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LCN12 lipocalin 12 [ Homo sapiens (human) ]

Gene ID: 286256, updated on 5-Mar-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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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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