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Aliases for LIMD1 Gene

Aliases for LIMD1 Gene

  • LIM Domains Containing 1 2 3 5

External Ids for LIMD1 Gene

Previous GeneCards Identifiers for LIMD1 Gene

  • GC03P044877
  • GC03P045455
  • GC03P045596

Summaries for LIMD1 Gene

GeneCards Summary for LIMD1 Gene

LIMD1 (LIM Domains Containing 1) is a Protein Coding gene. Among its related pathways are Hippo signaling pathway. GO annotations related to this gene include transcription corepressor activity. An important paralog of this gene is AJUBA.

UniProtKB/Swiss-Prot for LIMD1 Gene

  • Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation.

Gene Wiki entry for LIMD1 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMD1 Gene

Genomics for LIMD1 Gene

Regulatory Elements for LIMD1 Gene

Genomic Location for LIMD1 Gene

Chromosome:
3
Start:
45,555,394 bp from pter
End:
45,686,338 bp from pter
Size:
130,945 bases
Orientation:
Plus strand

Genomic View for LIMD1 Gene

Genes around LIMD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMD1 Gene

Proteins for LIMD1 Gene

  • Protein details for LIMD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UGP4-LIMD1_HUMAN
    Recommended name:
    LIM domain-containing protein 1
    Protein Accession:
    Q9UGP4
    Secondary Accessions:
    • Q17RQ1
    • Q9BQQ9
    • Q9NQ47

    Protein attributes for LIMD1 Gene

    Size:
    676 amino acids
    Molecular mass:
    72190 Da
    Quaternary structure:
    • Interacts (via LIM domains) with TRAF6. Found in a complex with TRAF6, PRKCZ and SQSTM1. Interacts (via LIM domains) SNAI2/SLUG (via SNAG domain) and SCRT1 (via SNAG domain) (By similarity). Interacts with SQSTM1 and RB1. Found in a complex composed of LIMD1, VHL, EGLN1/PHD2, TCEB2 AND CUL2. Interacts with EIF4E, AGO1, AGO2, DCP2, DDX6, LATS1, LATS2, EGLN1/PHD2, EGLN2/PHD1 and EGLN3/PHD3. Interacts (via LIM zinc-binding 2) with isoform 1 and isoform 3 of VHL. Interacts (via LIM domains) with SNAI1 (via SNAG domain).

neXtProt entry for LIMD1 Gene

Proteomics data for LIMD1 Gene at MOPED

Post-translational modifications for LIMD1 Gene

Other Protein References for LIMD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for LIMD1 (LIMD1)

No data available for DME Specific Peptides for LIMD1 Gene

Domains & Families for LIMD1 Gene

Gene Families for LIMD1 Gene

Protein Domains for LIMD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LIMD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UGP4

UniProtKB/Swiss-Prot:

LIMD1_HUMAN :
  • Contains 3 LIM zinc-binding domains.
  • Belongs to the zyxin/ajuba family.
Domain:
  • Contains 3 LIM zinc-binding domains.
Family:
  • Belongs to the zyxin/ajuba family.
genes like me logo Genes that share domains with LIMD1: view

Function for LIMD1 Gene

Molecular function for LIMD1 Gene

UniProtKB/Swiss-Prot Function:
Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation.
UniProtKB/Swiss-Prot Induction:
Down-regulated in lung cancer.
genes like me logo Genes that share phenotypes with LIMD1: view

Animal Models for LIMD1 Gene

MGI Knock Outs for LIMD1:

Animal Model Products

  • Taconic Biosciences Mouse Models for LIMD1

miRNA for LIMD1 Gene

miRTarBase miRNAs that target LIMD1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIMD1 Gene

Localization for LIMD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMD1 Gene

Cytoplasm. Nucleus. Cytoplasm, P-body. Cell junction, adherens junction. Cell junction, focal adhesion. Note=Shuttles between cytoplasm and nucleus but is localized predominantly to the cytoplasm. Found in the nucleus but not nucleoli. Colocalizes with VCL in the focal adhesions. Down-regulation and/or elimination of its expression from the nucleus of neoplastic cells correlates strongly with poor patient prognosis and aggressive forms of breast carcinoma. Conversely, strong nuclear localization correlates with low-tumor grade and better patient prognosis.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LIMD1 Gene COMPARTMENTS Subcellular localization image for LIMD1 gene
Compartment Confidence
nucleus 5
cytosol 3

No data available for Gene Ontology (GO) - Cellular Components for LIMD1 Gene

Pathways & Interactions for LIMD1 Gene

SuperPathways for LIMD1 Gene

Superpath Contained pathways
1 Hippo signaling pathway
genes like me logo Genes that share pathways with LIMD1: view

Pathways by source for LIMD1 Gene

1 KEGG pathway for LIMD1 Gene

Gene Ontology (GO) - Biological Process for LIMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 22286099
GO:0006351 transcription, DNA-templated IEA --
GO:0007275 multicellular organism development TAS 10647888
GO:0008360 regulation of cell shape IMP 21834987
GO:0016477 cell migration IMP 21834987
genes like me logo Genes that share ontologies with LIMD1: view

No data available for SIGNOR curated interactions for LIMD1 Gene

Drugs & Compounds for LIMD1 Gene

No Compound Related Data Available

Transcripts for LIMD1 Gene

Unigene Clusters for LIMD1 Gene

LIM domains containing 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LIMD1 Gene

No ASD Table

Relevant External Links for LIMD1 Gene

GeneLoc Exon Structure for
LIMD1
ECgene alternative splicing isoforms for
LIMD1

Expression for LIMD1 Gene

mRNA expression in normal human tissues for LIMD1 Gene

Protein differential expression in normal tissues from HIPED for LIMD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.0) and Pancreas (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LIMD1 Gene



SOURCE GeneReport for Unigene cluster for LIMD1 Gene Hs.193370

mRNA Expression by UniProt/SwissProt for LIMD1 Gene

Q9UGP4-LIMD1_HUMAN
Tissue specificity: Expressed in normal and breast cancer tissues (at protein level). Ubiquitous.
genes like me logo Genes that share expression patterns with LIMD1: view

Protein tissue co-expression partners for LIMD1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for LIMD1 Gene

Orthologs for LIMD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIMD1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LIMD1 35
  • 84.92 (n)
  • 83.78 (a)
LIMD1 36
  • 84 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIMD1 35
  • 84.86 (n)
  • 82.42 (a)
LIMD1 36
  • 82 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Limd1 35
  • 80.85 (n)
  • 78.2 (a)
Limd1 16
Limd1 36
  • 78 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LIMD1 35
  • 99.41 (n)
  • 99.26 (a)
LIMD1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Limd1 35
  • 80.97 (n)
  • 78.55 (a)
oppossum
(Monodelphis domestica)
Mammalia LIMD1 36
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIMD1 36
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIMD1 35
  • 81.38 (n)
  • 88.83 (a)
LIMD1 36
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIMD1 36
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17031 35
zebrafish
(Danio rerio)
Actinopterygii LOC562793 35
  • 70.32 (n)
  • 70.79 (a)
LIMD1 (1 of 2) 36
  • 54 (a)
OneToMany
LIMD1 (2 of 2) 36
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG11063 37
  • 66 (a)
Unc-115a 36
  • 10 (a)
OneToMany
Unc-115b 36
  • 11 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea zyx-1 37
  • 42 (a)
unc-115 36
  • 11 (a)
OneToOne
Species with no ortholog for LIMD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LIMD1 Gene

ENSEMBL:
Gene Tree for LIMD1 (if available)
TreeFam:
Gene Tree for LIMD1 (if available)

Paralogs for LIMD1 Gene

Paralogs for LIMD1 Gene

(7) SIMAP similar genes for LIMD1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LIMD1: view

Variants for LIMD1 Gene

Sequence variations from dbSNP and Humsavar for LIMD1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs3733113 - 45,596,122(-) AGATC(C/T)CAGGC reference, missense
rs2578662 - 45,594,986(-) TGTTG(C/T)CTGCA reference, missense
rs197946 -- 45,613,172(-) ctgaa(C/G)aaagc intron-variant, downstream-variant-500B
rs187884 -- 45,610,563(-) AGCCA(A/C)CATGC intron-variant
rs267208 -- 45,610,554(-) GCATG(C/T)CTGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LIMD1 Gene

Variant ID Type Subtype PubMed ID
esv34130 CNV Loss 18971310
esv2725221 CNV Deletion 23290073
esv2725222 CNV Deletion 23290073
nsv3795 CNV Insertion 18451855
esv2725223 CNV Deletion 23290073

Variation tolerance for LIMD1 Gene

Residual Variation Intolerance Score: 49.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.98; 36.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIMD1 Gene

HapMap Linkage Disequilibrium report
LIMD1
Human Gene Mutation Database (HGMD)
LIMD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIMD1 Gene

Disorders for LIMD1 Gene

Relevant External Links for LIMD1

Genetic Association Database (GAD)
LIMD1
Human Genome Epidemiology (HuGE) Navigator
LIMD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIMD1

No disorders were found for LIMD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LIMD1 Gene

Publications for LIMD1 Gene

  1. A novel gene containing LIM domains (LIMD1) is located within the common eliminated region 1 (C3CER1) in 3p21.3. (PMID: 10647888) Kiss H. … Dumanski J.P. (Hum. Genet. 1999) 2 3 4 67
  2. LIM domains-containing protein 1 (LIMD1), a tumor suppressor encoded at chromosome 3p21.3, binds pRB and represses E2F-driven transcription. (PMID: 15542589) Sharp T.V. … Boshoff C. (Proc. Natl. Acad. Sci. U.S.A. 2004) 3 23
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. (PMID: 24927181) Navarini A.A. … Barker J.N. (Nat Commun 2014) 3
  5. Regulation of YAP by mechanical strain through Jnk and Hippo signaling. (PMID: 25127217) Codelia V.A. … Irvine K.D. (Curr. Biol. 2014) 3

Products for LIMD1 Gene

Sources for LIMD1 Gene

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