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Aliases for LCN12 Gene

Aliases for LCN12 Gene

  • Lipocalin 12 2 3 5

External Ids for LCN12 Gene

Previous GeneCards Identifiers for LCN12 Gene

  • GC09P135205
  • GC09P137122
  • GC09P138963
  • GC09P139844
  • GC09P109306

Summaries for LCN12 Gene

Entrez Gene Summary for LCN12 Gene

  • 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]

GeneCards Summary for LCN12 Gene

LCN12 (Lipocalin 12) is a Protein Coding gene. Among its related pathways are Transport of vitamins, nucleosides, and related molecules and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include transporter activity and retinoic acid binding. An important paralog of this gene is LCN2.

UniProtKB/Swiss-Prot for LCN12 Gene

  • Binds all-trans retinoic acid and may act as a retinoid carrier protein within the epididymis. May play a role in male fertility (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCN12 Gene

Genomics for LCN12 Gene

Regulatory Elements for LCN12 Gene

Enhancers for LCN12 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09F136990 1.7 FANTOM5 Ensembl ENCODE 20.3 +47.2 47200 11.6 HDGF PKNOX1 ARNT CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 CBX5 ENSG00000238268 LCN12 ABCA2 ANAPC2 PRR31 C9orf139 SNHG7 LCNL1 RABL6 CCDC183
GH09F136942 1.2 ENCODE 26.7 -1.7 -1735 10.6 HDGF CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF302 LCN12 ENSG00000238268 DPH7 ANAPC2 SNHG7 LOC100418938 NDOR1 LCNL1 C8G
GH09F136925 1 Ensembl ENCODE 26.6 -21.8 -21845 3.7 CTCF ESRRA PKNOX1 RAD21 ZFHX2 ZNF316 POLR2A NFE2 ZNF600 MAFK LCN12 TRAF2 CCDC183 PRR31 MAMDC4 PHPT1 C9orf172 RABL6 CCDC183-AS1 ENSG00000238268
GH09F136965 1 Ensembl ENCODE 24.9 +16.9 16896 1.4 KLF1 ATF1 PKNOX1 ESRRA ZNF121 ZBTB48 CREM L3MBTL2 USF2 ZBTB8A LCN12 ENSG00000238268 PTGDS PRR31
GH09F136959 0.8 Ensembl ENCODE 24.2 +11.3 11307 2.6 SMARCA4 POLR2A NR3C1 ZIC2 ZBTB7A EGR2 LCN12 ENSG00000238268 PTGDS PRR31
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LCN12 on UCSC Golden Path with GeneCards custom track

Promoters for LCN12 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001317819 705 1401 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF207 FOS

Genomic Location for LCN12 Gene

Chromosome:
9
Start:
136,949,195 bp from pter
End:
136,955,498 bp from pter
Size:
6,304 bases
Orientation:
Plus strand

Genomic View for LCN12 Gene

Genes around LCN12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCN12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCN12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCN12 Gene

Proteins for LCN12 Gene

  • Protein details for LCN12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6JVE5-LCN12_HUMAN
    Recommended name:
    Epididymal-specific lipocalin-12
    Protein Accession:
    Q6JVE5
    Secondary Accessions:
    • A2AMJ7

    Protein attributes for LCN12 Gene

    Size:
    192 amino acids
    Molecular mass:
    21500 Da
    Quaternary structure:
    • Monomer.

neXtProt entry for LCN12 Gene

Post-translational modifications for LCN12 Gene

No Post-translational modifications

Antibody Products

  • Abcam antibodies for LCN12
  • Cloud-Clone Corp. Antibodies for LCN12

No data available for DME Specific Peptides for LCN12 Gene

Domains & Families for LCN12 Gene

Gene Families for LCN12 Gene

Suggested Antigen Peptide Sequences for LCN12 Gene

Graphical View of Domain Structure for InterPro Entry

Q6JVE5

UniProtKB/Swiss-Prot:

LCN12_HUMAN :
  • Belongs to the calycin superfamily. Lipocalin family.
Family:
  • Belongs to the calycin superfamily. Lipocalin family.
genes like me logo Genes that share domains with LCN12: view

Function for LCN12 Gene

Molecular function for LCN12 Gene

UniProtKB/Swiss-Prot Function:
Binds all-trans retinoic acid and may act as a retinoid carrier protein within the epididymis. May play a role in male fertility (By similarity).

Gene Ontology (GO) - Molecular Function for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001972 retinoic acid binding ISS --
GO:0005215 transporter activity IEA --
genes like me logo Genes that share ontologies with LCN12: view

Phenotypes for LCN12 Gene

GenomeRNAi human phenotypes for LCN12:
genes like me logo Genes that share phenotypes with LCN12: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCN12 Gene

Localization for LCN12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCN12 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCN12 gene
Compartment Confidence
extracellular 5
mitochondrion 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with LCN12: view

Pathways & Interactions for LCN12 Gene

genes like me logo Genes that share pathways with LCN12: view

Interacting Proteins for LCN12 Gene

Selected Interacting proteins: Q6JVE5-LCN12_HUMAN for LCN12 Gene via IID

Symbol External ID(s) Details
MYC

Gene Ontology (GO) - Biological Process for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006810 transport IEA --
GO:0015909 long-chain fatty acid transport TAS --
genes like me logo Genes that share ontologies with LCN12: view

No data available for SIGNOR curated interactions for LCN12 Gene

Transcripts for LCN12 Gene

Unigene Clusters for LCN12 Gene

Lipocalin 12:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCN12 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6
SP1:
SP2: -
SP3: - -

Relevant External Links for LCN12 Gene

GeneLoc Exon Structure for
LCN12
ECgene alternative splicing isoforms for
LCN12

Expression for LCN12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCN12 Gene

mRNA differential expression in normal tissues according to GTEx for LCN12 Gene

This gene is overexpressed in Thyroid (x13.7) and Liver (x4.8).

NURSA nuclear receptor signaling pathways regulating expression of LCN12 Gene:

LCN12

SOURCE GeneReport for Unigene cluster for LCN12 Gene:

Hs.440519
genes like me logo Genes that share expression patterns with LCN12: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for LCN12 Gene

Orthologs for LCN12 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LCN12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LCN12 34 35
  • 97.57 (n)
dog
(Canis familiaris)
Mammalia LCN12 34 35
  • 70.64 (n)
cow
(Bos Taurus)
Mammalia LCN12 34 35
  • 69.16 (n)
mouse
(Mus musculus)
Mammalia Lcn12 34 16 35
  • 68.27 (n)
rat
(Rattus norvegicus)
Mammalia Lcn12 34
  • 66.89 (n)
oppossum
(Monodelphis domestica)
Mammalia LCN12 35
  • 25 (a)
OneToOne
Species where no ortholog for LCN12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LCN12 Gene

ENSEMBL:
Gene Tree for LCN12 (if available)
TreeFam:
Gene Tree for LCN12 (if available)

Paralogs for LCN12 Gene

Paralogs for LCN12 Gene

(2) SIMAP similar genes for LCN12 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LCN12: view

Variants for LCN12 Gene

Sequence variations from dbSNP and Humsavar for LCN12 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs10666636 -- 136,951,022(+) ACCTG(-/GTGGGA/GTGGGAGGA)GGGGG intron-variant, upstream-variant-2KB
rs10781526 -- 136,953,451(+) ACTTT(A/G)GGGGC intron-variant
rs10870148 -- 136,950,052(+) GTGCC(C/T)CAAGG intron-variant, upstream-variant-2KB
rs111447188 -- 136,953,442(+) AATCC(C/T)AGCAC intron-variant
rs11145938 -- 136,947,303(+) CGAGC(A/C/T)GAGCT downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for LCN12 Gene

Variant ID Type Subtype PubMed ID
esv2422220 CNV deletion 17116639
esv2661667 CNV deletion 23128226
nsv469918 CNV loss 18288195
nsv524322 CNV loss 19592680
nsv615988 CNV loss 21841781
nsv818738 CNV gain 17921354
nsv951206 CNV deletion 24416366

Variation tolerance for LCN12 Gene

Residual Variation Intolerance Score: 82.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.47; 28.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LCN12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCN12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCN12 Gene

Disorders for LCN12 Gene

Relevant External Links for LCN12

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LCN12

No disorders were found for LCN12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LCN12 Gene

Publications for LCN12 Gene

  1. Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2. (PMID: 15363845) Suzuki K. … Orgebin-Crist M.-C. (Gene 2004) 2 3 4 22 64
  2. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. (PMID: 23291589) Lu Y. … Wong T.Y. (Nat. Genet. 2013) 3 64
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 4 64
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64

Products for LCN12 Gene

Sources for LCN12 Gene

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