Aliases for LIMD1 Gene

Aliases for LIMD1 Gene

  • LIM Domain Containing 1 2 3
  • LIM Domains Containing 1 2 3 5
  • LIM Domain-Containing Protein 1 3 4
  • LIMD1 5

External Ids for LIMD1 Gene

Previous GeneCards Identifiers for LIMD1 Gene

  • GC03P044877
  • GC03P045455
  • GC03P045596
  • GC03P045611

Summaries for LIMD1 Gene

GeneCards Summary for LIMD1 Gene

LIMD1 (LIM Domain Containing 1) is a Protein Coding gene. Diseases associated with LIMD1 include Wilson-Turner X-Linked Mental Retardation Syndrome. Among its related pathways are Cytoskeletal Signaling and Hippo signaling pathway. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity. An important paralog of this gene is WTIP.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIMD1 Gene

Genomics for LIMD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIMD1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIMD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIMD1

Top Transcription factor binding sites by QIAGEN in the LIMD1 gene promoter:
  • AML1a
  • AP-1
  • ATF-2
  • c-Jun
  • CP2
  • CUTL1
  • ER-alpha
  • IRF-2
  • STAT5A

Genomic Locations for LIMD1 Gene

Latest Assembly
chr3:45,555,394-45,686,341
(GRCh38/hg38)
Size:
130,948 bases
Orientation:
Plus strand

Previous Assembly
chr3:45,636,243-45,727,833
(GRCh37/hg19 by Entrez Gene)
Size:
91,591 bases
Orientation:
Plus strand

chr3:45,596,886-45,727,830
(GRCh37/hg19 by Ensembl)
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, ELOB 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

Post-translational modifications for LIMD1 Gene

Other Protein References for LIMD1 Gene

No data available for DME Specific Peptides for LIMD1 Gene

Domains & Families for LIMD1 Gene

Gene Families for LIMD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for LIMD1 Gene

InterPro:
Blocks:
  • Zn-binding protein, LIM

Suggested Antigen Peptide Sequences for LIMD1 Gene

GenScript: Design optimal peptide antigens:
  • LIM domain-containing protein 1 (LIMD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UGP4

UniProtKB/Swiss-Prot:

LIMD1_HUMAN :
  • Belongs to the zyxin/ajuba family.
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.

Phenotypes From GWAS Catalog for LIMD1 Gene

Gene Ontology (GO) - Molecular Function for LIMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity IEA,ISS --
GO:0005515 protein binding IPI 15542589
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMD1: view
genes like me logo Genes that share phenotypes with LIMD1: view

Animal Models for LIMD1 Gene

MGI Knock Outs for LIMD1:

miRNA for LIMD1 Gene

miRTarBase miRNAs that target LIMD1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMD1

No data available for Enzyme Numbers (IUBMB) , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIMD1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 4
cytoskeleton 2
extracellular 1
mitochondrion 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA,IDA 20616046
GO:0005634 nucleus IBA,IDA 15542589
GO:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex IBA 21873635
GO:0005737 cytoplasm IEA,IDA 15542589
genes like me logo Genes that share ontologies with LIMD1: view

Pathways & Interactions for LIMD1 Gene

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

Gene Ontology (GO) - Biological Process for LIMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 22286099
GO:0002076 osteoblast development IEA,ISS --
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0007010 cytoskeleton organization IMP 21834987
GO:0008360 regulation of cell shape 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

mRNA/cDNA for LIMD1 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMD1

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

No ASD Table

Relevant External Links for LIMD1 Gene

GeneLoc Exon Structure for
LIMD1

Expression for LIMD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for LIMD1 Gene



Protein tissue co-expression partners for LIMD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIMD1

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.

Evidence on tissue expression from TISSUES for LIMD1 Gene

  • Liver(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LIMD1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
Chimpanzee
(Pan troglodytes)
Mammalia LIMD1 29 30
  • 99.41 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LIMD1 29 30
  • 84.92 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIMD1 29 30
  • 84.86 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Limd1 29
  • 80.97 (n)
Mouse
(Mus musculus)
Mammalia Limd1 29 16 30
  • 80.85 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LIMD1 30
  • 59 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LIMD1 30
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LIMD1 29 30
  • 81.38 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIMD1 30
  • 52 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.17031 29
Zebrafish
(Danio rerio)
Actinopterygii LOC562793 29
  • 70.32 (n)
LIMD1 (2 of 2) 30
  • 58 (a)
OneToMany
LIMD1 (1 of 2) 30
  • 54 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG11063 31
  • 66 (a)
Unc-115b 30
  • 11 (a)
OneToMany
Unc-115a 30
  • 10 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea zyx-1 31
  • 42 (a)
unc-115 30
  • 11 (a)
OneToOne
Species where no ortholog for LIMD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for LIMD1: view image
Alliance of Genome Resources:
Additional Orthologs for LIMD1

Paralogs for LIMD1 Gene

Paralogs for LIMD1 Gene

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

  • LIMD1_HUMAN
  • C9JRJ5_HUMAN
genes like me logo Genes that share paralogs with LIMD1: view

Variants for LIMD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIMD1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs114236922 Benign: not provided 45,596,273(+) A/G
NM_014240.3(LIMD1):c.1394A>G (p.Lys465Arg)
MISSENSE
rs150103800 Benign: not provided 45,596,139(+) C/T
NM_014240.3(LIMD1):c.1260C>T (p.Asp420=)
SYNONYMOUS
rs2578662 -- p.Gly36Asp
rs3733113 -- p.Gly415Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LIMD1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv2725221 CNV deletion 23290073
esv2725222 CNV deletion 23290073
esv2725223 CNV deletion 23290073
esv34130 CNV loss 18971310
nsv3795 CNV insertion 18451855

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)

Additional Variant Information for LIMD1 Gene

Human Gene Mutation Database (HGMD)
LIMD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMD1
Leiden Open Variation Database (LOVD)
LIMD1

SNP Genotyping and Copy Number Assays for research

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

Disorders for LIMD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LIMD1 Gene - From: COP

Disorder Aliases PubMed IDs
wilson-turner x-linked mental retardation syndrome
  • wts
- elite association - COSMIC cancer census association via MalaCards
Search LIMD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LIMD1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LIMD1: view

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

Publications for LIMD1 Gene

  1. LIM domains-containing protein 1 (LIMD1), a tumor suppressor encoded at chromosome 3p21.3, binds pRB and represses E2F-driven transcription. (PMID: 15542589) Sharp TV … Boshoff C (Proceedings of the National Academy of Sciences of the United States of America 2004) 3 4 22
  2. A novel gene containing LIM domains (LIMD1) is located within the common eliminated region 1 (C3CER1) in 3p21.3. (PMID: 10647888) Kiss H … Dumanski JP (Human genetics 1999) 2 3 4
  3. The LIMD1 protein bridges an association between the prolyl hydroxylases and VHL to repress HIF-1 activity. (PMID: 22286099) Foxler DE … Sharp TV (Nature cell biology 2012) 3 4
  4. Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration. (PMID: 21834987) Bai SW … Ridley AJ (BMC biology 2011) 3 4
  5. Ajuba LIM proteins are negative regulators of the Hippo signaling pathway. (PMID: 20303269) Das Thakur M … Longmore GD (Current biology : CB 2010) 3 4

Products for LIMD1 Gene

Sources for LIMD1 Gene