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LIMS3 Gene

protein-coding   GIFtS: 37
GCID: GC02P110656

LIM And Senescent Cell Antigen-Like Domains 3

  Search for LIMS3
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LIM And Senescent Cell Antigen-Like Domains 31 2
Pinch 21 2
Particularly Interesting New Cys-His Protein 32 3
PINCH-32 3
LIM And Senescent Cell Antigen-Like-Containing Domain Protein 32
PINCH33

External Ids:    HGNC: 300471   Entrez Gene: 966262   Ensembl: ENSG000002569777   UniProtKB: P0CW193   

Export aliases for LIMS3 gene to outside databases

Previous GC identifers: GC02P110392 GC02P110013


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for LIMS3 Gene:
LIMS3 (LIM and senescent cell antigen-like domains 3) is a protein-coding gene. An important paralog of this gene is LIMS1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LIMS3 gene promoter:
         NF-1   NF-1/L   AP-1   RelA   YY1   GATA-1   PPAR-gamma1   COMP1   SEF-1 (1)   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLIMS3 promoter sequence
   Search Chromatin IP Primers for LIMS3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LIMS3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q13   Ensembl cytogenetic band:  2q13   HGNC cytogenetic band: 2q13

LIMS3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LIMS3 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P110656:  view genomic region     (about GC identifiers)

Start:
110,656,005 bp from pter      End:
110,683,202 bp from pter
Size:
27,198 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for LIMS3

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LIMS3_HUMAN, P0CW19 (See protein sequence)
Recommended Name: LIM and senescent cell antigen-like-containing domain protein 3  
Size: 117 amino acids; 13251 Da
Secondary accessions: Q9HB10

Explore the universe of human proteins at neXtProt for LIMS3: NX_P0CW19

Explore proteomics data for LIMS3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See LIMS3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_277049.1  
    ENSEMBL proteins: 
     ENSP00000405165   ENSP00000450675  

    LIMS3 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR017351 PINCH
     IPR001781 Znf_LIM

    Graphical View of Domain Structure for InterPro Entry P0CW19

    ProtoNet protein and cluster: P0CW19

    UniProtKB/Swiss-Prot: LIMS3_HUMAN, P0CW19
    Similarity: Contains 1 LIM zinc-binding domain


    Find genes that share domains with LIMS3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with LIMS3           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LIMS3
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    1 qRT-PCR Assays for microRNA that regulate LIMS3:
    hsa-miR-642a
    SwitchGear 3'UTR luciferase reporter plasmidLIMS3 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    LIMS3_HUMAN, P0CW19: Cytoplasm (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    nucleus3

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with LIMS3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LIMS3
    Interactions:

        Search GeneGlobe Interaction Network for LIMS3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    Selected Interacting proteins for LIMS3 (ENSP000004051654) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    LDB3ENSP000003552964STRING: ENSP00000355296
    PDLIM5ENSP000003217464STRING: ENSP00000321746
    PDLIM7ENSP000003480994STRING: ENSP00000348099
    PXNENSP000002283074STRING: ENSP00000228307
    TGFB1I1ENSP000003783324STRING: ENSP00000378332
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LIMS3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for LIMS3 gene: 
    NM_033514.4  

    Unigene Cluster for LIMS3:

    LIM and senescent cell antigen-like domains 3
    Hs.535619  [show with all ESTs]
    Unigene Representative Sequence: NR_027145
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000437679(uc002tff.3) ENST00000482065 ENST00000479168 ENST00000487150
    ENST00000553749
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate LIMS3:
    hsa-miR-642a
    SwitchGear 3'UTR luciferase reporter plasmidLIMS3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LIMS3
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    GenScript: all cDNA clones in your preferred vector: LIMS3 (NM_033514)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LIMS3
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat LIMS3
      QuantiFast Probe-based Assays in human, mouse, rat LIMS3

    Additional mRNA sequence: 

    AF288404.1 AK298340.1 AK312178.1 BC054477.1 BC171890.1 NR_027145.2 NR_027467.2 NR_038099.1 

    12 DOTS entries:

    DT.101960929  DT.91754540  DT.412543  DT.437332  DT.95161695  DT.95336173  DT.100816049  DT.121031862 
    DT.121031905  DT.314499  DT.91712046  DT.97794076 

    Selected AceView cDNA sequences (see all 123):

    AL133596 AA936147 AW085495 AI820499 AI821344 AU122254 CB216310 CK430290 
    C18914 AI025828 AI318413 BQ013290 AA570650 AI252658 AL703551 CB993644 
    CB216573 BV196052 AI364163 CB991028 BC054477 AW438901 CF994716 AW189703 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LIMS3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTGATGTGC
    LIMS3 Expression
    About this image

    LIMS3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LIMS3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.535619

    UniProtKB/Swiss-Prot: LIMS3_HUMAN, P0CW19
    Tissue specificity: Detected in testis

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LIMS3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for LIMS3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    (see all 5)
    Uncharacterized protein
    (see all 5)


    (see all 5)
    many ↔ many
    many ↔ many
    (see all 5)
    10(36180-42573) ENSGALG00000027405
    JH375335.1(7775-9525)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    23(a)
    1 → many
    3(107508842-107530508)
    zebrafish
    (Danio rerio)
    Actinopterygii lims16
    lims26
    LIM and senescent cell antigen-like domains 2
    15(a)
    15(a)
    many ↔ many
    many ↔ many
    11(34434877-34454717) ENSDARG00000026985
    9(423983-430060) ENSDARG00000014976
    fruit fly
    (Drosophila melanogaster)
    Insecta stck6
    steamer duck
    10(a)
    1 → many
    3R(4182689-4185686)
    worm
    (Caenorhabditis elegans)
    Secernentea unc-976
    Protein UNC-97 (unc-97) mRNA, complete cds
    7(a)
    1 → many
    X(5593133-5594965) WBGene00006826
            Species with no ortholog for LIMS3

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LIMS3 gene
    LIMS3L1 2  LIMS12  PDLIM72  FHL32  FHL52  LDB32  LPXN2  FHL12  
    ENSG000002572072  TGFB1I12  PDLIM52  PXN2  FHL22  LIMS22  
    7 SIMAP similar genes for LIMS3 using alignment to 2 protein entries:     LIMS3_HUMAN (see all proteins):
    LIMS3L    LIMS1    LIMS2    LHX4    CRIP1    LHx4
    PXN

    Find genes that share paralogs with LIMS3           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for LIMS3
    PGOHUM00000240252 PGOHUM00000240841


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for LIMS3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2751812CNV Loss17911159
    nsv508157CNV Loss20534489
    nsv874777CNV Gain21882294
    dgv4263n71CNV Gain21882294
    esv28875CNV Gain+Loss19812545
    nsv469649CNV Complex16826518
    nsv510884CNV Complex20534489

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LIMS3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with LIMS3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Molecular cloning and characterization of a novel splice variant of the LIM domain family gene, PINCH 2, in human testis. (PubMed id 17435276)1 Liu Y....Li J. (Mol. Biotechnol. 2007)
    4. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
    5. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. (PubMed id 15342556)1 Suzuki Y.... Sugano S. (Genome Res. 2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    8. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 96626 HGNC: 30047 AceView: LOC339692 Ensembl:ENSG00000256977 euGenes: HUgn96626
    ECgene: LIMS3 H-InvDB: LIMS3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LIMS3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LIMS3 gene:
    Search GeneIP for patents involving LIMS3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     Custom PCR Arrays for LIMS3 Search Chromatin IP Primers for LIMS3
     Pre-validated RT2 qPCR Primer Assay in human, mouse / rat LIMS3  Search GeneGlobe Interaction Network for LIMS3
     Regulatory tfbs in LIMS3 promoter
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LIMS3
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     Search Addgene for plasmids for LIMS3
      Search eBioscience for proteins for LIMS3
      Search eBioscience for elisas for LIMS3
      eBioscience FlowRNA Probe Sets
           
    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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