable transcription corepressor activity. Involved in several processes, including negative regulation of hippo signaling; regulation of gene expression; and response to hypoxia. Acts upstream of or within P-body assembly and gene silencing by miRNA. Located in several cellular components, including P-body; adherens junction; and focal adhesion. Part of RISC complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lung (RPKM 16.2), thyroid (RPKM 9.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LIMD1 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45594751..45686341)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45610699..45702290)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45636243..45727833)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377061 Neighboring gene uncharacterized LOC105377062 Neighboring gene NANOG hESC enhancer GRCh37_chr3:45387482-45388007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45430895-45431470 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45434289-45435488 Neighboring gene MPRA-validated peak4627 silencer Neighboring gene leucyl-tRNA synthetase 2, mitochondrial Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45534631-45534827 Neighboring gene LARS2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45549416-45550282 Neighboring gene Sharpr-MPRA regulatory region 486 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45585473-45585699 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45586492-45586702 Neighboring gene Sharpr-MPRA regulatory region 4333 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:45592715-45593914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45608597-45609123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14283 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45638615-45639114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45649345-45649845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45671459-45671960 Neighboring gene Sharpr-MPRA regulatory region 10324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45688585-45689086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19785 Neighboring gene LIMD1 antisense RNA 1 Neighboring gene tRNA-Arg (anticodon ACG) 2-1 Neighboring gene SAC1 like phosphatidylinositide phosphatase Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45769094-45769290 Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Pol gag-pol HIV-1 Pol is identified to have a physical interaction with LIM domains containing 1 (LIMD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with LIM domains containing 1 (LIMD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within P-body assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in miRNA-mediated gene silencing by inhibition of translation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within miRNA-mediated post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of hippo signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of hippo signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in osteoblast development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to hypoxia IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to hypoxia IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in P-body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of RISC complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    LIM domain-containing protein 1
    Names
    LIM domains containing 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_014240.3NP_055055.1  LIM domain-containing protein 1

      See identical proteins and their annotated locations for NP_055055.1

      Status: VALIDATED

      Source sequence(s)
      AC098476, AC099539, AJ132408, BC117236, BU428864
      Consensus CDS
      CCDS2729.1
      UniProtKB/Swiss-Prot
      Q17RQ1, Q9BQQ9, Q9NQ47, Q9UGP4
      UniProtKB/TrEMBL
      C9JRJ5
      Related
      ENSP00000273317.4, ENST00000273317.5
      Conserved Domains (4) summary
      cd09352
      Location:472525
      LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins
      cd09355
      Location:537589
      LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins
      cd09438
      Location:597658
      LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins
      cl26464
      Location:69443
      Atrophin-1; Atrophin-1 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      45594751..45686341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534207.4XP_011532509.1  LIM domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45610699..45702290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348293.1XP_054204268.1  LIM domain-containing protein 1 isoform X1