Human Gene LIMS1 (ENST00000414829.2) Description and Page Index
  Description: Contains 1 LIM zinc-binding domain. (from UniProt F8WC86)
RefSeq Summary (NM_001193485): 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: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript 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 :: SRR1660805.66489.1, SRR6380201.36391.25 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000414829.2
Gencode Gene: ENSG00000169756.16
Transcript (Including UTRs)
   Position: hg38 chr2:108,655,053-108,662,303 Size: 7,251 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr2:108,655,075-108,662,240 Size: 7,166 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:108,655,053-108,662,303)mRNA (may differ from genome)Protein (117 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
LynxMGIPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=LIM and senescent cell antigen-like-containing domain protein 1;
SIMILARITY: Contains 1 LIM zinc-binding domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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 -1.6022-0.073 Picture PostScript Text
3' UTR -15.4063-0.244 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
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain

ModBase Predicted Comparative 3D Structure on F8WC86
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 orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

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

-  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.

-  Other Names for This Gene
  Alternate Gene Symbols: AK312178, F8WC86, F8WC86_HUMAN, uc061msm.1, uc061msm.2
UCSC ID: uc061msm.2
RefSeq Accession: NM_001193485
Protein: F8WC86

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