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Aliases for LIMS3 Gene

Aliases for LIMS3 Gene

  • LIM Zinc Finger Domain Containing 3 2 3 5
  • Particularly Interesting New Cys-His Protein 3 3 4
  • LIM And Senescent Cell Antigen-Like Domains 3 2 3
  • LIM-Type Zinc Finger Domains 3 2 3
  • Pinch 2 2 3
  • PINCH-3 3 4
  • LIM And Senescent Cell Antigen-Like-Containing Domain Protein 3 3
  • PINCH3 4

External Ids for LIMS3 Gene

Previous GeneCards Identifiers for LIMS3 Gene

  • GC02P110392
  • GC02P110013
  • GC02P110656

Summaries for LIMS3 Gene

GeneCards Summary for LIMS3 Gene

LIMS3 (LIM Zinc Finger Domain Containing 3) is a Protein Coding gene. An important paralog of this gene is LIMS4.

Additional gene information for LIMS3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMS3 Gene

Genomics for LIMS3 Gene

GeneHancer (GH) Regulatory Elements for LIMS3 Gene

Promoters and enhancers for LIMS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I109899 Promoter 0.5 Ensembl 550.8 +1.1 1073 0.6 ENSG00000284337 LIMS3 LIMS3-LOC440895 LOC105373547
GH02I109898 Promoter 0.5 EPDnew 550.8 0.0 -18 0.1 ENSG00000284337 LIMS3 LIMS3-LOC440895 LOC102724848
GH02I109902 Promoter 0.5 EPDnew 550.8 +0.2 244 0.1 ENSG00000284337 LIMS3 LIMS3-LOC440895 LOC105373547
GH02I109689 Enhancer 1.3 Ensembl ENCODE dbSUPER 7.8 -206.4 -206368 5.9 PKNOX1 FOXA2 MLX ARID4B NEUROD1 SIN3A DMAP1 ZNF48 YY1 ATF7 LIMS3 SMIM37 ENSG00000184115 ENSG00000186148 LOC105373545 BMS1P19 GC02M109642 GC02M109641
GH02I110099 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 5.2 +206.5 206477 11.8 PKNOX1 FOXA2 ARID4B SIN3A BRCA1 GTF3C2 GLIS2 FOS SP3 REST GC02M110047 SMIM37 LINC01106 MALL ENSG00000231536 ENSG00000186148 LIMS3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LIMS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIMS3 gene promoter:

Genomic Locations for LIMS3 Gene

Genomic Locations for LIMS3 Gene
27,198 bases
Plus strand

Genomic View for LIMS3 Gene

Genes around LIMS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMS3 Gene

Proteins for LIMS3 Gene

  • Protein details for LIMS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM and senescent cell antigen-like-containing domain protein 3
    Protein Accession:
    Secondary Accessions:
    • A0A0A6YYD2
    • B4DPH6
    • Q9HB10

    Protein attributes for LIMS3 Gene

    117 amino acids
    Molecular mass:
    13251 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LIMS3 Gene


neXtProt entry for LIMS3 Gene

Post-translational modifications for LIMS3 Gene

No Post-translational modifications

Other Protein References for LIMS3 Gene

No data available for DME Specific Peptides for LIMS3 Gene

Domains & Families for LIMS3 Gene

Gene Families for LIMS3 Gene

Protein Domains for LIMS3 Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LIMS3: view

No data available for UniProtKB/Swiss-Prot for LIMS3 Gene

Function for LIMS3 Gene

Gene Ontology (GO) - Molecular Function for LIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMS3: view

Phenotypes for LIMS3 Gene

GenomeRNAi human phenotypes for LIMS3:
genes like me logo Genes that share phenotypes with LIMS3: view

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LIMS3 Gene

Localization for LIMS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMS3 Gene


Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Focal adhesion sites (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane IEA --
GO:0005925 focal adhesion IEA --
GO:0016020 membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LIMS3: view

No data available for Subcellular locations from COMPARTMENTS for LIMS3 Gene

Pathways & Interactions for LIMS3 Gene

SuperPathways for LIMS3 Gene

No Data Available

Interacting Proteins for LIMS3 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: P0CW19-LIMS3_HUMAN ENSP00000405165 for LIMS3 Gene via IID STRING

Gene Ontology (GO) - Biological Process for LIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045216 cell-cell junction organization IEA --
genes like me logo Genes that share ontologies with LIMS3: view

No data available for Pathways by source and SIGNOR curated interactions for LIMS3 Gene

Drugs & Compounds for LIMS3 Gene

No Compound Related Data Available

Transcripts for LIMS3 Gene

Unigene Clusters for LIMS3 Gene

LIM and senescent cell antigen-like domains 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIMS3 Gene

No ASD Table

Relevant External Links for LIMS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LIMS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIMS3 Gene

mRNA differential expression in normal tissues according to GTEx for LIMS3 Gene

This gene is overexpressed in Artery - Aorta (x8.2) and Muscle - Skeletal (x7.3).

Protein differential expression in normal tissues from HIPED for LIMS3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LIMS3 Gene

Protein tissue co-expression partners for LIMS3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LIMS3 Gene:


SOURCE GeneReport for Unigene cluster for LIMS3 Gene:


mRNA Expression by UniProt/SwissProt for LIMS3 Gene:

Tissue specificity: Detected in testis.

Evidence on tissue expression from TISSUES for LIMS3 Gene

  • Kidney(4)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with LIMS3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMS3 Gene

Orthologs for LIMS3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIMS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Mus musculus)
Mammalia Lims1 34
  • 27 (a)
(Canis familiaris)
Mammalia -- 34
  • 26 (a)
(Bos Taurus)
Mammalia MGC142792 34
  • 15 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 15 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 14 (a)
(Gallus gallus)
Aves LIMS1 34
  • 15 (a)
-- 34
-- 34
-- 34
-- 34
(Anolis carolinensis)
Reptilia -- 34
  • 23 (a)
(Danio rerio)
Actinopterygii lims1 34
  • 15 (a)
lims2 34
  • 15 (a)
fruit fly
(Drosophila melanogaster)
Insecta stck 34
  • 10 (a)
(Caenorhabditis elegans)
Secernentea unc-97 34
  • 7 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11312 34
  • 12 (a)
Species where no ortholog for LIMS3 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for LIMS3 Gene

Gene Tree for LIMS3 (if available)
Gene Tree for LIMS3 (if available)

Paralogs for LIMS3 Gene

(7) SIMAP similar genes for LIMS3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LIMS3: view

Variants for LIMS3 Gene

Sequence variations from dbSNP and Humsavar for LIMS3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1005579223 -- 109,918,035(+) C/T genic_downstream_transcript_variant, intron_variant
rs1018746136 -- 109,918,055(+) T/C genic_downstream_transcript_variant, intron_variant
rs1045007142 -- 109,909,210(+) A/G genic_downstream_transcript_variant, intron_variant
rs1046064705 -- 109,914,514(+) T/A genic_downstream_transcript_variant, intron_variant
rs1047215453 -- 109,915,194(+) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LIMS3 Gene

Variant ID Type Subtype PubMed ID
nsv979092 CNV duplication 23825009
nsv979089 CNV duplication 23825009
nsv510884 OTHER complex 20534489
nsv508157 CNV deletion 20534489
nsv469649 CNV loss 16826518
nsv1149522 OTHER inversion 26484159
nsv1003103 CNV gain+loss 25217958
esv3584010 CNV loss 25503493
esv3575292 CNV gain 25503493
esv28875 CNV gain+loss 19812545
esv2751812 CNV loss 17911159
dgv730e214 CNV gain 21293372
dgv4047n100 CNV loss 25217958
dgv4037n100 CNV gain 25217958
dgv1163e212 CNV loss 25503493
dgv1162e212 CNV gain 25503493

Additional Variant Information for LIMS3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for LIMS3 Gene

Disorders for LIMS3 Gene

Additional Disease Information for LIMS3

No disorders were found for LIMS3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LIMS3 Gene

Publications for LIMS3 Gene

  1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  5. Molecular cloning and characterization of a novel splice variant of the LIM domain family gene, PINCH 2, in human testis. (PMID: 17435276) Liu Y … Li J (Molecular biotechnology 2007) 3 58

Products for LIMS3 Gene

Sources for LIMS3 Gene

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