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    LCN8 lipocalin 8 [ Homo sapiens (human) ]

    Gene ID: 138307, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LCN8provided by HGNC
    Official Full Name
    lipocalin 8provided by HGNC
    Primary source
    HGNC:HGNC:27038
    See related
    Ensembl:ENSG00000204001 MIM:612902; AllianceGenome:HGNC:27038
    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
    EP17; LCN5
    Summary
    Members of the lipocalin family, such as LCN8, 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 LCN8 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136754386..136758543, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148987564..148991721, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139648838..139652995, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene lipocalin 10 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 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139657693-139658340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29326 Neighboring gene uncharacterized LOC107987143

    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. Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB. Li FL, et al. EMBO J, 2022 Sep 1. PMID 35844135, Free PMC Article
    4. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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 small molecule binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in response to hormone 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-8
    Names
    epididymis secretory sperm binding protein
    lipocalin 5

    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_001345934.2 → NP_001332863.1  epididymal-specific lipocalin-8 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK090647, AL355987, AY301268
      Consensus CDS
      CCDS87717.1
      UniProtKB/Swiss-Prot
      A1L4A8, A6NMN9, Q5T5R4, Q6JVE9
      Related
      ENSP00000482512.1, ENST00000612714.1

    2. NM_178469.4 → NP_848564.2  epididymal-specific lipocalin-8 isoform 2

      See identical proteins and their annotated locations for NP_848564.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK126902, AL355987, BC042109
      Consensus CDS
      CCDS35183.1
      UniProtKB/TrEMBL
      A0A384MDK0
      Related
      ENSP00000360753.3, ENST00000371688.8
      Conserved Domains (1) summary
      pfam00061
      Location:11 → 134
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    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
      136754386..136758543 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014272.3 → XP_016869761.1  epididymal-specific lipocalin-8 isoform X1

    RNA

    1. XR_007061246.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      148987564..148991721 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361981.1 → XP_054217956.1  epididymal-specific lipocalin-8 isoform X1

    RNA

    1. XR_008487941.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6JVE9.1 GenPept UniProtKB/Swiss-Prot:Q6JVE9

    Gene LinkOut

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

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