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Aliases for LCN1 Gene

Aliases for LCN1 Gene

  • Lipocalin 1 2 3 5
  • Von Ebner Gland Protein 2 3 4
  • Tear Prealbumin 2 3 4
  • Lipocalin 1 (Tear Prealbumin) 2 3
  • Tear Lipocalin 2 4
  • VEG Protein 3 4
  • VEGP 3 4
  • TLC 3 4
  • TP 3 4
  • Lipocalin 1 (Protein Migrating Faster Than Albumin, Tear Prealbumin) 2
  • Protein Migrating Faster Than Albumin 3
  • Lipocalin 1-Like 2 2
  • PMFA 3

External Ids for LCN1 Gene

Previous GeneCards Identifiers for LCN1 Gene

  • GC09P127140
  • GC09P130184
  • GC09P131936
  • GC09P133852
  • GC09P135639
  • GC09P137553
  • GC09P138413
  • GC09P107875

Summaries for LCN1 Gene

Entrez Gene Summary for LCN1 Gene

  • This gene encodes a member of the lipocalin family of small secretory proteins. Lipocalins are extracellular transport proteins that bind to a variety of hydrophobic ligands. The encoded protein is the primary lipid binding protein in tears and is overproduced in response to multiple stimuli including infection and stress. The encoded protein may be a marker for chromosome aneuploidy as well as an autoantigen in Sjogren's syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and two pseudogenes of this gene are also located on the long arm of chromosome 9. [provided by RefSeq, Nov 2011]

GeneCards Summary for LCN1 Gene

LCN1 (Lipocalin 1) is a Protein Coding gene. Diseases associated with LCN1 include stromal keratitis and lacrimal apparatus disease. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Transport of vitamins, nucleosides, and related molecules. GO annotations related to this gene include cysteine-type endopeptidase inhibitor activity. An important paralog of this gene is OBP2A.

UniProtKB/Swiss-Prot for LCN1 Gene

  • Could play a role in taste reception. Could be necessary for the concentration and delivery of sapid molecules in the gustatory system. Can bind various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampicin and even to microbial siderophores. Exhibits an extremely wide ligand pocket.

Gene Wiki entry for LCN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCN1 Gene

Genomics for LCN1 Gene

Regulatory Elements for LCN1 Gene

Genomic Location for LCN1 Gene

Chromosome:
9
Start:
135,521,297 bp from pter
End:
135,526,540 bp from pter
Size:
5,244 bases
Orientation:
Plus strand

Genomic View for LCN1 Gene

Genes around LCN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCN1 Gene

Proteins for LCN1 Gene

  • Protein details for LCN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P31025-LCN1_HUMAN
    Recommended name:
    Lipocalin-1
    Protein Accession:
    P31025
    Secondary Accessions:
    • Q5T8A1

    Protein attributes for LCN1 Gene

    Size:
    176 amino acids
    Molecular mass:
    19250 Da
    Quaternary structure:
    • Homodimer (By similarity). Binds to LMBR1L which may mediate its endocytosis.

    Three dimensional structures from OCA and Proteopedia for LCN1 Gene

neXtProt entry for LCN1 Gene

Proteomics data for LCN1 Gene at MOPED

Post-translational modifications for LCN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LCN1 Gene

Antibody Products

No data available for DME Specific Peptides for LCN1 Gene

Domains & Families for LCN1 Gene

Gene Families for LCN1 Gene

Suggested Antigen Peptide Sequences for LCN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P31025

UniProtKB/Swiss-Prot:

LCN1_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 LCN1: view

Function for LCN1 Gene

Molecular function for LCN1 Gene

GENATLAS Biochemistry:
lipocalin 1,component of human tear,expressed by lacrymal,salivary glands,trachea and of nasal mucus (lipophilic ligand carrier protein superfamily,lipocalin family,Kernel group) involved in the transport of hydrophobic ligands
UniProtKB/Swiss-Prot Function:
Could play a role in taste reception. Could be necessary for the concentration and delivery of sapid molecules in the gustatory system. Can bind various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampicin and even to microbial siderophores. Exhibits an extremely wide ligand pocket.

Phenotypes for LCN1 Gene

genes like me logo Genes that share phenotypes with LCN1: view

Animal Model Products

miRNA for LCN1 Gene

miRTarBase miRNAs that target LCN1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LCN1 Gene

Localization for LCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCN1 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LCN1 Gene COMPARTMENTS Subcellular localization image for LCN1 gene
Compartment Confidence
extracellular 5

Gene Ontology (GO) - Cellular Components for LCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with LCN1: view

Pathways & Interactions for LCN1 Gene

genes like me logo Genes that share pathways with LCN1: view

Gene Ontology (GO) - Biological Process for LCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001895 retina homeostasis IEP 23580065
GO:0010951 negative regulation of endopeptidase activity TAS 8999869
GO:0015909 long-chain fatty acid transport TAS --
GO:0050909 sensory perception of taste IEA --
genes like me logo Genes that share ontologies with LCN1: view

No data available for SIGNOR curated interactions for LCN1 Gene

Drugs & Compounds for LCN1 Gene

(12) Drugs for LCN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(11) Additional Compounds for LCN1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LCN1: view

Transcripts for LCN1 Gene

Unigene Clusters for LCN1 Gene

Lipocalin 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LCN1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5
SP1: -
SP2: - -
SP3: -
SP4:

Relevant External Links for LCN1 Gene

GeneLoc Exon Structure for
LCN1
ECgene alternative splicing isoforms for
LCN1

Expression for LCN1 Gene

mRNA expression in normal human tissues for LCN1 Gene

mRNA differential expression in normal tissues according to GTEx for LCN1 Gene

This gene is overexpressed in Esophagus - Mucosa (x31.8) and Pituitary (x7.1).

Protein differential expression in normal tissues from HIPED for LCN1 Gene

This gene is overexpressed in Saliva (54.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LCN1 Gene



SOURCE GeneReport for Unigene cluster for LCN1 Gene Hs.530311

mRNA Expression by UniProt/SwissProt for LCN1 Gene

P31025-LCN1_HUMAN
Tissue specificity: Mainly expressed in lachrymal and salivary glands. Also expressed in the prostate.
genes like me logo Genes that share expression patterns with LCN1: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for LCN1 Gene

Orthologs for LCN1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LCN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LCN1 35
  • 99.05 (n)
  • 98.3 (a)
LCN1 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LCN1 36
  • 52 (a)
OneToOne
LOC511158 35
  • 70.33 (n)
  • 53.18 (a)
dog
(Canis familiaris)
Mammalia LCN1 35
  • 72.67 (n)
  • 58.14 (a)
LCN1 36
  • 56 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lcn3 36
  • 37 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 31 (a)
ManyToMany
-- 36
  • 39 (a)
ManyToMany
-- 36
  • 32 (a)
ManyToMany
-- 36
  • 31 (a)
ManyToMany
-- 36
  • 37 (a)
ManyToMany
-- 36
  • 32 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 26 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Vegp2 35
  • 72.95 (n)
  • 61.14 (a)
Species with no ortholog for LCN1:
  • 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)
  • 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 LCN1 Gene

ENSEMBL:
Gene Tree for LCN1 (if available)
TreeFam:
Gene Tree for LCN1 (if available)

Paralogs for LCN1 Gene

Paralogs for LCN1 Gene

(4) SIMAP similar genes for LCN1 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for LCN1 Gene

genes like me logo Genes that share paralogs with LCN1: view

Variants for LCN1 Gene

Sequence variations from dbSNP and Humsavar for LCN1 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs3827832 -- 135,522,988(+) GGGGG(G/T)TTGGG intron-variant
rs34145173 -- 135,524,587(+) CACTC(C/T)GGGAG intron-variant
rs12379612 -- 135,525,791(+) AGAGG(C/T)TGGAG intron-variant
rs55884352 -- 135,523,894(+) AGCAC(A/G/T)TGGCA reference, missense
rs35905708 -- 135,522,949(+) GCAGC(C/T)TGGGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LCN1 Gene

Variant ID Type Subtype PubMed ID
esv2739138 CNV Deletion 23290073
nsv894247 CNV Gain 21882294
dgv8366n71 CNV Loss 21882294
dgv8367n71 CNV Loss 21882294
nsv894253 CNV Loss 21882294
nsv466656 CNV Gain 19166990

Variation tolerance for LCN1 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LCN1 Gene

HapMap Linkage Disequilibrium report
LCN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCN1 Gene

Disorders for LCN1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LCN1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
stromal keratitis
lacrimal apparatus disease
  • lacrimal apparatus diseases
pulmonary large cell neuroendocrine carcinoma
  • large cell lung neuroendocrine carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search LCN1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LCN1

Genetic Association Database (GAD)
LCN1
Human Genome Epidemiology (HuGE) Navigator
LCN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LCN1
genes like me logo Genes that share disorders with LCN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCN1 Gene

Publications for LCN1 Gene

  1. The 1.8-A crystal structure of human tear lipocalin reveals an extended branched cavity with capacity for multiple ligands. (PMID: 15489503) Breustedt D.A. … Skerra A. (J. Biol. Chem. 2005) 3 4 23 67
  2. Assignment of the human tear lipocalin gene (LCN1) to 9q34 by in situ hybridization. (PMID: 8276406) Lassagne H. … Gachon A.M. (Genomics 1993) 2 3 23
  3. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity. (PMID: 19770509) Breustedt D.A. … Skerra A. (Acta Crystallogr. D Biol. Crystallogr. 2009) 3 23
  4. Oligomeric state of lipocalin-1 (LCN1) by multiangle laser light scattering and fluorescence anisotropy decay. (PMID: 17869594) Gasymov O.K. … Glasgow B.J. (Biochim. Biophys. Acta 2007) 3 23
  5. Evidence for internal and external binding sites on human tear lipocalin. (PMID: 17945179) Gasymov O.K. … Glasgow B.J. (Arch. Biochem. Biophys. 2007) 3 23

Products for LCN1 Gene

Sources for LCN1 Gene

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