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

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.

No data available for Entrez Gene 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

Regulatory Elements for LIMS3 Gene

Enhancers for LIMS3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F109689 1.2 Ensembl ENCODE 7.8 -206.4 -206368 5.9 PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF48 YY1 SP5 ZHX2 MIER2 LIMS3 LINC00116 ENSG00000184115 ENSG00000186148 LOC105373545 BMS1P19
GH02F110099 1.6 FANTOM5 Ensembl ENCODE 5.2 +206.5 206478 11.8 PKNOX1 ARID4B SIN3A BRCA1 GTF3C2 GLIS2 FOS ZNF263 SP3 JUNB LINC00116 LINC01106 MALL ENSG00000231536 ENSG00000186148 LIMS3 GC02M110047
GH02F109698 1.1 Ensembl ENCODE 6.6 -196.9 -196937 5.9 ELF3 PKNOX1 MLX ZNF133 ZFP64 ARID4B RAD21 RFX5 SCRT2 RCOR1 LIMS3 ENSG00000186148 LINC00116 LINC01106 LOC105373545 GC02M109641 GC02M109642
GH02F109888 0.4 Ensembl 0.4 -9.7 -9728 0.6 HLF LIMS3 LOC102724848
GH02F109889 0.2 Ensembl 0.4 -8.4 -8427 0.4 LIMS3 LOC102724848
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LIMS3 on UCSC Golden Path with GeneCards custom track

Promoters for LIMS3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001826085 1172 2401 OSR2 RAD51 MTA2 TARDBP NBN TBX21

Genomic Location for LIMS3 Gene

109,898,428 bp from pter
109,934,429 bp from pter
36,002 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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LIMS3 Gene

No data available for DME Specific Peptides for LIMS3 Gene

Domains & Families for LIMS3 Gene

Protein Domains for LIMS3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Contains 1 LIM zinc-binding domain.
  • Contains 1 LIM zinc-binding domain.
genes like me logo Genes that share domains with LIMS3: view

Function for LIMS3 Gene

Gene Ontology (GO) - Molecular Function for LIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
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

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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


Gene Ontology (GO) - Cellular Components for LIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm 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: ENSP00000405165 P0CW19-LIMS3_HUMAN for LIMS3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for LIMS3 Gene


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

Transcripts for LIMS3 Gene

Unigene Clusters for LIMS3 Gene

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

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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.
genes like me logo Genes that share expression patterns with LIMS3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery 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 35
  • 27 (a)
(Canis familiaris)
Mammalia -- 35
  • 26 (a)
(Bos Taurus)
Mammalia MGC142792 35
  • 15 (a)
(Monodelphis domestica)
Mammalia -- 35
  • 15 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 14 (a)
(Gallus gallus)
Aves LIMS1 35
  • 15 (a)
-- 35
-- 35
-- 35
-- 35
(Anolis carolinensis)
Reptilia -- 35
  • 23 (a)
(Danio rerio)
Actinopterygii lims1 35
  • 15 (a)
lims2 35
  • 15 (a)
fruit fly
(Drosophila melanogaster)
Insecta stck 35
  • 10 (a)
(Caenorhabditis elegans)
Secernentea unc-97 35
  • 7 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11312 35
  • 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 Sequence Context AA Info Type
rs112366401 -- 109,914,018(+) GAGAA(G/T)TACAG intron-variant
rs1132994 -- 109,905,883(+) AGGAA(C/T)GAACG intron-variant, reference, stop-gained
rs113406090 -- 109,896,502(+) TGTCC(C/T)CATCC upstream-variant-2KB
rs113434358 -- 109,917,082(+) ATAGC(C/T)CACTG intron-variant
rs113458393 -- 109,924,100(+) CAGGA(A/G)GCTGA intron-variant, upstream-variant-2KB

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

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

Relevant External Links 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

Relevant External Links for LIMS3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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 L.W. … Wilson R.K. (Nature 2005) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64
  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. (Mol. Biotechnol. 2007) 3 64

Products for LIMS3 Gene

Sources for LIMS3 Gene

Loading form....