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Aliases for LCN2 Gene

Aliases for LCN2 Gene

  • Lipocalin 2 2 3 5
  • Oncogene 24p3 2 3 4
  • 25 KDa Alpha-2-Microglobulin-Related Subunit Of MMP-9 3 4
  • Neutrophil Gelatinase-Associated Lipocalin 2 3
  • Siderocalin LCN2 3 4
  • NGAL 3 4
  • P25 3 4
  • Migration-Stimulating Factor Inhibitor 3
  • Lipocalin 2 (Oncogene 24p3) 2
  • Siderocalin 2
  • Lipocalin-2 4
  • 24p3 3
  • MSFI 3
  • HNL 4

External Ids for LCN2 Gene

Previous GeneCards Identifiers for LCN2 Gene

  • GC09P122026
  • GC09P122558
  • GC09P124365
  • GC09P126287
  • GC09P127991
  • GC09P129951
  • GC09P130911
  • GC09P100525

Summaries for LCN2 Gene

Entrez Gene Summary for LCN2 Gene

  • This gene encodes a protein that belongs to the lipocalin family. Members of this family transport small hydrophobic molecules such as lipids, steroid hormones and retinoids. The protein encoded by this gene is a neutrophil gelatinase-associated lipocalin and plays a role in innate immunity by limiting bacterial growth as a result of sequestering iron-containing siderophores. The presence of this protein in blood and urine is an early biomarker of acute kidney injury. This protein is thought to be be involved in multiple cellular processes, including maintenance of skin homeostasis, and suppression of invasiveness and metastasis. Mice lacking this gene are more susceptible to bacterial infection than wild type mice. [provided by RefSeq, Sep 2015]

GeneCards Summary for LCN2 Gene

LCN2 (Lipocalin 2) is a Protein Coding gene. Diseases associated with LCN2 include Klebsiella Infection and Kidney Disease. Among its related pathways are Defensins and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include protein homodimerization activity and iron ion binding. An important paralog of this gene is LCN12.

UniProtKB/Swiss-Prot for LCN2 Gene

  • Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.

Gene Wiki entry for LCN2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCN2 Gene

Genomics for LCN2 Gene

Regulatory Elements for LCN2 Gene

Enhancers for LCN2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09G127962 2 FANTOM5 Ensembl ENCODE dbSUPER 10 -175.7 -175724 22.2 CREB3L1 FEZF1 DMAP1 YY1 ZNF263 SP3 NFYC TBX21 PPARGC1A MEF2D PIP5KL1 DPM2 SPOUT1 LOC101929270 ENSG00000227218 SLC25A25 NAIF1 ENSG00000230848 ODF2-AS1 CDK9
GH09G128070 1.7 FANTOM5 ENCODE dbSUPER 10.7 -76.2 -76240 4.9 HDGF FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 FOS DPM2 ENSG00000227218 LCN2 C9orf16 CIZ1 ENSG00000230536 SLC25A25-AS1 SLC25A25 TOR2A SH2D3C
GH09G128097 1.6 Ensembl ENCODE dbSUPER 11.3 -48.2 -48198 9.0 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 NAIF1 PTGES2 CIZ1 PTGES2-AS1 SLC25A25-AS1 SLC25A25 LCN2 C9orf16 DNM1 ENSG00000230536
GH09G128077 1.6 Ensembl ENCODE dbSUPER 10.7 -68.8 -68802 5.6 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 YY1 ZNF766 FOS ENSG00000230848 SLC25A25-AS1 DPM2 ENSG00000227218 LCN2 C9orf16 CIZ1 ENSG00000230536 NAIF1 GC09P128094
GH09G127951 1.6 Ensembl ENCODE dbSUPER 10.2 -194.6 -194587 5.4 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 ZNF766 PIP5KL1 SPOUT1 FAM102A ENSG00000230848 CDK9 PTRH1 LCN2 C9orf16 CIZ1 LOC101929270
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LCN2 on UCSC Golden Path with GeneCards custom track

Genomic Location for LCN2 Gene

Chromosome:
9
Start:
128,149,071 bp from pter
End:
128,153,455 bp from pter
Size:
4,385 bases
Orientation:
Plus strand

Genomic View for LCN2 Gene

Genes around LCN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCN2 Gene

Proteins for LCN2 Gene

  • Protein details for LCN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P80188-NGAL_HUMAN
    Recommended name:
    Neutrophil gelatinase-associated lipocalin
    Protein Accession:
    P80188
    Secondary Accessions:
    • A6NII8
    • B4DWV4
    • B7ZAA2
    • P30150
    • Q5SYV9
    • Q5SYW0
    • Q6FGL5
    • Q92683

    Protein attributes for LCN2 Gene

    Size:
    198 amino acids
    Molecular mass:
    22588 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Heterodimer; disulfide-linked with MMP9.
    SequenceCaution:
    • Sequence=CAI13824.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LCN2 Gene

    Alternative splice isoforms for LCN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LCN2 Gene

Post-translational modifications for LCN2 Gene

  • Glycosylation at posLast=8585
  • Modification sites at PhosphoSitePlus

Other Protein References for LCN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for LCN2 (Lipocalin-2/NGAL)
  • Cell Signaling Technology (CST) Antibodies for LCN2 (LCN2)

No data available for DME Specific Peptides for LCN2 Gene

Domains & Families for LCN2 Gene

Gene Families for LCN2 Gene

Suggested Antigen Peptide Sequences for LCN2 Gene

Graphical View of Domain Structure for InterPro Entry

P80188

UniProtKB/Swiss-Prot:

NGAL_HUMAN :
  • Belongs to the calycin superfamily. Lipocalin family.
Family:
  • Belongs to the calycin superfamily. Lipocalin family.
genes like me logo Genes that share domains with LCN2: view

Function for LCN2 Gene

Molecular function for LCN2 Gene

GENATLAS Biochemistry:
neutrophil gelatinase-associated lipocalin 2,25kDa,found at moderate levels,only in breast and lung,component of human tear (lipophilic ligand carrier protein superfamily,lipocalin family,Kernel group),modulator of inflammation,involved in the transport of hydrophobic ligands
UniProtKB/Swiss-Prot Function:
Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.
UniProtKB/Swiss-Prot Induction:
Expression is activated by the oncoprotein BCR-ABL; BCR-ABL misregulates expression via the JAK/STAT pathway and binding of STAT5A to the promoter.

Gene Ontology (GO) - Molecular Function for LCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002020 protease binding IEA --
GO:0005215 transporter activity IEA --
GO:0005506 iron ion binding ISS --
GO:0036094 small molecule binding IEA --
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with LCN2: view
genes like me logo Genes that share phenotypes with LCN2: view

Animal Models for LCN2 Gene

MGI Knock Outs for LCN2:

Animal Model Products

  • Taconic Biosciences Mouse Models for LCN2

CRISPR Products

miRNA for LCN2 Gene

miRTarBase miRNAs that target LCN2

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for LCN2

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LCN2 Gene

Localization for LCN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCN2 Gene

Secreted. Note=Upon binding to the SLC22A17 (24p3R) receptor, it is internalized.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCN2 gene
Compartment Confidence
extracellular 5
cytosol 3
cytoskeleton 2
mitochondrion 2
nucleus 2
plasma membrane 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS,IEA --
GO:0005615 extracellular space IDA 16502470
GO:0005829 cytosol IEA --
GO:0035580 specific granule lumen TAS --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with LCN2: view

Pathways & Interactions for LCN2 Gene

genes like me logo Genes that share pathways with LCN2: view

Pathways by source for LCN2 Gene

1 KEGG pathway for LCN2 Gene

Gene Ontology (GO) - Biological Process for LCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006879 cellular iron ion homeostasis TAS --
GO:0006915 apoptotic process IEA --
genes like me logo Genes that share ontologies with LCN2: view

No data available for SIGNOR curated interactions for LCN2 Gene

Drugs & Compounds for LCN2 Gene

(25) Drugs for LCN2 Gene - From: DrugBank, ClinicalTrials, ApexBio, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin A Approved, Vet_approved Nutra 492
2,3,-Dihydroxybenzoylserine Experimental Pharma Target 0
2,3-Dihydroxy-Benzoic Acid Experimental Pharma Target 0
Carboxymycobactin S Experimental Pharma Target 0
Carboxymycobactin T Experimental Pharma Target 0

(11) Additional Compounds for LCN2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(1) ApexBio Compounds for LCN2 Gene

Compound Action Cas Number
SB-3CT gelatinases inhibitor, potent and selective 292605-14-2
genes like me logo Genes that share compounds with LCN2: view

Transcripts for LCN2 Gene

Unigene Clusters for LCN2 Gene

Lipocalin 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for LCN2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCN2 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8
SP1: - - - - - -
SP2: - - -
SP3: - - - -
SP4: - - - - - - - - - - -
SP5:
SP6: -
SP7: - -

Relevant External Links for LCN2 Gene

GeneLoc Exon Structure for
LCN2
ECgene alternative splicing isoforms for
LCN2

Expression for LCN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LCN2 Gene

This gene is overexpressed in Whole Blood (x12.3), Minor Salivary Gland (x10.8), Esophagus - Mucosa (x7.7), Vagina (x4.7), and Stomach (x4.3).

Protein differential expression in normal tissues from HIPED for LCN2 Gene

This gene is overexpressed in Neutrophil (31.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LCN2 Gene



NURSA nuclear receptor signaling pathways regulating expression of LCN2 Gene:

LCN2

SOURCE GeneReport for Unigene cluster for LCN2 Gene:

Hs.204238

mRNA Expression by UniProt/SwissProt for LCN2 Gene:

P80188-NGAL_HUMAN
Tissue specificity: Expressed in bone marrow and in tissues that are prone to exposure to microorganism. High expression is found in bone marrow as well as in uterus, prostate, salivary gland, stomach, appendix, colon, trachea and lung. Not found in the small intestine or peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for LCN2 Gene

  • Blood(4.8)
  • Pancreas(4.8)
  • Bone marrow(4.7)
  • Liver(4.5)
  • Saliva(4.1)
  • Intestine(3.8)
  • Kidney(3.6)
  • Urine(3.4)
  • Gall bladder(3)
  • Stomach(3)
  • Lung(2.8)
  • Heart(2.2)
  • Skin(2.2)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with LCN2: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCN2 Gene

Orthologs for LCN2 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LCN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LCN2 34 35
  • 99.33 (n)
dog
(Canis familiaris)
Mammalia LCN2 34 35
  • 77.72 (n)
cow
(Bos Taurus)
Mammalia LCN2 34 35
  • 77.33 (n)
mouse
(Mus musculus)
Mammalia Lcn2 34 16 35
  • 72.25 (n)
rat
(Rattus norvegicus)
Mammalia Lcn2 34
  • 71.32 (n)
oppossum
(Monodelphis domestica)
Mammalia LCN2 35
  • 41 (a)
OneToOne
Species where no ortholog for LCN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LCN2 Gene

ENSEMBL:
Gene Tree for LCN2 (if available)
TreeFam:
Gene Tree for LCN2 (if available)

Paralogs for LCN2 Gene

Paralogs for LCN2 Gene

(2) SIMAP similar genes for LCN2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LCN2: view

Variants for LCN2 Gene

Sequence variations from dbSNP and Humsavar for LCN2 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000597275 -- 128,149,840(+) CCCCC(A/C)ATCCC intron-variant
rs1000705447 -- 128,149,277(+) ACTCC(A/G)GGAAT upstream-variant-2KB
rs1000781104 -- 128,148,009(+) GCAGA(G/T)GATAC upstream-variant-2KB
rs1001390633 -- 128,153,281(+) CCCCA(C/G)CCATC intron-variant
rs1001627576 -- 128,148,358(+) CGTTA(G/T)TCCCA upstream-variant-2KB

Variation tolerance for LCN2 Gene

Residual Variation Intolerance Score: 89.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.32; 26.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LCN2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCN2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LCN2 Gene

Disorders for LCN2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for LCN2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
klebsiella infection
  • klebsiella
kidney disease
  • nephropathy
transient cerebral ischemia
  • tia
urinary system disease
  • non-neoplastic urinary tract disease
asthenopia
  • accommodative strain
- elite association - COSMIC cancer census association via MalaCards
Search LCN2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LCN2

Genetic Association Database (GAD)
LCN2
Human Genome Epidemiology (HuGE) Navigator
LCN2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LCN2
genes like me logo Genes that share disorders with LCN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCN2 Gene

Publications for LCN2 Gene

  1. Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin. (PMID: 10684642) Goetz D.H. … Strong R.K. (Biochemistry 2000) 3 4 22 64
  2. Molecular cloning and expression of a cDNA encoding NGAL: a lipocalin expressed in human neutrophils. (PMID: 8060329) Bundgaard J.R. … Kjeldsen L. (Biochem. Biophys. Res. Commun. 1994) 3 4 22 64
  3. Isolation and primary structure of NGAL, a novel protein associated with human neutrophil gelatinase. (PMID: 7683678) Kjeldsen L. … Borregaard N. (J. Biol. Chem. 1993) 2 3 4 64
  4. Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection. (PMID: 20587610) Ucisik-Akkaya E. … Dorak M.T. (Mol. Hum. Reprod. 2010) 3 46 64
  5. Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot". (PMID: 20628624) Johnatty S.E. … . (PLoS Genet. 2010) 3 46 64

Products for LCN2 Gene

  • Addgene plasmids for LCN2

Sources for LCN2 Gene

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