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LCN1 lipocalin 1 [ Homo sapiens (human) ]

Gene ID: 3933, updated on 13-Feb-2019

Summary

Official Symbol
LCN1provided by HGNC
Official Full Name
lipocalin 1provided by HGNC
Primary source
HGNC:HGNC:6525
See related
Ensembl:ENSG00000160349 MIM:151675
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
TP; TLC; PMFA; VEGP
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See LCN1 in Genome Data Viewer
Location:
9q34.3
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (135521296..135526540)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (138413284..138418386)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene chromosome 9 open reading frame 116 Neighboring gene uncharacterized LOC101928525 Neighboring gene mitochondrial ribosomal protein S2 Neighboring gene odorant binding protein 2A Neighboring gene uncharacterized LOC107987040

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC71975

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chloride ion binding IDA
Inferred from Direct Assay
more info
PubMed 
cysteine-type endopeptidase inhibitor activity TAS
Traceable Author Statement
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
small molecule binding IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
long-chain fatty acid transport TAS
Traceable Author Statement
more info
 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
proteolysis TAS
Traceable Author Statement
more info
PubMed 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
retina homeostasis HEP PubMed 
sensory perception of taste IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lipocalin-1
Names
VEG protein
Von Ebner gland protein
protein migrating faster than albumin
tear prealbumin

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_001252617.1NP_001239546.1  lipocalin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001239546.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    CK429694, CK431106, M90424
    Consensus CDS
    CCDS6991.1
    UniProtKB/Swiss-Prot
    P31025
    UniProtKB/TrEMBL
    A0A024R8D7
    Related
    ENSP00000263598.2, ENST00000263598.6
    Conserved Domains (1) summary
    pfam00061
    Location:32169
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  2. NM_001252618.1NP_001239547.1  lipocalin-1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, which results in a translational frameshift, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    CD721968, CK431106, M90424
    UniProtKB/Swiss-Prot
    P31025
    Conserved Domains (1) summary
    pfam00061
    Location:32135
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  3. NM_001252619.1NP_001239548.1  lipocalin-1 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region, which results in a translational frameshift, compared to variant 1. The encoded isoform (3) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    CK430667, CK431106, M90424
    UniProtKB/Swiss-Prot
    P31025
    Conserved Domains (1) summary
    pfam00061
    Location:32132
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
  4. NM_002297.3NP_002288.1  lipocalin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002288.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the shortest isoform (1). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    CK431106, M90424, X62418
    Consensus CDS
    CCDS6991.1
    UniProtKB/Swiss-Prot
    P31025
    UniProtKB/TrEMBL
    A0A024R8D7
    Related
    ENSP00000360846.3, ENST00000371781.3
    Conserved Domains (1) summary
    pfam00061
    Location:32169
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    135521296..135526540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518675.2XP_011516977.1  lipocalin-1 isoform X1

    Conserved Domains (1) summary
    pfam00061
    Location:96233
    Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family
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