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

LCN2 (lipocalin 2)

Identity

Alias_nameslipocalin 2 (oncogene 24p3)
Alias_symbol (synonym)NGAL
24p3
Other aliasMSFI
p25
HGNC (Hugo) LCN2
LocusID (NCBI) 3934
Atlas_Id 41133
Location 9q34.11  [Link to chromosome band 9q34]
Location_base_pair Starts at 128149430 and ends at 128153455 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CIZ1 (9q34.11) / LCN2 (9q34.11)DNM1 (9q34.11) / LCN2 (9q34.11)LCN2 (9q34.11) / MKL2 (16p13.12)
LCN2 (9q34.11) / NAPRT (8q24.3)POP4 (19q12) / LCN2 (9q34.11)TXNRD1 (12q23.3) / LCN2 (9q34.11)
DNM1 9q34.11 / LCN2 9q34.11

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)LCN2   6526
Cards
Entrez_Gene (NCBI)LCN2  3934  lipocalin 2
Aliases24p3; MSFI; NGAL; p25
GeneCards (Weizmann)LCN2
Ensembl hg19 (Hinxton)ENSG00000148346 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000148346 [Gene_View]  chr9:128149430-128153455 [Contig_View]  LCN2 [Vega]
ICGC DataPortalENSG00000148346
TCGA cBioPortalLCN2
AceView (NCBI)LCN2
Genatlas (Paris)LCN2
WikiGenes3934
SOURCE (Princeton)LCN2
Genetics Home Reference (NIH)LCN2
Genomic and cartography
GoldenPath hg38 (UCSC)LCN2  -     chr9:128149430-128153455 +  9q34.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LCN2  -     9q34.11   [Description]    (hg19-Feb_2009)
EnsemblLCN2 - 9q34.11 [CytoView hg19]  LCN2 - 9q34.11 [CytoView hg38]
Mapping of homologs : NCBILCN2 [Mapview hg19]  LCN2 [Mapview hg38]
OMIM600181   
Gene and transcription
Genbank (Entrez)AK301694 AK307311 AK316217 AW778875 BC033089
RefSeq transcript (Entrez)NM_005564
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LCN2
Cluster EST : UnigeneHs.204238 [ NCBI ]
CGAP (NCI)Hs.204238
Alternative Splicing GalleryENSG00000148346
Gene ExpressionLCN2 [ NCBI-GEO ]   LCN2 [ EBI - ARRAY_EXPRESS ]   LCN2 [ SEEK ]   LCN2 [ MEM ]
Gene Expression Viewer (FireBrowse)LCN2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3934
GTEX Portal (Tissue expression)LCN2
Protein : pattern, domain, 3D structure
UniProt/SwissProtP80188   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP80188  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP80188
Splice isoforms : SwissVarP80188
PhosPhoSitePlusP80188
Domaine pattern : Prosite (Expaxy)LIPOCALIN (PS00213)   
Domains : Interpro (EBI)Calycin    Calycin-like    LCN2/LCN12    Lipocalin    Lipocalin_CS    Lipocln_cytosolic_FA-bd_dom   
Domain families : Pfam (Sanger)Lipocalin (PF00061)   
Domain families : Pfam (NCBI)pfam00061   
Conserved Domain (NCBI)LCN2
DMDM Disease mutations3934
Blocks (Seattle)LCN2
PDB (SRS)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
PDB (PDBSum)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
PDB (IMB)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
PDB (RSDB)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
Structural Biology KnowledgeBase1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
SCOP (Structural Classification of Proteins)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
CATH (Classification of proteins structures)1DFV    1L6M    1NGL    1QQS    1X71    1X89    1X8U    3BY0    3CBC    3CMP    3DSZ    3DTQ    3FW4    3FW5    3HWD    3HWE    3HWF    3HWG    3I0A    3K3L    3PEC    3PED    3T1D    3TF6    3TZS    3U03    3U0D    4GH7    4IAW    4IAX    4K19    4MVI    4MVK    4MVL    4QAE    4ZFX    4ZHC    4ZHD    4ZHF    4ZHG    4ZHH    5JR8   
SuperfamilyP80188
Human Protein AtlasENSG00000148346
Peptide AtlasP80188
HPRD02551
IPIIPI00299547   IPI01013763   IPI00643623   
Protein Interaction databases
DIP (DOE-UCLA)P80188
IntAct (EBI)P80188
FunCoupENSG00000148346
BioGRIDLCN2
STRING (EMBL)LCN2
ZODIACLCN2
Ontologies - Pathways
QuickGOP80188
Ontology : AmiGOprotease binding  transporter activity  iron ion binding  extracellular region  extracellular region  extracellular space  cytosol  ion transport  cellular iron ion homeostasis  response to virus  response to herbicide  response to mycotoxin  positive regulation of gene expression  siderophore transport  antimicrobial humoral response  positive regulation of cell projection organization  cellular response to nutrient levels  specific granule lumen  small molecule binding  response to drug  protein homodimerization activity  neutrophil degranulation  innate immune response  extracellular exosome  protein homotrimerization  cellular response to hydrogen peroxide  cellular response to lipopolysaccharide  cellular response to interleukin-1  cellular response to tumor necrosis factor  extrinsic apoptotic signaling pathway in absence of ligand  
Ontology : EGO-EBIprotease binding  transporter activity  iron ion binding  extracellular region  extracellular region  extracellular space  cytosol  ion transport  cellular iron ion homeostasis  response to virus  response to herbicide  response to mycotoxin  positive regulation of gene expression  siderophore transport  antimicrobial humoral response  positive regulation of cell projection organization  cellular response to nutrient levels  specific granule lumen  small molecule binding  response to drug  protein homodimerization activity  neutrophil degranulation  innate immune response  extracellular exosome  protein homotrimerization  cellular response to hydrogen peroxide  cellular response to lipopolysaccharide  cellular response to interleukin-1  cellular response to tumor necrosis factor  extrinsic apoptotic signaling pathway in absence of ligand  
NDEx NetworkLCN2
Atlas of Cancer Signalling NetworkLCN2
Wikipedia pathwaysLCN2
Orthology - Evolution
OrthoDB3934
GeneTree (enSembl)ENSG00000148346
Phylogenetic Trees/Animal Genes : TreeFamLCN2
HOVERGENP80188
HOGENOMP80188
Homologs : HomoloGeneLCN2
Homology/Alignments : Family Browser (UCSC)LCN2
Gene fusions - Rearrangements
Fusion : MitelmanDNM1/LCN2 [9q34.11/9q34.11]  [t(9;9)(q34;q34)]  
Fusion: TCGADNM1 9q34.11 LCN2 9q34.11 HNSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLCN2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LCN2
dbVarLCN2
ClinVarLCN2
1000_GenomesLCN2 
Exome Variant ServerLCN2
ExAC (Exome Aggregation Consortium)LCN2 (select the gene name)
Genetic variants : HAPMAP3934
Genomic Variants (DGV)LCN2 [DGVbeta]
DECIPHERLCN2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLCN2 
Mutations
ICGC Data PortalLCN2 
TCGA Data PortalLCN2 
Broad Tumor PortalLCN2
OASIS PortalLCN2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLCN2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLCN2
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 LCN2
DgiDB (Drug Gene Interaction Database)LCN2
DoCM (Curated mutations)LCN2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LCN2 (select a term)
intoGenLCN2
Cancer3DLCN2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600181   
Orphanet
MedgenLCN2
Genetic Testing Registry LCN2
NextProtP80188 [Medical]
TSGene3934
GENETestsLCN2
Huge Navigator LCN2 [HugePedia]
snp3D : Map Gene to Disease3934
BioCentury BCIQLCN2
ClinGenLCN2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3934
Chemical/Pharm GKB GenePA30309
Clinical trialLCN2
Miscellaneous
canSAR (ICR)LCN2 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLCN2
EVEXLCN2
GoPubMedLCN2
iHOPLCN2
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 : Fri May 19 12:22:15 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.