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    LCN10 lipocalin 10 [ Homo sapiens (human) ]

    Gene ID: 414332, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LCN10provided by HGNC
    Official Full Name
    lipocalin 10provided by HGNC
    Primary source
    HGNC:HGNC:20892
    See related
    Ensembl:ENSG00000187922 MIM:612904; AllianceGenome:HGNC:20892
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Members of the lipocalin family, such as LCN10, have a common structure consisting of an 8-stranded antiparallel beta-barrel that forms a cup-shaped ligand-binding pocket or calyx. Lipocalins generally bind small hydrophobic ligands and transport them to specific cells (Suzuki et al., 2004 [PubMed 15363845]).[supplied by OMIM, Aug 2009]
    Expression
    Broad expression in spleen (RPKM 4.2), endometrium (RPKM 3.9) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LCN10 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136738170..136742940, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148971348..148976118, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139632622..139637392, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene cuticle collagen 2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20538 Neighboring gene small nucleolar RNA, H/ACA box 17B Neighboring gene small nucleolar RNA host gene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139623217-139623386 Neighboring gene small nucleolar RNA, H/ACA box 17A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139627044-139627888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139629713-139630212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20539 Neighboring gene uncharacterized LOC100128593 Neighboring gene lipocalin 6 Neighboring gene microRNA 6722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29324 Neighboring gene lipocalin 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Lipocalin 10 as a New Prognostic Biomarker in Sepsis-Induced Myocardial Dysfunction and Mortality: A Pilot Study. Wang L, et al. Mediators Inflamm, 2021. PMID 34121925, Free PMC Article
    2. Lipocalin 10 is essential for protection against inflammation-triggered vascular leakage by activating LDL receptor-related protein 2-slingshot homologue 1 signalling pathway. Zhao H, et al. Cardiovasc Res, 2023 Aug 19. PMID 37392461, Free PMC Article
    3. Loss of Lipocalin 10 Exacerbates Diabetes-Induced Cardiomyopathy via Disruption of Nr4a1-Mediated Anti-Inflammatory Response in Macrophages. Li Q, et al. Front Immunol, 2022. PMID 35757735, Free PMC Article
    4. Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2. Suzuki K, et al. Gene, 2004 Sep 15. PMID 15363845
    5. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Bartolec TK, et al. Proc Natl Acad Sci U S A, 2023 Apr 25. PMID 37071682, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lipocalin 10 is essential for protection against inflammation-triggered vascular leakage by activating LDL receptor-related protein 2-slingshot homologue 1 signalling pathway.
      Title: Lipocalin 10 is essential for protection against inflammation-triggered vascular leakage by activating LDL receptor-related protein 2-slingshot homologue 1 signalling pathway.
    2. Loss of Lipocalin 10 Exacerbates Diabetes-Induced Cardiomyopathy via Disruption of Nr4a1-Mediated Anti-Inflammatory Response in Macrophages.
      Title: Loss of Lipocalin 10 Exacerbates Diabetes-Induced Cardiomyopathy via Disruption of Nr4a1-Mediated Anti-Inflammatory Response in Macrophages.
    3. Lipocalin 10 as a New Prognostic Biomarker in Sepsis-Induced Myocardial Dysfunction and Mortality: A Pilot Study.
      Title: Lipocalin 10 as a New Prognostic Biomarker in Sepsis-Induced Myocardial Dysfunction and Mortality: A Pilot Study.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: LCN6

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables small molecule binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    epididymal-specific lipocalin-10

    NCBI Reference Sequences (RefSeq)

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    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_001001712.3 → NP_001001712.2  epididymal-specific lipocalin-10 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001001712.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL355987
      Consensus CDS
      CCDS35182.2
      UniProtKB/TrEMBL
      B7ZMD1
      Related
      ENSP00000418491.1, ENST00000497771.6

    2. NM_001368089.1 → NP_001355018.1  epididymal-specific lipocalin-10 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL355987, AY301271
      Consensus CDS
      CCDS94536.1
      UniProtKB/Swiss-Prot
      A2RUU3, B0QZ79, Q6JVE6
      Related
      ENSP00000420564.1, ENST00000474369.1

    3. NM_001368090.1 → NP_001355019.1  epididymal-specific lipocalin-10 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      AL355987, BC144441
      Consensus CDS
      CCDS94537.1
      UniProtKB/TrEMBL
      B7ZMD1, E9PK15
      Related
      ENSP00000431726.1, ENST00000527229.5
      Conserved Domains (1) summary
      cl10502
      Location:36 → 108
      lipocalin_FABP; lipocalin/cytosolic fatty acid-binding protein family

    RNA

    1. NR_160514.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355987, BC171741

    2. NR_160515.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355987, HY166769

    3. NR_160516.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355987, DA965366

    4. NR_160517.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL355987
      Related
      ENST00000341040.11

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      136738170..136742940 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      148971348..148976118 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6JVE6.1 GenPept UniProtKB/Swiss-Prot:Q6JVE6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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