Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LIMD1 Gene

Aliases for LIMD1 Gene

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

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 Cytoskeletal Signaling and CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity. An important paralog of this gene is WTIP.

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

Additional gene information for LIMD1 Gene

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

Genomics for LIMD1 Gene

GeneHancer (GH) Regulatory Elements for LIMD1 Gene

Promoters and enhancers for LIMD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J045638 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 43.8 +88.2 88216 9.6 HDGF PKNOX1 FOXA2 ARNT ARID4B YY1 SLC30A9 E2F8 FOS SP5 LIMD1 SACM1L RN7SL145P LARS2-AS1 LIMD1-AS1 EXOSC7 XCR1 ZDHHC3 LARS2 CLEC3B
GH03J045631 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 36.9 +76.2 76214 1.2 HDGF HDAC1 ATF1 PKNOX1 TAF9B NFRKB TCF12 GATA2 ETV6 CREM LIMD1 LARS2-AS1 LARS2 SACM1L GC03M045664 PIR32515
GH03J045659 Enhancer 1.2 Ensembl ENCODE dbSUPER 44.7 +104.8 104840 1.9 ELF3 RB1 ARID4B RAD21 YY1 ZNF614 ZNF143 FOS IKZF2 THAP11 LIMD1 LIMD1-AS1 SACM1L LARS2-AS1 LARS2 GC03M045664 PIR32515
GH03J045687 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 21.4 +136.5 136502 8.2 ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC SACM1L RN7SL145P LIMD1 ZDHHC3 ZNF502 ZNF501 EXOSC7 LARS2-AS1 XCR1 CCR9
GH03J045635 Enhancer 1.2 Ensembl ENCODE dbSUPER 37.2 +80.6 80632 1.6 FOXA2 ARID4B SIN3A RAD21 RARA ETS1 RFX5 RCOR1 ATF7 FOS LIMD1 LARS2-AS1 ENSG00000236869 CLEC3B GC03M045664 PIR32515
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LIMD1 Gene

Genomic Locations for LIMD1 Gene
chr3:45,555,394-45,686,338
(GRCh38/hg38)
Size:
130,945 bases
Orientation:
Plus strand
chr3:45,596,886-45,727,830
(GRCh37/hg19)
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

ENSEMBL proteins:
REFSEQ proteins:

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

Blocks:
InterPro:
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 :
  • 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 ISS,IEA --
GO:0005515 protein binding IPI 15542589
GO:0008270 zinc ion binding TAS 10647888
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:

Animal Model Products

miRNA for LIMD1 Gene

miRTarBase miRNAs that target LIMD1

Clone Products

  • Addgene plasmids 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (3)
  • Nucleus (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 IDA 20616046
GO:0005634 nucleus IDA,IEA 15542589
GO:0005667 transcription factor complex IBA --
GO:0005737 cytoplasm IEA,IDA 15542589
GO:0005829 cytosol TAS --
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 ISS,IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 10647888
GO:0007010 cytoskeleton organization 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

Unigene Clusters for LIMD1 Gene

LIM domains containing 1:
Representative Sequences:

Clone Products

  • Addgene plasmids 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
ECgene alternative splicing isoforms for
LIMD1

Expression for LIMD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of LIMD1 Gene:

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(4.2)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with LIMD1: view

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 34 33
  • 99.41 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LIMD1 34 33
  • 84.92 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LIMD1 34 33
  • 84.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Limd1 33
  • 80.97 (n)
mouse
(Mus musculus)
Mammalia Limd1 16 34 33
  • 80.85 (n)
oppossum
(Monodelphis domestica)
Mammalia LIMD1 34
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIMD1 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIMD1 34 33
  • 81.38 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIMD1 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17031 33
zebrafish
(Danio rerio)
Actinopterygii LOC562793 33
  • 70.32 (n)
LIMD1 (2 of 2) 34
  • 58 (a)
OneToMany
LIMD1 (1 of 2) 34
  • 54 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG11063 35
  • 66 (a)
Unc-115b 34
  • 11 (a)
OneToMany
Unc-115a 34
  • 10 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea zyx-1 35
  • 42 (a)
unc-115 34
  • 11 (a)
OneToOne
Species where no ortholog for LIMD1 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LIMD1: view image

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 from dbSNP and Humsavar for LIMD1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000023870 -- 45,612,075(+) C/G intron_variant
rs1000038919 -- 45,594,877(+) A/G 5_prime_UTR_variant
rs1000092219 -- 45,662,770(+) G/A/T genic_downstream_transcript_variant, intron_variant
rs1000124140 -- 45,594,283(+) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000160114 -- 45,598,023(+) T/G intron_variant

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LIMD1 Gene

Additional Disease Information for LIMD1

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

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. 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 58
  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 58
  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 58
  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 58
  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 58

Products for LIMD1 Gene

Sources for LIMD1 Gene

Content
Loading form....