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    LCN12 lipocalin 12 [ Homo sapiens (human) ]

    Gene ID: 286256, updated on 17-Jun-2024

    Summary

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    Official Symbol
    LCN12provided by HGNC
    Official Full Name
    lipocalin 12provided by HGNC
    Primary source
    HGNC:HGNC:28733
    See related
    Ensembl:ENSG00000184925 MIM:612905; AllianceGenome:HGNC:28733
    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 LCN12, 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
    Biased expression in thyroid (RPKM 11.7), spleen (RPKM 1.8) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LCN12 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136949197..136956538)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149183558..149189824)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139846725..139849949)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139837603-139838368 Neighboring gene F-box and WD repeat domain containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20562 Neighboring gene complement C8 gamma chain Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20563 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139847365-139847546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139853309-139853809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139862419-139862920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139862921-139863420 Neighboring gene long intergenic non-protein coding RNA 2692 Neighboring gene uncharacterized LOC124902312

    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. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. Lu Y, et al. Nat Genet, 2013 Feb. PMID 23291589, Free PMC Article
    3. Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. Lee N, et al. Sci Rep, 2016 Dec 15. PMID 27976729, 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) 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

    EBI GWAS Catalog

    Description
    Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
    EBI GWAS Catalog

    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

    Clone Names

    • MGC34753, MGC48935

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables retinoic acid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    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-12
    Names
    epididymis secretory sperm binding protein
    lipocalcin 12

    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_178536.4 → NP_848631.2  epididymal-specific lipocalin-12 precursor

      See identical proteins and their annotated locations for NP_848631.2

      Status: VALIDATED

      Source sequence(s)
      AI681012, AL807752, AY301272, BX281250
      Consensus CDS
      CCDS7018.2
      UniProtKB/Swiss-Prot
      A2AMJ7, Q6JVE5
      UniProtKB/TrEMBL
      A0A384MDV4
      Related
      ENSP00000360696.3, ENST00000371633.8
      Conserved Domains (1) summary
      pfam00061
      Location:40 → 184
      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
      136949197..136956538
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717065.4 → XP_006717128.1  epididymal-specific lipocalin-12 isoform X2

      See identical proteins and their annotated locations for XP_006717128.1

      UniProtKB/TrEMBL
      Q8IW14
      Conserved Domains (1) summary
      pfam00061
      Location:40 → 184
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    2. XM_011518562.3 → XP_011516864.1  epididymal-specific lipocalin-12 isoform X2

      See identical proteins and their annotated locations for XP_011516864.1

      UniProtKB/TrEMBL
      Q8IW14
      Conserved Domains (1) summary
      pfam00061
      Location:40 → 184
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    3. XM_011518560.3 → XP_011516862.1  epididymal-specific lipocalin-12 isoform X1

      Conserved Domains (1) summary
      pfam00061
      Location:67 → 211
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    4. XM_017014631.2 → XP_016870120.2  epididymal-specific lipocalin-12 isoform X4

    5. XM_047423247.1 → XP_047279203.1  epididymal-specific lipocalin-12 isoform X3

    RNA

    1. XR_007061284.1 RNA Sequence

    2. XR_001746278.2 RNA Sequence

    3. XR_001746279.3 RNA Sequence

    4. XR_001746280.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      149183558..149189824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362773.1 → XP_054218748.1  epididymal-specific lipocalin-12 isoform X2

      UniProtKB/TrEMBL
      Q8IW14

    2. XM_054362774.1 → XP_054218749.1  epididymal-specific lipocalin-12 isoform X2

      UniProtKB/TrEMBL
      Q8IW14

    3. XM_054362772.1 → XP_054218747.1  epididymal-specific lipocalin-12 isoform X1

    4. XM_054362771.1 → XP_054218746.1  epididymal-specific lipocalin-12 isoform X2

      UniProtKB/TrEMBL
      Q8IW14

    5. XM_054362776.1 → XP_054218751.1  epididymal-specific lipocalin-12 isoform X4

    6. XM_054362775.1 → XP_054218750.1  epididymal-specific lipocalin-12 isoform X3

    RNA

    1. XR_008487993.1 RNA Sequence

    2. XR_008487989.1 RNA Sequence

    3. XR_008487990.1 RNA Sequence

    4. XR_008487992.1 RNA Sequence

    5. XR_008487991.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6JVE5.1 GenPept UniProtKB/Swiss-Prot:Q6JVE5

    Gene LinkOut

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