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LCN9 lipocalin 9 [ Homo sapiens (human) ]

Gene ID: 392399, updated on 5-Mar-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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Location:
9q34.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (135663309..135666961)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (147889683..147893335)
105.20220307 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)

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 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
    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_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
    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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