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

    Gene ID: 8994, updated on 19-Mar-2017
    Official Symbol
    LIMD1provided by HGNC
    Official Full Name
    LIM domains containing 1provided by HGNC
    Primary source
    HGNC:HGNC:6612
    See related
    Ensembl:ENSG00000144791 MIM:604543; Vega:OTTHUMG00000133453
    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
    Orthologs
    Location:
    3p21.31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 3 NC_000003.12 (45594181..45681263)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45636323..45722755)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377061 Neighboring gene uncharacterized LOC105377062 Neighboring gene leucyl-tRNA synthetase 2, mitochondrial Neighboring gene LARS2 antisense RNA 1 Neighboring gene LIMD1 antisense RNA 1 Neighboring gene transfer RNA-Arg (ACG) 2-1 Neighboring gene SAC1 suppressor of actin mutations 1 like (yeast) Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

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

    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

    • Cellular response to hypoxia, organism-specific biosystem (from REACTOME)
      Cellular response to hypoxia, organism-specific biosystemOxygen plays a central role in the functioning of human cells: it is both essential for normal metabolism and toxic. To begin the annotation of stress responses in Reactome, we have annotated one asp...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • Hippo signaling pathway, organism-specific biosystem (from KEGG)
      Hippo signaling pathway, organism-specific biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
    • Hippo signaling pathway, conserved biosystem (from KEGG)
      Hippo signaling pathway, conserved biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
    • Hippo signaling pathway -multiple species, organism-specific biosystem (from KEGG)
      Hippo signaling pathway -multiple species, organism-specific biosystemHippo signaling pathways control diverse aspects of cell proliferation, survival, and morphogenesis in eukaryotes. The core organization of these networks is conserved over a billion years of evoluti...
    • Hippo signaling pathway -multiple species, conserved biosystem (from KEGG)
      Hippo signaling pathway -multiple species, conserved biosystemHippo signaling pathways control diverse aspects of cell proliferation, survival, and morphogenesis in eukaryotes. The core organization of these networks is conserved over a billion years of evoluti...
    • Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha, organism-specific biosystem (from REACTOME)
      Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha, organism-specific biosystemHIF-alpha subunits, comprising HIF1A (Bruick and McKnight 2001, Ivan et al. 2001, Jaakkola et al. 2001), HIF2A (Percy et al. 2008, Furlow et al. 2009), and HIF3A (Maynard et al. 2003), are hydroxylat...
    • Regulation of Hypoxia-inducible Factor (HIF) by oxygen, organism-specific biosystem (from REACTOME)
      Regulation of Hypoxia-inducible Factor (HIF) by oxygen, organism-specific biosystemIn the presence of oxygen members of the transcription factor family HIF-alpha, comprising HIF1A, HIF2A (EPAS1), and HIF3A, are hydroxylated on proline residues by PHD1 (EGLN2), PHD2 (EGLN1), and PHD...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cytoplasmic mRNA processing body assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    gene silencing by miRNA IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of hippo signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    osteoblast development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of gene silencing by miRNA IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
    Traceable Author Statement
    more info
     
    regulation of transcription, DNA-templated TAS
    Traceable Author Statement
    more info
    PubMed 
    response to hypoxia IDA
    Inferred from Direct Assay
    more info
    PubMed 
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    P-body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RISC complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    transcription factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Preferred Names
    LIM domain-containing protein 1

    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_014240.2NP_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
      Q9UGP4
      Related
      ENSP00000273317, OTTHUMP00000164657, ENST00000273317, OTTHUMT00000257327
      Conserved Domains (3) 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

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p7 Primary Assembly

      Range
      45594181..45681263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534207.2XP_011532509.1  LIM domain-containing protein 1 isoform X1

    Alternate CHM1_1.1

    Genomic

    1. NC_018914.2 Alternate CHM1_1.1

      Range
      45586336..45672049
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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