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    LCN9 lipocalin 9 [ Homo sapiens (human) ]

    Gene ID: 392399, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LCN9provided by HGNC
    Official Full Name
    lipocalin 9provided by HGNC
    Primary source
    HGNC:HGNC:17442
    See related
    Ensembl:ENSG00000148386 MIM:612903; AllianceGenome:HGNC:17442
    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
    Also known as
    HEL129
    Summary
    Members of the lipocalin family, such as LCN9, 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
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See LCN9 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 (135663309..135666961)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (147889683..147893335)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (138555155..138558807)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene lipocalin 1-like Neighboring gene glycosyltransferase 6 domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138553165-138553666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138558544-138559044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138559045-138559545 Neighboring gene uncharacterized LOC105376317 Neighboring gene uncharacterized LOC105376318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138586423-138586937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20488 Neighboring gene spermatogenesis and oogenesis specific basic helix-loop-helix 1

    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. Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2. Suzuki K, et al. Gene, 2004 Sep 15. PMID 15363845
    2. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
    3. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
    4. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small molecule binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    epididymal-specific lipocalin-9
    Names
    MUP-like lipocalin
    epididymis luminal protein 129

    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_001393661.1 → NP_001380590.1  epididymal-specific lipocalin-9 precursor

      Status: VALIDATED

      Source sequence(s)
      AL158822
      Consensus CDS
      CCDS94528.1
      UniProtKB/TrEMBL
      A0AAA9WZE8
      Related
      ENSP00000482296.2, ENST00000619315.2
      Conserved Domains (1) summary
      cl10502
      Location:21 → 139
      lipocalin_FABP; lipocalin/cytosolic fatty acid-binding protein family

    RNA

    1. NR_171893.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL158822
      Related
      ENST00000277526.8

    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
      135663309..135666961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      147889683..147893335
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001001676.1: Suppressed sequence

      Description
      NM_001001676.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WX39.3 GenPept UniProtKB/Swiss-Prot:Q8WX39

    Gene LinkOut

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

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