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LCN2 lipocalin 2 [ Homo sapiens (human) ]

Gene ID: 3934, updated on 4-Dec-2019

Summary

Official Symbol
LCN2provided by HGNC
Official Full Name
lipocalin 2provided by HGNC
Primary source
HGNC:HGNC:6526
See related
Ensembl:ENSG00000148346 MIM:600181
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p25; 24p3; MSFI; NGAL
Summary
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]
Expression
Biased expression in gall bladder (RPKM 1027.2), bone marrow (RPKM 834.0) and 5 other tissues See more
Orthologs

Genomic context

See LCN2 in Genome Data Viewer
Location:
9q34.11
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (128149453..128153453)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130911732..130915734)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene prostaglandin E synthase 2 Neighboring gene PTGES2 antisense RNA 1 (head to head) Neighboring gene chromosome 9 open reading frame 16 Neighboring gene CDKN1A interacting zinc finger protein 1 Neighboring gene dynamin 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • Antimicrobial peptides, organism-specific biosystem (from REACTOME)
    Antimicrobial peptides, organism-specific biosystemAntimicrobial peptides (AMPs) are small molecular weight proteins with broad spectrum of antimicrobial activity against bacteria, viruses, and fungi (Zasloff M 2002; Radek K & Gallo R 2007). The majo...
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • IL-17 signaling pathway, organism-specific biosystem (from KEGG)
    IL-17 signaling pathway, organism-specific biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • IL-17 signaling pathway, conserved biosystem (from KEGG)
    IL-17 signaling pathway, conserved biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Interleukin-4 and 13 signaling, organism-specific biosystem (from REACTOME)
    Interleukin-4 and 13 signaling, organism-specific biosystemInterleukin-4 (IL4) is a principal regulatory cytokine during the immune response, crucially important in allergy and asthma (Nelms et al. 1999). When resting T cells are antigen-activated and expand...
  • Iron uptake and transport, organism-specific biosystem (from REACTOME)
    Iron uptake and transport, organism-specific biosystemThe transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell ...
  • Metal sequestration by antimicrobial proteins, organism-specific biosystem (from REACTOME)
    Metal sequestration by antimicrobial proteins, organism-specific biosystemMetals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et...
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
    Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enterobactin binding IDA
Inferred from Direct Assay
more info
PubMed 
iron ion binding IDA
Inferred from Direct Assay
more info
PubMed 
iron ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protease binding IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
small molecule binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
antimicrobial humoral response TAS
Traceable Author Statement
more info
 
cellular iron ion homeostasis TAS
Traceable Author Statement
more info
 
cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
cellular response to interleukin-1 IEA
Inferred from Electronic Annotation
more info
 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
cellular response to nutrient levels IEA
Inferred from Electronic Annotation
more info
 
cellular response to tumor necrosis factor IEA
Inferred from Electronic Annotation
more info
 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
defense response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
extrinsic apoptotic signaling pathway in absence of ligand IEA
Inferred from Electronic Annotation
more info
 
innate immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of cell projection organization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
protein homotrimerization IEA
Inferred from Electronic Annotation
more info
 
response to herbicide IEA
Inferred from Electronic Annotation
more info
 
response to mycotoxin IEA
Inferred from Electronic Annotation
more info
 
response to virus IEA
Inferred from Electronic Annotation
more info
 
sequestering of iron ion IDA
Inferred from Direct Assay
more info
PubMed 
siderophore transport ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extracellular region HDA PubMed 
extracellular region ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
specific granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
neutrophil gelatinase-associated lipocalin
Names
25 kDa alpha-2-microglobulin-related subunit of MMP-9
migration-stimulating factor inhibitor
oncogene 24p3
siderocalin LCN2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_005564.5NP_005555.2  neutrophil gelatinase-associated lipocalin precursor

    See identical proteins and their annotated locations for NP_005555.2

    Status: REVIEWED

    Source sequence(s)
    BC033089, BM977724, BX644845
    Consensus CDS
    CCDS6892.1
    UniProtKB/Swiss-Prot
    P80188
    Related
    ENSP00000277480.2, ENST00000277480.7
    Conserved Domains (1) summary
    pfam00061
    Location:49193
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    128149453..128153453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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