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Aliases for LIMS1 Gene

Aliases for LIMS1 Gene

  • LIM Zinc Finger Domain Containing 1 2 3 5
  • Particularly Interesting New Cys-His Protein 1 2 3 4
  • LIM And Senescent Cell Antigen-Like Domains 1 2 3
  • Renal Carcinoma Antigen NY-REN-48 3 4
  • LIM-Type Zinc Finger Domains 1 2 3
  • Senescent Cell Antigen 2 3
  • PINCH-1 3 4
  • PINCH1 3 4
  • PINCH 3 4
  • LIM And Senescent Cell Antigen-Like-Containing Domain Protein 1 3

External Ids for LIMS1 Gene

Previous GeneCards Identifiers for LIMS1 Gene

  • GC02P107110
  • GC02P107684
  • GC02P108755
  • GC02P108772
  • GC02P108826
  • GC02P109150

Summaries for LIMS1 Gene

Entrez Gene Summary for LIMS1 Gene

  • The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

GeneCards Summary for LIMS1 Gene

LIMS1 (LIM Zinc Finger Domain Containing 1) is a Protein Coding gene. Diseases associated with LIMS1 include Conotruncal Heart Malformations. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Cell junction organization. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is LIMS2.

UniProtKB/Swiss-Prot for LIMS1 Gene

  • Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.

Gene Wiki entry for LIMS1 Gene

Additional gene information for LIMS1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMS1 Gene

Genomics for LIMS1 Gene

Regulatory Elements for LIMS1 Gene

Enhancers for LIMS1 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
GH02H108583 2.1 FANTOM5 Ensembl ENCODE dbSUPER 25.8 +56.3 56328 14.2 PKNOX1 ARNT ZNF766 CBX5 ZNF143 FOS JUNB REST SMARCB1 ZNF592 GCC2 LIMS1 RANBP2 PIR40245
GH02H108631 1.8 VISTA Ensembl ENCODE dbSUPER 14.4 +102.6 102551 10.8 HDGF PKNOX1 FOXA2 ARID4B TCF12 GATA2 ZNF143 FOS RUNX3 JUNB GCC2 LIMS1 RPL37P12 LIMS1-AS1 PIR40245
GH02H108611 1.9 FANTOM5 Ensembl ENCODE dbSUPER 8.5 +83.5 83454 13.3 HDGF PKNOX1 ARNT SIN3A FEZF1 TCF12 ZNF121 ZNF766 CBX5 GATA2 GCC2 LIMS1 SULT1C4 LIMS1-AS1 RANBP2 PIR40245
GH02H108785 1.1 ENCODE 5.9 +252.4 252439 2.3 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 PAF1 GCC2 LIMS1 CCDC138 RPL39P16
GH02H109030 1.5 FANTOM5 Ensembl ENCODE 2.7 +497.7 497666 3.3 PKNOX1 FEZF1 ZNF2 ETS1 GLIS2 ATF7 ZNF592 NFIL3 ZNF610 GLIS1 RANBP2 LIMS1 LOC105373543 PIR45653
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LIMS1 on UCSC Golden Path with GeneCards custom track

Promoters for LIMS1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000121383 145 2601 HDGF FOXA2 ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 SP3

Genomic Locations for LIMS1 Gene

Genomic Locations for LIMS1 Gene
chr2:108,534,355-108,687,246
(GRCh38/hg38)
Size:
152,892 bases
Orientation:
Plus strand
chr2:109,150,811-109,303,702
(GRCh37/hg19)

Genomic View for LIMS1 Gene

Genes around LIMS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMS1 Gene

Proteins for LIMS1 Gene

  • Protein details for LIMS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48059-LIMS1_HUMAN
    Recommended name:
    LIM and senescent cell antigen-like-containing domain protein 1
    Protein Accession:
    P48059
    Secondary Accessions:
    • B2RAJ4
    • B7Z483
    • B7Z7R3
    • B7Z907
    • Q53TE0
    • Q9BS44

    Protein attributes for LIMS1 Gene

    Size:
    325 amino acids
    Molecular mass:
    37251 Da
    Quaternary structure:
    • Interacts (via LIM zinc-binding 5) with TGFB1I1 (By similarity). Interacts with integrin-linked protein kinase 1 (ILK) via the first LIM domain, and in competition with LIMS2. Part of the heterotrimeric IPP complex composed of integrin-linked kinase (ILK), LIMS1 or LIMS2, and PARVA. Interacts with SH3/SH2 adapter NCK2, thereby linking the complex to cell surface receptors.

    Three dimensional structures from OCA and Proteopedia for LIMS1 Gene

    Alternative splice isoforms for LIMS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIMS1 Gene

Post-translational modifications for LIMS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for LIMS1 (LIMS1)
  • Abcam antibodies for LIMS1

No data available for DME Specific Peptides for LIMS1 Gene

Domains & Families for LIMS1 Gene

Gene Families for LIMS1 Gene

Protein Domains for LIMS1 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LIMS1: view

No data available for UniProtKB/Swiss-Prot for LIMS1 Gene

Function for LIMS1 Gene

Molecular function for LIMS1 Gene

UniProtKB/Swiss-Prot Function:
Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.

Phenotypes From GWAS Catalog for LIMS1 Gene

Gene Ontology (GO) - Molecular Function for LIMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10574708
GO:0008270 zinc ion binding IDA 19074270
GO:0019901 protein kinase binding IPI 20926685
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMS1: view
genes like me logo Genes that share phenotypes with LIMS1: view

Animal Models for LIMS1 Gene

MGI Knock Outs for LIMS1:

Animal Model Products

CRISPR Products

miRNA for LIMS1 Gene

miRTarBase miRNAs that target LIMS1

Clone Products

  • Addgene plasmids for LIMS1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIMS1 Gene

Localization for LIMS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMS1 Gene

Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side.

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 LIMS1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
nucleus 3

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for LIMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IEA --
GO:0005911 cell-cell junction IMP 20926685
GO:0005925 colocalizes_with focal adhesion IEA,IDA 19117955
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LIMS1: view

Pathways & Interactions for LIMS1 Gene

genes like me logo Genes that share pathways with LIMS1: view

Pathways by source for LIMS1 Gene

Gene Ontology (GO) - Biological Process for LIMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001837 NOT epithelial to mesenchymal transition IMP 20926685
GO:0007569 cell aging TAS 7517666
GO:0010628 positive regulation of gene expression IMP 20926685
GO:0010811 positive regulation of cell-substrate adhesion IMP 20926685
GO:0033209 tumor necrosis factor-mediated signaling pathway IMP 21343177
genes like me logo Genes that share ontologies with LIMS1: view

No data available for SIGNOR curated interactions for LIMS1 Gene

Drugs & Compounds for LIMS1 Gene

(2) Drugs for LIMS1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LIMS1: view

Transcripts for LIMS1 Gene

Unigene Clusters for LIMS1 Gene

LIM and senescent cell antigen-like domains 1:
Representative Sequences:

CRISPR Products

Clone Products

  • Addgene plasmids for LIMS1

Alternative Splicing Database (ASD) splice patterns (SP) for LIMS1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
SP1: - - - - -
SP2: - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - - - - - - -
SP7: - - - - - -
SP8: -
SP9: - - - -
SP10: - -
SP11: - - - - - - -
SP12:

Relevant External Links for LIMS1 Gene

GeneLoc Exon Structure for
LIMS1
ECgene alternative splicing isoforms for
LIMS1

Expression for LIMS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIMS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LIMS1 Gene

This gene is overexpressed in Platelet (21.5) and Peripheral blood mononuclear cells (11.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LIMS1 Gene



Protein tissue co-expression partners for LIMS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LIMS1 Gene:

LIMS1

SOURCE GeneReport for Unigene cluster for LIMS1 Gene:

Hs.597715

mRNA Expression by UniProt/SwissProt for LIMS1 Gene:

P48059-LIMS1_HUMAN
Tissue specificity: Expressed in most tissues except in the brain.

Evidence on tissue expression from TISSUES for LIMS1 Gene

  • Blood(4.3)
  • Bone marrow(4.2)
  • Heart(3.1)
  • Lung(2.9)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with LIMS1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMS1 Gene

Orthologs for LIMS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIMS1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIMS1 33
  • 99.41 (n)
cow
(Bos Taurus)
Mammalia MGC142792 34
  • 96 (a)
OneToMany
LIMS1 33
  • 89.91 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 91 (a)
OneToMany
LIMS1 33
  • 90.01 (n)
mouse
(Mus musculus)
Mammalia Lims1 16 34 33
  • 90.72 (n)
rat
(Rattus norvegicus)
Mammalia Lims1 33
  • 90.72 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 88 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 82 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 86 (a)
ManyToMany
-- 34
  • 84 (a)
ManyToMany
LIMS1 33 34
  • 82.87 (n)
-- 34
  • 79 (a)
ManyToMany
-- 34
  • 69 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 92 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia lims1 33
  • 82.87 (n)
Str.8448 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.12605 33
zebrafish
(Danio rerio)
Actinopterygii lims1 33 34
  • 80.85 (n)
lims2 34
  • 73 (a)
ManyToMany
wufc32c03 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5292 33
fruit fly
(Drosophila melanogaster)
Insecta stck 35 33 34
  • 65.2 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003429 33
  • 64.35 (n)
worm
(Caenorhabditis elegans)
Secernentea unc-97 35 33 34
  • 63.03 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11312 34
  • 67 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4597 33
Species where no ortholog for LIMS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for LIMS1 Gene

ENSEMBL:
Gene Tree for LIMS1 (if available)
TreeFam:
Gene Tree for LIMS1 (if available)

Paralogs for LIMS1 Gene

Variants for LIMS1 Gene

Sequence variations from dbSNP and Humsavar for LIMS1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000001917 -- 108,610,219(+) TTTTT(C/T)ATTTT intron-variant
rs1000051096 -- 108,617,347(+) TGGAA(A/G)ATGTT intron-variant
rs1000051512 -- 108,650,172(+) TTTCA(A/G)TCAAA intron-variant
rs1000077616 -- 108,588,053(+) AGTTA(A/C)CTCTT intron-variant, upstream-variant-2KB
rs1000087061 -- 108,679,217(+) CTCAC(A/G)CCTGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LIMS1 Gene

Variant ID Type Subtype PubMed ID
nsv961855 CNV duplication 23825009
nsv961854 CNV duplication 23825009
nsv834328 CNV gain 17160897
nsv527491 CNV loss 19592680
nsv521122 CNV loss 19592680
nsv1149522 OTHER inversion 26484159
nsv1139724 CNV duplication 24896259
esv3591929 CNV loss 21293372
esv2759081 CNV gain 17122850
esv2720498 CNV deletion 23290073
dgv4036n100 CNV gain 25217958
dgv153e55 CNV gain 17911159

Variation tolerance for LIMS1 Gene

Gene Damage Index Score: 2.56; 44.60% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIMS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMS1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIMS1 Gene

Disorders for LIMS1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LIMS1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
conotruncal heart malformations
  • conotruncal heart malformations, variable
- elite association - COSMIC cancer census association via MalaCards
Search LIMS1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LIMS1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIMS1
genes like me logo Genes that share disorders with LIMS1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIMS1 Gene

Publications for LIMS1 Gene

  1. Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase. (PMID: 19117955) Yang Y … Qin J (The Journal of biological chemistry 2009) 3 4 22 60
  2. The structural basis of integrin-linked kinase-PINCH interactions. (PMID: 19074270) Chiswell BP … Calderwood DA (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4 22 60
  3. Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling. (PMID: 12794636) Velyvis A … Qin J (Nature structural biology 2003) 3 4 22 60
  4. Solution structure of the focal adhesion adaptor PINCH LIM1 domain and characterization of its interaction with the integrin-linked kinase ankyrin repeat domain. (PMID: 11078733) Velyvis A … Qin J (The Journal of biological chemistry 2001) 3 4 22 60
  5. The LIM-only protein PINCH directly interacts with integrin-linked kinase and is recruited to integrin-rich sites in spreading cells. (PMID: 10022929) Tu Y … Wu C (Molecular and cellular biology 1999) 2 3 4 60

Products for LIMS1 Gene

  • Addgene plasmids for LIMS1

Sources for LIMS1 Gene

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