Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

LIMS1 (LIM zinc finger domain containing 1)

Identity

Alias_namesLIM and senescent cell antigen-like domains 1
LIM-type zinc finger domains 1
Alias_symbol (synonym)PINCH
PINCH1
Other aliasPINCH-1
HGNC (Hugo) LIMS1
LocusID (NCBI) 3987
Atlas_Id 45926
Location 2q12.3  [Link to chromosome band 2q12]
Location_base_pair Starts at 108607161 and ends at 108687246 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
LIMS1 (2q12.3) / RNF185 (22q12.2)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

4T>
Nomenclature
HGNC (Hugo)LIMS1   6616
Cards
Entrez_Gene (NCBI)LIMS1  3987  LIM zinc finger domain containing 1
AliasesPINCH; PINCH-1; PINCH1
GeneCards (Weizmann)LIMS1
Ensembl hg19 (Hinxton)ENSG00000169756 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000169756 [Gene_View]  chr2:108607161-108687246 [Contig_View]  LIMS1 [Vega]
ICGC DataPortalENSG00000169756
TCGA cBioPortalLIMS1
AceView (NCBI)LIMS1
Genatlas (Paris)LIMS1
WikiGenes3987
SOURCE (Princeton)LIMS1
Genetics Home Reference (NIH)LIMS1Genomic and cartography
GoldenPath hg38 (UCSC)LIMS1  -     chr2:108607161-108687246 +  2q12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LIMS1  -     2q12.3   [Description]    (hg19-Feb_2009)
EnsemblLIMS1 - 2q12.3 [CytoView hg19]  LIMS1 - 2q12.3 [CytoView hg38]
Mapping of homologs : NCBILIMS1 [Mapview hg19]  LIMS1 [Mapview hg38]
OMIM602567   
Gene and transcription
Genbank (Entrez)AF527759 AF527760 AF527761 AF527762 AF527763
RefSeq transcript (Entrez)NM_001193482 NM_001193483 NM_001193484 NM_001193485 NM_001193488 NM_004987
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LIMS1
Cluster EST : UnigeneHs.613268 [ NCBI ]
CGAP (NCI)Hs.613268
Alternative Splicing GalleryENSG00000169756
Gene ExpressionLIMS1 [ NCBI-GEO ]   LIMS1 [ EBI - ARRAY_EXPRESS ]   LIMS1 [ SEEK ]   LIMS1 [ MEM ]
Gene Expression Viewer (FireBrowse)LIMS1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3987
GTEX Portal (Tissue expression)LIMS1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP48059   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP48059  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP48059
Splice isoforms : SwissVarP48059
PhosPhoSitePlusP48059
Domaine pattern : Prosite (Expaxy)LIM_DOMAIN_1 (PS00478)    LIM_DOMAIN_2 (PS50023)   
Domains : Interpro (EBI)PINCH    Znf_LIM   
Domain families : Pfam (Sanger)LIM (PF00412)   
Domain families : Pfam (NCBI)pfam00412   
Domain families : Smart (EMBL)LIM (SM00132)  
Conserved Domain (NCBI)LIMS1
DMDM Disease mutations3987
Blocks (Seattle)LIMS1
PDB (SRS)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
PDB (PDBSum)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
PDB (IMB)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
PDB (RSDB)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
Structural Biology KnowledgeBase1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
SCOP (Structural Classification of Proteins)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
CATH (Classification of proteins structures)1G47    1NYP    1U5S    2COR    2D8X    2KBX    3F6Q    4HI8    4HI9   
SuperfamilyP48059
Human Protein AtlasENSG00000169756
Peptide AtlasP48059
HPRD03978
IPIIPI00788612   IPI00930460   IPI00917739   IPI00847665   IPI00917064   IPI00917194   IPI00917579   IPI00941481   
Protein Interaction databases
DIP (DOE-UCLA)P48059
IntAct (EBI)P48059
FunCoupENSG00000169756
BioGRIDLIMS1
STRING (EMBL)LIMS1
ZODIACLIMS1
Ontologies - Pathways
QuickGOP48059
Ontology : AmiGOepithelial to mesenchymal transition  protein binding  cytosol  plasma membrane  cell-cell junction  focal adhesion  focal adhesion  cell aging  zinc ion binding  positive regulation of gene expression  positive regulation of cell-substrate adhesion  protein kinase binding  tumor necrosis factor-mediated signaling pathway  cell junction assembly  positive regulation of GTPase activity  establishment of protein localization  negative regulation of transcription, DNA-templated  perinuclear region of cytoplasm  regulation of epithelial cell proliferation  positive regulation of focal adhesion assembly  cellular response to transforming growth factor beta stimulus  positive regulation of substrate adhesion-dependent cell spreading  positive regulation of NIK/NF-kappaB signaling  
Ontology : EGO-EBIepithelial to mesenchymal transition  protein binding  cytosol  plasma membrane  cell-cell junction  focal adhesion  focal adhesion  cell aging  zinc ion binding  positive regulation of gene expression  positive regulation of cell-substrate adhesion  protein kinase binding  tumor necrosis factor-mediated signaling pathway  cell junction assembly  positive regulation of GTPase activity  establishment of protein localization  negative regulation of transcription, DNA-templated  perinuclear region of cytoplasm  regulation of epithelial cell proliferation  positive regulation of focal adhesion assembly  cellular response to transforming growth factor beta stimulus  positive regulation of substrate adhesion-dependent cell spreading  positive regulation of NIK/NF-kappaB signaling  
NDEx NetworkLIMS1
Atlas of Cancer Signalling NetworkLIMS1
Wikipedia pathwaysLIMS1
Orthology - Evolution
OrthoDB3987
GeneTree (enSembl)ENSG00000169756
Phylogenetic Trees/Animal Genes : TreeFamLIMS1
HOVERGENP48059
HOGENOMP48059
Homologs : HomoloGeneLIMS1
Homology/Alignments : Family Browser (UCSC)LIMS1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLIMS1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LIMS1
dbVarLIMS1
ClinVarLIMS1
1000_GenomesLIMS1 
Exome Variant ServerLIMS1
ExAC (Exome Aggregation Consortium)LIMS1 (select the gene name)
Genetic variants : HAPMAP3987
Genomic Variants (DGV)LIMS1 [DGVbeta]
DECIPHERLIMS1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLIMS1 
Mutations
ICGC Data PortalLIMS1 
TCGA Data PortalLIMS1 
Broad Tumor PortalLIMS1
OASIS PortalLIMS1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLIMS1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLIMS1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LIMS1
DgiDB (Drug Gene Interaction Database)LIMS1
DoCM (Curated mutations)LIMS1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LIMS1 (select a term)
intoGenLIMS1
Cancer3DLIMS1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602567   
Orphanet
MedgenLIMS1
Genetic Testing Registry LIMS1
NextProtP48059 [Medical]
TSGene3987
GENETestsLIMS1
Target ValidationLIMS1
Huge Navigator LIMS1 [HugePedia]
snp3D : Map Gene to Disease3987
BioCentury BCIQLIMS1
ClinGenLIMS1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3987
Chemical/Pharm GKB GenePA30389
Clinical trialLIMS1
Miscellaneous
canSAR (ICR)LIMS1 (select the gene name)
Probes
Litterature
PubMed69 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLIMS1
EVEXLIMS1
GoPubMedLIMS1
iHOPLIMS1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 25 19:15:28 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.