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LCN8 lipocalin 8 [ Homo sapiens (human) ]

Gene ID: 138307, updated on 5-Mar-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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Location:
9q34.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136754386..136758543, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148987564..148991721, complement)
105.20220307 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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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)

Genotypes

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_2023_10

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

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