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

Gene ID: 8994, updated on 7-Oct-2018

Summary

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
Expression
Ubiquitous expression in lung (RPKM 16.2), thyroid (RPKM 9.3) and 25 other tissues See more
Orthologs

Genomic context

See LIMD1 in Genome Data Viewer
Location:
3p21.31
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (45594105..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 like phosphatidylinositide phosphatase 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
transcription corepressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding TAS
Traceable Author Statement
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to hypoxia IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
P-body IDA
Inferred from Direct Assay
more info
PubMed 
RISC complex IDA
Inferred from Direct Assay
more info
PubMed 
adherens junction IBA
Inferred from Biological aspect of Ancestor
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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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
PubMed 

General protein information

Preferred Names
LIM domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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
    ENSP00000273317.4, OTTHUMP00000164657, ENST00000273317.4, OTTHUMT00000257327
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    45594105..45681263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534207.3XP_011532509.1  LIM domain-containing protein 1 isoform X1

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