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PDLIM1 (PDZ and LIM domain 1)

Identity

Alias_namesCLIM1
PDZ and LIM domain 1 (elfin)
Alias_symbol (synonym)CLP-36
hCLIM1
CLP36
Other aliasHEL-S-112
HGNC (Hugo) PDLIM1
LocusID (NCBI) 9124
Atlas_Id 55262
Location 10q23.33  [Link to chromosome band 10q23]
Location_base_pair Starts at 96997325 and ends at 97050905 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
KCNN3 (1q21.3) / PDLIM1 (10q23.33)PDLIM1 (10q23.33) / PPP1CB (2p23.2)PDLIM1 (10q23.33) / SORBS1 (10q24.1)
PDLIM1 10q23.33 / SORBS1 10q24.1

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

Nomenclature
HGNC (Hugo)PDLIM1   2067
Cards
Entrez_Gene (NCBI)PDLIM1  9124  PDZ and LIM domain 1
AliasesCLIM1; CLP-36; CLP36; HEL-S-112; 
hCLIM1
GeneCards (Weizmann)PDLIM1
Ensembl hg19 (Hinxton)ENSG00000107438 [Gene_View]  chr10:96997325-97050905 [Contig_View]  PDLIM1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000107438 [Gene_View]  chr10:96997325-97050905 [Contig_View]  PDLIM1 [Vega]
ICGC DataPortalENSG00000107438
TCGA cBioPortalPDLIM1
AceView (NCBI)PDLIM1
Genatlas (Paris)PDLIM1
WikiGenes9124
SOURCE (Princeton)PDLIM1
Genetics Home Reference (NIH)PDLIM1
Genomic and cartography
GoldenPath hg19 (UCSC)PDLIM1  -     chr10:96997325-97050905 -  10q23.33   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PDLIM1  -     10q23.33   [Description]    (hg38-Dec_2013)
EnsemblPDLIM1 - 10q23.33 [CytoView hg19]  PDLIM1 - 10q23.33 [CytoView hg38]
Mapping of homologs : NCBIPDLIM1 [Mapview hg19]  PDLIM1 [Mapview hg38]
OMIM605900   
Gene and transcription
Genbank (Entrez)AJ310549 AK091847 AK314792 BC000915 BC018755
RefSeq transcript (Entrez)NM_020992
RefSeq genomic (Entrez)NC_000010 NC_018921 NT_030059 NW_004929376
Consensus coding sequences : CCDS (NCBI)PDLIM1
Cluster EST : UnigeneHs.368525 [ NCBI ]
CGAP (NCI)Hs.368525
Alternative Splicing GalleryENSG00000107438
Gene ExpressionPDLIM1 [ NCBI-GEO ]   PDLIM1 [ EBI - ARRAY_EXPRESS ]   PDLIM1 [ SEEK ]   PDLIM1 [ MEM ]
Gene Expression Viewer (FireBrowse)PDLIM1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9124
GTEX Portal (Tissue expression)PDLIM1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00151   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00151  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00151
Splice isoforms : SwissVarO00151
PhosPhoSitePlusO00151
Domaine pattern : Prosite (Expaxy)LIM_DOMAIN_1 (PS00478)    LIM_DOMAIN_2 (PS50023)    PDZ (PS50106)   
Domains : Interpro (EBI)DUF4749    PDLIM1    PDZ    ZASP    Znf_LIM   
Domain families : Pfam (Sanger)DUF4749 (PF15936)    LIM (PF00412)    PDZ (PF00595)   
Domain families : Pfam (NCBI)pfam15936    pfam00412    pfam00595   
Domain families : Smart (EMBL)LIM (SM00132)  PDZ (SM00228)  ZM (SM00735)  
Conserved Domain (NCBI)PDLIM1
DMDM Disease mutations9124
Blocks (Seattle)PDLIM1
PDB (SRS)1X62    2PKT   
PDB (PDBSum)1X62    2PKT   
PDB (IMB)1X62    2PKT   
PDB (RSDB)1X62    2PKT   
Structural Biology KnowledgeBase1X62    2PKT   
SCOP (Structural Classification of Proteins)1X62    2PKT   
CATH (Classification of proteins structures)1X62    2PKT   
SuperfamilyO00151
Human Protein AtlasENSG00000107438
Peptide AtlasO00151
HPRD09326
IPIIPI00010414   
Protein Interaction databases
DIP (DOE-UCLA)O00151
IntAct (EBI)O00151
FunCoupENSG00000107438
BioGRIDPDLIM1
STRING (EMBL)PDLIM1
ZODIACPDLIM1
Ontologies - Pathways
QuickGOO00151
Ontology : AmiGOresponse to hypoxia  transcription coactivator activity  transcription factor complex  cytoplasm  cytoskeleton  focal adhesion  regulation of transcription, DNA-templated  response to oxidative stress  zinc ion binding  
Ontology : EGO-EBIresponse to hypoxia  transcription coactivator activity  transcription factor complex  cytoplasm  cytoskeleton  focal adhesion  regulation of transcription, DNA-templated  response to oxidative stress  zinc ion binding  
NDEx NetworkPDLIM1
Atlas of Cancer Signalling NetworkPDLIM1
Wikipedia pathwaysPDLIM1
Orthology - Evolution
OrthoDB9124
GeneTree (enSembl)ENSG00000107438
Phylogenetic Trees/Animal Genes : TreeFamPDLIM1
HOVERGENO00151
HOGENOMO00151
Homologs : HomoloGenePDLIM1
Homology/Alignments : Family Browser (UCSC)PDLIM1
Gene fusions - Rearrangements
Fusion : MitelmanPDLIM1/SORBS1 [10q23.33/10q24.1]  
Fusion: TCGAPDLIM1 10q23.33 SORBS1 10q24.1 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDLIM1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDLIM1
dbVarPDLIM1
ClinVarPDLIM1
1000_GenomesPDLIM1 
Exome Variant ServerPDLIM1
ExAC (Exome Aggregation Consortium)PDLIM1 (select the gene name)
Genetic variants : HAPMAP9124
Genomic Variants (DGV)PDLIM1 [DGVbeta]
DECIPHER (Syndromes)10:96997325-97050905  ENSG00000107438
CONAN: Copy Number AnalysisPDLIM1 
Mutations
ICGC Data PortalPDLIM1 
TCGA Data PortalPDLIM1 
Broad Tumor PortalPDLIM1
OASIS PortalPDLIM1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDLIM1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDLIM1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PDLIM1
DgiDB (Drug Gene Interaction Database)PDLIM1
DoCM (Curated mutations)PDLIM1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDLIM1 (select a term)
intoGenPDLIM1
Cancer3DPDLIM1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605900   
Orphanet
MedgenPDLIM1
Genetic Testing Registry PDLIM1
NextProtO00151 [Medical]
TSGene9124
GENETestsPDLIM1
Huge Navigator PDLIM1 [HugePedia]
snp3D : Map Gene to Disease9124
BioCentury BCIQPDLIM1
ClinGenPDLIM1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9124
Chemical/Pharm GKB GenePA33158
Clinical trialPDLIM1
Miscellaneous
canSAR (ICR)PDLIM1 (select the gene name)
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDLIM1
EVEXPDLIM1
GoPubMedPDLIM1
iHOPPDLIM1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:20:53 CET 2017

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