Human Gene LIMS1 (ENST00000544547.6_8) from GENCODE V47lift37
  Description: LIM zinc finger domain containing 1, transcript variant 5 (from RefSeq NM_001193483.3)
Gencode Transcript: ENST00000544547.6_8
Gencode Gene: ENSG00000169756.17_17
Transcript (Including UTRs)
   Position: hg19 chr2:109,150,926-109,303,702 Size: 152,777 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr2:109,151,019-109,300,455 Size: 149,437 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:109,150,926-109,303,702)mRNA (may differ from genome)Protein (337 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LIMS1_HUMAN
DESCRIPTION: RecName: Full=LIM and senescent cell antigen-like-containing domain protein 1; AltName: Full=Particularly interesting new Cys-His protein 1; Short=PINCH-1; AltName: Full=Renal carcinoma antigen NY-REN-48;
FUNCTION: Effector of integrin and growth factor signaling, coupling surface receptors to downstream signaling molecules involved in the regulation of cell survival, cell proliferation and cell differentiation. Focal adhesion protein part of the complex ILK-PINCH. This complex is considered to be one of the convergence points of integrin- and growth factor-signaling pathway.
SUBUNIT: Interacts (via LIM zinc-binding 5) with TGFB1I1 (By similarity). Interacts (via LIM zinc-binding 1) with ILK. Interacts with SH3/SH2 adapter NCK2.
SUBCELLULAR LOCATION: Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side.
TISSUE SPECIFICITY: Expressed in most tissues except in the brain.
SIMILARITY: Contains 5 LIM zinc-binding domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LIMS1
Diseases sorted by gene-association score: conotruncal heart malformations (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.04 RPKM in Adipose - Subcutaneous
Total median expression: 303.88 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.2093-0.378 Picture PostScript Text
3' UTR -798.403247-0.246 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017351 - PINCH
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain

SCOP Domains:
48695 - Multiheme cytochromes
47240 - Ferritin-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1G47 - NMR MuPIT 1NYP - NMR MuPIT 1U5S - NMR MuPIT 2COR - NMR MuPIT 2D8X - NMR MuPIT 2KBX - NMR MuPIT 3F6Q - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P48059
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0019901 protein kinase binding
GO:0046872 metal ion binding

Biological Process:
GO:0007569 cell aging
GO:0010628 positive regulation of gene expression
GO:0010811 positive regulation of cell-substrate adhesion
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0034329 cell junction assembly
GO:0043547 positive regulation of GTPase activity
GO:0045184 establishment of protein localization
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051894 positive regulation of focal adhesion assembly
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
GO:1901224 positive regulation of NIK/NF-kappaB signaling
GO:0001837 epithelial to mesenchymal transition
GO:0050678 regulation of epithelial cell proliferation

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK296992 - Homo sapiens cDNA FLJ55516 complete cds, highly similar to Particularly interesting new Cys-His protein.
AF527761 - Homo sapiens tissue-type lung LIM-like protein 1C mRNA, complete sequence.
AK314217 - Homo sapiens cDNA, FLJ94954, Homo sapiens LIM and senescent cell antigen-like domains 1 (LIMS1),mRNA.
U09284 - Homo sapiens PINCH protein mRNA, complete cds.
AF527763 - Homo sapiens tissue-type melanoma LIM-like protein 1E mRNA, complete sequence.
BC005341 - Homo sapiens LIM and senescent cell antigen-like domains 1, mRNA (cDNA clone MGC:12432 IMAGE:3838632), complete cds.
AF527762 - Homo sapiens tissue-type melanoma LIM-like protein 1D mRNA, complete sequence.
AK304260 - Homo sapiens cDNA FLJ55509 complete cds, highly similar to Particularly interesting newCys-His protein.
AF527760 - Homo sapiens tissue-type blood LIM-like protein 1B mRNA, complete sequence.
AK310547 - Homo sapiens cDNA, FLJ17589.
AF527759 - Homo sapiens tissue-type placenta LIM-like protein 1A mRNA, complete sequence.
AK312178 - Homo sapiens cDNA, FLJ92465, highly similar to Homo sapiens LIM and senescent cell antigen-like domains 3 (LIMS3), mRNA.
AK302411 - Homo sapiens cDNA FLJ55165 complete cds, highly similar to Particularly interesting new Cys-His protein.
CU675127 - Synthetic construct Homo sapiens gateway clone IMAGE:100018939 5' read LIMS1 mRNA.
AB463831 - Synthetic construct DNA, clone: pF1KB6473, Homo sapiens LIMS1 gene for LIM and senescent cell antigen-like domains 1, without stop codon, in Flexi system.
KJ897130 - Synthetic construct Homo sapiens clone ccsbBroadEn_06524 LIMS1 gene, encodes complete protein.
EU446859 - Synthetic construct Homo sapiens clone IMAGE:100070064; IMAGE:100012068; FLH258303.01L LIM and senescent cell antigen-like domains 1 (LIMS1) gene, encodes complete protein.
LF322450 - JP 2014500723-A/129953: Polycomb-Associated Non-Coding RNAs.
JD027242 - Sequence 8266 from Patent EP1572962.
JD031651 - Sequence 12675 from Patent EP1572962.
JD035410 - Sequence 16434 from Patent EP1572962.
LF322452 - JP 2014500723-A/129955: Polycomb-Associated Non-Coding RNAs.
LF322453 - JP 2014500723-A/129956: Polycomb-Associated Non-Coding RNAs.
AK098109 - Homo sapiens cDNA FLJ40790 fis, clone TRACH2007324.
JD561228 - Sequence 542252 from Patent EP1572962.
BC015843 - Homo sapiens LIM and senescent cell antigen-like domains 1, mRNA (cDNA clone IMAGE:4337964), with apparent retained intron.
LF322456 - JP 2014500723-A/129959: Polycomb-Associated Non-Coding RNAs.
LF322457 - JP 2014500723-A/129960: Polycomb-Associated Non-Coding RNAs.
JD266251 - Sequence 247275 from Patent EP1572962.
AK025661 - Homo sapiens cDNA: FLJ22008 fis, clone HEP06934.
AL110164 - Homo sapiens mRNA; cDNA DKFZp586I0324 (from clone DKFZp586I0324).
LF322458 - JP 2014500723-A/129961: Polycomb-Associated Non-Coding RNAs.
JD481439 - Sequence 462463 from Patent EP1572962.
JD159614 - Sequence 140638 from Patent EP1572962.
JD560870 - Sequence 541894 from Patent EP1572962.
JD542358 - Sequence 523382 from Patent EP1572962.
JD211812 - Sequence 192836 from Patent EP1572962.
JD410422 - Sequence 391446 from Patent EP1572962.
BC022365 - Homo sapiens cDNA clone IMAGE:4730629.
MA558027 - JP 2018138019-A/129953: Polycomb-Associated Non-Coding RNAs.
MA558029 - JP 2018138019-A/129955: Polycomb-Associated Non-Coding RNAs.
MA558030 - JP 2018138019-A/129956: Polycomb-Associated Non-Coding RNAs.
MA558033 - JP 2018138019-A/129959: Polycomb-Associated Non-Coding RNAs.
MA558034 - JP 2018138019-A/129960: Polycomb-Associated Non-Coding RNAs.
MA558035 - JP 2018138019-A/129961: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P48059 (Reactome details) participates in the following event(s):

R-HSA-430311 Rsu-1 interacts with Pinch1
R-HSA-446391 Formation of the PINCH-ILK-parvin complex
R-HSA-446388 Regulation of cytoskeletal remodeling and cell spreading by IPP complex components
R-HSA-446353 Cell-extracellular matrix interactions
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAJ4, B7Z483, B7Z7R3, B7Z907, ENST00000544547.1, ENST00000544547.2, ENST00000544547.3, ENST00000544547.4, ENST00000544547.5, LIMS1_HUMAN, NM_001193483, P48059, PINCH, PINCH1, Q53TE0, Q9BS44, uc324vrf.1, uc324vrf.2
UCSC ID: ENST00000544547.6_8
RefSeq Accession: NM_001193483.3
Protein: P48059 (aka LIMS1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.