Human Gene SLC39A12 (uc001ipo.2) Description and Page Index
  Description: Homo sapiens solute carrier family 39 (zinc transporter), member 12 (SLC39A12), transcript variant 1, mRNA.
RefSeq Summary (NM_001145195): Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008].
Transcript (Including UTRs)
   Position: hg19 chr10:18,240,768-18,332,221 Size: 91,454 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr10:18,242,206-18,331,762 Size: 89,557 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:18,240,768-18,332,221)mRNA (may differ from genome)Protein (691 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: S39AC_HUMAN
DESCRIPTION: RecName: Full=Zinc transporter ZIP12; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 8; Short=LZT-Hs8; AltName: Full=Solute carrier family 39 member 12; AltName: Full=Zrt- and Irt-like protein 12; Short=ZIP-12;
FUNCTION: Acts as a zinc-influx transporter (Potential). May be partly involved in the outbreak of schizophrenia.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Expressed in brain and eye.
SIMILARITY: Belongs to the ZIP transporter (TC 2.A.5) family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC39A12
CDC HuGE Published Literature: SLC39A12
Positive Disease Associations: Blood Pressure , Body Height , Clozapine , Hypertension , Inflammatory Bowel Diseases , Lipids , Triglycerides , Waist Circumference
Related Studies:
  1. Blood Pressure
    Georg B Ehret et al. Nature 2011, Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk., Nature. [PubMed 21909115]
  2. Body Height
    , , . [PubMed 0]
  3. Clozapine
    D E Adkins et al. Molecular psychiatry 2011, Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs., Molecular psychiatry. [PubMed 20195266]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.87 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 88.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.52273-0.229 Picture PostScript Text
3' UTR -85.00459-0.185 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003689 - ZIP

Pfam Domains:
PF02535 - ZIP Zinc transporter

ModBase Predicted Comparative 3D Structure on Q504Y0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005385 zinc ion transmembrane transporter activity
GO:0046873 metal ion transmembrane transporter activity

Biological Process:
GO:0006811 ion transport
GO:0006829 zinc II ion transport
GO:0006882 cellular zinc ion homeostasis
GO:0007165 signal transduction
GO:0010975 regulation of neuron projection development
GO:0030001 metal ion transport
GO:0031113 regulation of microtubule polymerization
GO:0055085 transmembrane transport
GO:0071578 zinc II ion transmembrane import

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0048471 perinuclear region of cytoplasm
GO:1903561 extracellular vesicle


-  Descriptions from all associated GenBank mRNAs
  AK055061 - Homo sapiens cDNA FLJ30499 fis, clone BRAWH2000443, weakly similar to Human breast cancer, estrogen regulated LIV-1 protein (LIV-1) mRNA.
BC035118 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone IMAGE:5263281), complete cds.
BC047635 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone MGC:51099 IMAGE:4820920), complete cds.
JD036397 - Sequence 17421 from Patent EP1572962.
AK295294 - Homo sapiens cDNA FLJ50768 complete cds, highly similar to Homo sapiens solute carrier family 39 (zinc transporter), member 12 (SLC39A12), mRNA.
BC094700 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone MGC:104205 IMAGE:30407123), complete cds.
JD037190 - Sequence 18214 from Patent EP1572962.
AK303735 - Homo sapiens cDNA FLJ53949 complete cds, highly similar to Homo sapiens solute carrier family 39 (zinc transporter), member 12 (SLC39A12), mRNA.
BC143551 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone MGC:177079 IMAGE:9052062), complete cds.
BC117323 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone MGC:150932 IMAGE:40125874), complete cds.
BC065917 - Homo sapiens solute carrier family 39 (zinc transporter), member 12, mRNA (cDNA clone IMAGE:5752160), partial cds.
KJ906458 - Synthetic construct Homo sapiens clone ccsbBroadEn_16128 SLC39A12 gene, encodes complete protein.
HQ258343 - Synthetic construct Homo sapiens clone IMAGE:100072652 solute carrier family 39 (zinc transporter), member 12 (SLC39A12) gene, encodes complete protein.
KJ900470 - Synthetic construct Homo sapiens clone ccsbBroadEn_09864 SLC39A12 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZL35, C9JJL4, NM_001145195, NP_001138667, Q49AN8, Q4G0L3, Q504Y0, Q5VWV8, Q5VWV9, Q6NZY5, Q96NN4, S39AC_HUMAN, ZIP12
UCSC ID: uc001ipo.2
RefSeq Accession: NM_001145195
Protein: Q504Y0 (aka S39AC_HUMAN)
CCDS: CCDS44362.1, CCDS60493.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145195.1
exon count: 13CDS single in 3' UTR: no RNA size: 2808
ORF size: 2076CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4352.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.