Human Gene LIMS2 (ENST00000355119.9_9) from GENCODE V47lift37
  Description: LIM zinc finger domain containing 2, transcript variant 3 (from RefSeq NM_001161403.3)
Gencode Transcript: ENST00000355119.9_9
Gencode Gene: ENSG00000072163.20_13
Transcript (Including UTRs)
   Position: hg19 chr2:128,396,001-128,433,104 Size: 37,104 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr2:128,396,856-128,432,598 Size: 35,743 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 (chr2:128,396,001-128,433,104)mRNA (may differ from genome)Protein (341 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LIMS2_HUMAN
DESCRIPTION: RecName: Full=LIM and senescent cell antigen-like-containing domain protein 2; AltName: Full=LIM-like protein 2; AltName: Full=Particularly interesting new Cys-His protein 2; Short=PINCH-2;
FUNCTION: Competes with LIMS1 for binding to ILK. Plays a role in modulating cell spreading and migration.
SUBUNIT: Interacts with TGFB1I1 (By similarity). Interacts with integrin-linked protein kinase 1 (ILK) via the first LIM domain. Detected in a complex with ILK and PARVA.
SUBCELLULAR LOCATION: Nucleus (Potential). Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side.
SIMILARITY: Contains 5 LIM zinc-binding domains.
SEQUENCE CAUTION: Sequence=AAM77350.1; Type=Frameshift; Positions=331;

-  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: LIMS2
Diseases sorted by gene-association score: muscular dystrophy, limb-girdle, type 2w* (1350), muscular dystrophy (5)
* = Manually curated disease association

-  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: 176.69 RPKM in Colon - Sigmoid
Total median expression: 1628.15 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 -183.94506-0.364 Picture PostScript Text
3' UTR -335.10855-0.392 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
3IXE - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q7Z4I7
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    
 RGD    
      
      

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

Biological Process:
GO:0034329 cell junction assembly
GO:0043066 negative regulation of apoptotic process
GO:0045216 cell-cell junction organization
GO:0050680 negative regulation of epithelial cell proliferation
GO:0098609 cell-cell adhesion
GO:2000178 negative regulation of neural precursor cell proliferation
GO:2000346 negative regulation of hepatocyte proliferation
GO:2001046 positive regulation of integrin-mediated signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  AK123014 - Homo sapiens cDNA FLJ16826 fis, clone UTERU3006687, highly similar to Homo sapiens LIM and senescent cell antigen-like domains 1 (LIMS1).
AL512716 - Homo sapiens mRNA; cDNA DKFZp547D192 (from clone DKFZp547D192).
BC008977 - Homo sapiens LIM and senescent cell antigen-like domains 2, mRNA (cDNA clone IMAGE:4158414), partial cds.
BC001370 - Homo sapiens LIM and senescent cell antigen-like domains 2, mRNA (cDNA clone IMAGE:3051392), complete cds.
AF527769 - Homo sapiens tissue-type brain LIM-like protein 2F mRNA, complete cds.
AF527768 - Homo sapiens tissue-type brain LIM-like protein 2E mRNA, complete cds.
AF527770 - Homo sapiens tissue-type brain LIM-like protein 2G mRNA, complete cds.
AF527767 - Homo sapiens tissue-type uterus LIM-like protein 2D mRNA, complete cds.
AF527764 - Homo sapiens tissue-type brain LIM-like protein 2A mRNA, complete cds.
BC065816 - Homo sapiens LIM and senescent cell antigen-like domains 2, mRNA (cDNA clone MGC:75000 IMAGE:6181259), complete cds.
AF527765 - Homo sapiens tissue-type lung LIM-like protein 2B mRNA, complete cds.
AF527766 - Homo sapiens tissue-type spleen LIM-like protein 2C mRNA, complete cds.
JD057303 - Sequence 38327 from Patent EP1572962.
AK093692 - Homo sapiens cDNA FLJ36373 fis, clone THYMU2008111, moderately similar to PINCH PROTEIN.
AX748263 - Sequence 1788 from Patent EP1308459.
AK091763 - Homo sapiens cDNA FLJ34444 fis, clone HLUNG2001814, highly similar to PINCH PROTEIN.
AK091652 - Homo sapiens cDNA FLJ34333 fis, clone FEBRA2009276, highly similar to PINCH PROTEIN.
AX747112 - Sequence 637 from Patent EP1308459.
AK094954 - Homo sapiens cDNA FLJ37635 fis, clone BRCOC2017856, highly similar to PINCH PROTEIN.
AF520987 - Homo sapiens LIMS2 (LIMS2) mRNA, complete cds.
AK055363 - Homo sapiens cDNA FLJ30801 fis, clone FEBRA2001217, highly similar to Homo sapiens LIM and senescent cell antigen-like domains 2 (LIMS2), mRNA.
AK022470 - Homo sapiens cDNA FLJ12408 fis, clone MAMMA1002869, highly similar to PINCH PROTEIN.
AK000906 - Homo sapiens cDNA FLJ10044 fis, clone HEMBA1001088, moderately similar to PINCH PROTEIN.
AK095790 - Homo sapiens cDNA FLJ38471 fis, clone FEBRA2022055, highly similar to PINCH PROTEIN.
JD069132 - Sequence 50156 from Patent EP1572962.
JD351348 - Sequence 332372 from Patent EP1572962.
JD026751 - Sequence 7775 from Patent EP1572962.
JD477203 - Sequence 458227 from Patent EP1572962.
JD272747 - Sequence 253771 from Patent EP1572962.
JD124891 - Sequence 105915 from Patent EP1572962.
JD338022 - Sequence 319046 from Patent EP1572962.
JD087908 - Sequence 68932 from Patent EP1572962.
AK297645 - Homo sapiens cDNA FLJ56117 complete cds, highly similar to Homo sapiens LIM and senescent cell antigen-like domains 2 (LIMS2), mRNA.
JD471719 - Sequence 452743 from Patent EP1572962.
JD494237 - Sequence 475261 from Patent EP1572962.
JD532918 - Sequence 513942 from Patent EP1572962.
JD151502 - Sequence 132526 from Patent EP1572962.
JD537579 - Sequence 518603 from Patent EP1572962.
JD092290 - Sequence 73314 from Patent EP1572962.
JD250530 - Sequence 231554 from Patent EP1572962.
JD148575 - Sequence 129599 from Patent EP1572962.
JD253833 - Sequence 234857 from Patent EP1572962.
JD127290 - Sequence 108314 from Patent EP1572962.
JD055559 - Sequence 36583 from Patent EP1572962.
JD239858 - Sequence 220882 from Patent EP1572962.
JD454842 - Sequence 435866 from Patent EP1572962.
JD192408 - Sequence 173432 from Patent EP1572962.
JD392013 - Sequence 373037 from Patent EP1572962.
JD127191 - Sequence 108215 from Patent EP1572962.
JD390608 - Sequence 371632 from Patent EP1572962.
AF484961 - Homo sapiens PINCH-2 mRNA, complete cds.
KJ902856 - Synthetic construct Homo sapiens clone ccsbBroadEn_12250 LIMS2 gene, encodes complete protein.
AB463832 - Synthetic construct DNA, clone: pF1KB6527, Homo sapiens LIMS2 gene for LIM and senescent cell antigen-like domains 2, without stop codon, in Flexi system.
JD031651 - Sequence 12675 from Patent EP1572962.

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

Protein Q7Z4I7 (Reactome details) participates in the following event(s):

R-HSA-446391 Formation of the PINCH-ILK-parvin complex
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: A6NLH0, B4DMV1, ENST00000355119.1, ENST00000355119.2, ENST00000355119.3, ENST00000355119.4, ENST00000355119.5, ENST00000355119.6, ENST00000355119.7, ENST00000355119.8, F5H6E6, LIMS2_HUMAN, NM_001161403, PINCH2, Q7Z4I2, Q7Z4I6, Q7Z4I7, Q7Z4I8, Q8NFE7, Q9HA13, uc317yye.1, uc317yye.2
UCSC ID: ENST00000355119.9_9
RefSeq Accession: NM_001161403.3
Protein: Q7Z4I7 (aka LIMS2_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.