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    LCN1 lipocalin 1 [ Homo sapiens (human) ]

    Gene ID: 3933, updated on 12-May-2017
    Official Symbol
    LCN1provided by HGNC
    Official Full Name
    lipocalin 1provided by HGNC
    Primary source
    HGNC:HGNC:6525
    See related
    Ensembl:ENSG00000160349 MIM:151675; Vega:OTTHUMG00000020908
    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]
    Orthologs
    Location:
    9q34.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    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 
    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 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    sensory perception of taste IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    lipocalin-1
    Names
    VEG protein
    Von Ebner gland protein
    protein migrating faster than albumin
    tear prealbumin

    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, OTTHUMP00000022539, ENST00000263598.6, OTTHUMT00000054992
      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, OTTHUMP00000022540, ENST00000371781.3, OTTHUMT00000054993
      Conserved Domains (1) summary
      pfam00061
      Location:32169
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 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

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      138561863..138566965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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