Human Gene LIMS1 (ENST00000544547.5) Description and Page Index
  Description: Homo sapiens LIM zinc finger domain containing 1 (LIMS1), transcript variant 5, mRNA. (from RefSeq NM_001193483)
RefSeq Summary (NM_001193483): 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]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660803.39265.1, SRR1660805.235810.1 [ECO:0000332] ##Evidence-Data-END##
Gencode Transcript: ENST00000544547.5
Gencode Gene: ENSG00000169756.16
Transcript (Including UTRs)
   Position: hg38 chr2:108,534,355-108,687,238 Size: 152,884 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr2:108,534,563-108,683,999 Size: 149,437 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:108,534,355-108,687,238)mRNA (may differ from genome)Protein (337 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
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.

-  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

-  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 -112.10208-0.539 Picture PostScript Text
3' UTR -797.703239-0.246 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help



To conserve bandwidth, only the images from the first 3 structures are shown.
3F6Q - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P48059
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
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  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.
MA558027 - JP 2018138019-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.
MA558029 - JP 2018138019-A/129955: Polycomb-Associated Non-Coding RNAs.
LF322453 - JP 2014500723-A/129956: Polycomb-Associated Non-Coding RNAs.
MA558030 - JP 2018138019-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.
MA558033 - JP 2018138019-A/129959: Polycomb-Associated Non-Coding RNAs.
LF322457 - JP 2014500723-A/129960: Polycomb-Associated Non-Coding RNAs.
MA558034 - JP 2018138019-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.
MA558035 - JP 2018138019-A/129961: Polycomb-Associated Non-Coding RNAs.
JD481439 - Sequence 462463 from Patent EP1572962.
JD410422 - Sequence 391446 from Patent EP1572962.
BC022365 - Homo sapiens cDNA clone IMAGE:4730629.

-  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, LIMS1_HUMAN, NM_001193483, P48059, PINCH, PINCH1, Q53TE0, Q9BS44, uc002tel.1, uc002tel.2, uc002tel.3, uc002tel.4
UCSC ID: uc002tel.4
RefSeq Accession: NM_001193483
Protein: P48059 (aka LIMS1_HUMAN)
CCDS: CCDS2078.1, CCDS54383.1, CCDS54382.1

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