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    Lcn2 lipocalin 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 170496, updated on 9-Dec-2024

    Summary

    Official Symbol
    Lcn2provided by RGD
    Official Full Name
    lipocalin 2provided by RGD
    Primary source
    RGD:69408
    See related
    EnsemblRapid:ENSRNOG00000013973 AllianceGenome:RGD:69408
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Sip24
    Summary
    Enables enterobactin binding activity; identical protein binding activity; and protease binding activity. Involved in several processes, including cellular response to cytokine stimulus; memory; and regulation of hippocampal neuron apoptotic process. Located in extracellular space. Used to study intrahepatic cholangiocarcinoma and retinal degeneration. Biomarker of several diseases, including acute kidney failure; congenital diaphragmatic hernia; obesity; transient cerebral ischemia; and traumatic brain injury. Human ortholog(s) of this gene implicated in urinary tract infection. Orthologous to human LCN2 (lipocalin 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 27.4), Lung (RPKM 18.2) and 8 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Lcn2 in Genome Data Viewer
    Location:
    3p12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (36078432..36081851, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (15680688..15684033, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (11414189..11417534, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486070 Neighboring gene CDKN1A interacting zinc finger protein 1 Neighboring gene bublin coiled coil protein Neighboring gene uncharacterized LOC120101523 Neighboring gene prostaglandin E synthase 2 Neighboring gene solute carrier family 25 member 25 Neighboring gene nuclear apoptosis inducing factor 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables enterobactin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables enterobactin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables enterobactin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables iron ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables iron ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables iron ion sequestering activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables iron ion sequestering activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protease binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small molecule binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in acute-phase response IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to X-ray IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to amyloid-beta IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to hydrogen peroxide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to increased oxygen levels IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to interleukin-1 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to interleukin-6 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to nerve growth factor stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to nutrient levels IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to tumor necrosis factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in defense response to bacterium ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in defense response to bacterium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within extrinsic apoptotic signaling pathway in absence of ligand ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in innate immune response ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in innate immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in long-term memory IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of hippocampal neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of cell projection organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cold-induced thermogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endothelial tube morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of hippocampal neuron apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of iron ion import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of reactive oxygen species biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of reactive oxygen species metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to bacterium IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within response to bacterium ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to blue light IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to fructose IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to herbicide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to iron(II) ion IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to kainic acid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to mycotoxin IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to nutrient levels IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to oxidative stress IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to toxic substance IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within response to virus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to xenobiotic stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to xenobiotic stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in short-term memory IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in siderophore transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in siderophore transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle lumen IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular region ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    neutrophil gelatinase-associated lipocalin
    Names
    NGAL
    alpha-2-microglobulin-related protein
    alpha-2U globulin-related protein
    lipocalin 2 (oncogene 24p3)
    lipocalin 24p3
    p25
    siderocalin LCN2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_130741.2NP_570097.2  neutrophil gelatinase-associated lipocalin precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/Swiss-Prot
      P30152, Q5HZF1
      UniProtKB/TrEMBL
      A6JU59
      Related
      ENSRNOP00000018776.3, ENSRNOT00000018776.7

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      36078432..36081851 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063283026.1XP_063139096.1  neutrophil gelatinase-associated lipocalin isoform X2

    2. XM_063283025.1XP_063139095.1  neutrophil gelatinase-associated lipocalin isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZNE2