Human Gene SLC22A3 (uc003qti.4)
  Description: Homo sapiens solute carrier family 22 (extraneuronal monoamine transporter), member 3 (SLC22A3), mRNA.
RefSeq Summary (NM_021977): Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:160,769,405-160,873,611 Size: 104,207 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr6:160,769,452-160,872,088 Size: 102,637 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:160,769,405-160,873,611)mRNA (may differ from genome)Protein (556 aa)
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neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S22A3_HUMAN
DESCRIPTION: RecName: Full=Solute carrier family 22 member 3; AltName: Full=Extraneuronal monoamine transporter; Short=EMT; AltName: Full=Organic cation transporter 3;
FUNCTION: Mediates potential-dependent transport of a variety of organic cations. May play a significant role in the disposition of cationic neurotoxins and neurotransmitters in the brain.
INTERACTION: P00519:ABL1; NbExp=2; IntAct=EBI-1752674, EBI-375543;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in placenta, skeletal muscle, prostate, aorta, liver, fetal lung, salivary gland, adrenal gland, kidney and brain cortex. No expression detected in spleen.
SIMILARITY: Belongs to the major facilitator (TC 2.A.1) superfamily. Organic cation transporter (TC 2.A.1.19) family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC22A3
CDC HuGE Published Literature: SLC22A3
Positive Disease Associations: Colonic Neoplasms , Colony-Forming Units Assay , coronary artery disease , Hepatitis C, Chronic , Lipoproteins , methamphetamine dependence substance abuse , prostate cancer , Prostatic Neoplasms
Related Studies:
  1. Colonic Neoplasms
    R Cui et al. Gut 2011, Common variant in 6q26-q27 is associated with distal colon cancer in an Asian population., Gut. [PubMed 21242260]
    We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal colon cancer in an Asian population. These findings would further extend our understanding of the role of common genetic variants in the aetiology of CRC.
  2. Colony-Forming Units Assay
    Stanley Y Shaw et al. Circulation. Cardiovascular genetics 2011, Genetic and clinical correlates of early-outgrowth colony-forming units., Circulation. Cardiovascular genetics. [PubMed 21493818]
    In a community-based sample, early-outgrowth CFUs are inversely associated with select cardiovascular risk factors. Furthermore, genetic variants at the SLC22A3-LPAL2-LPA locus are associated with both decreased CFUs and an increased risk of myocardial infarction. These findings are consistent with the hypothesis that decreased circulating angiogenic cell populations promote susceptibility to myocardial infarction.
  3. coronary artery disease
    Tregouet ,et al. 2009, Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease, Nature genetics 2009 41- 3 : 283-5. [PubMed 19198611]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC22A3
Diseases sorted by gene-association score: extragonadal seminoma (11), cerebral palsy, ataxic, autosomal recessive (7), chromosome 3q29 microdeletion syndrome (6), diabetes mellitus, insulin-dependent, 8 (6), prostate cancer susceptibility (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 38.15 RPKM in Nerve - Tibial
Total median expression: 300.44 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 -16.9047-0.360 Picture PostScript Text
3' UTR -424.841523-0.279 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
IPR011701 - MFS
IPR020846 - MFS_dom
IPR016196 - MFS_dom_general_subst_transpt
IPR004749 - Orgcat_transp
IPR005829 - Sugar_transporter_CS

Pfam Domains:
PF00083 - Sugar (and other) transporter
PF07690 - Major Facilitator Superfamily

SCOP Domains:
103473 - MFS general substrate transporter

ModBase Predicted Comparative 3D Structure on O75751
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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:0005215 transporter activity
GO:0005329 dopamine transmembrane transporter activity
GO:0005515 protein binding
GO:0008514 organic anion transmembrane transporter activity
GO:0015101 organic cation transmembrane transporter activity
GO:0015651 quaternary ammonium group transmembrane transporter activity
GO:0019534 toxin transporter activity

Biological Process:
GO:0006811 ion transport
GO:0006855 drug transmembrane transport
GO:0015695 organic cation transport
GO:0015697 quaternary ammonium group transport
GO:0015711 organic anion transport
GO:0015844 monoamine transport
GO:0015872 dopamine transport
GO:0032098 regulation of appetite
GO:0051608 histamine transport
GO:0051615 histamine uptake
GO:0055085 transmembrane transport
GO:1901998 toxin transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC144280 - Homo sapiens cDNA clone IMAGE:9052800.
AK314590 - Homo sapiens cDNA, FLJ95424, Homo sapiens solute carrier family 22 (extraneuronal monoaminetransporter), member 3 (SLC22A3), mRNA.
AJ001417 - Homo sapiens mRNA for extraneuronal monoamine transporter.
BC156538 - Synthetic construct Homo sapiens clone IMAGE:100063252, MGC:190724 solute carrier family 22 (extraneuronal monoamine transporter), member 3 (SLC22A3) mRNA, encodes complete protein.
BC172500 - Synthetic construct Homo sapiens clone IMAGE:100069194, MGC:199205 solute carrier family 22 (extraneuronal monoamine transporter), member 3 (SLC22A3) mRNA, encodes complete protein.
JD408543 - Sequence 389567 from Patent EP1572962.
BX640965 - Homo sapiens mRNA; cDNA DKFZp686N10184 (from clone DKFZp686N10184).
AF078749 - Homo sapiens organic cation transporter 3 (SLC22A3) mRNA, partial cds.
AK125826 - Homo sapiens cDNA FLJ43838 fis, clone TESTI4006053.
JD448034 - Sequence 429058 from Patent EP1572962.
JD282228 - Sequence 263252 from Patent EP1572962.
JD195496 - Sequence 176520 from Patent EP1572962.
JD058419 - Sequence 39443 from Patent EP1572962.
JD239174 - Sequence 220198 from Patent EP1572962.
JD305644 - Sequence 286668 from Patent EP1572962.
JD452113 - Sequence 433137 from Patent EP1572962.
JD089690 - Sequence 70714 from Patent EP1572962.
BC070300 - Homo sapiens cDNA clone IMAGE:4716887, partial cds.
JD046881 - Sequence 27905 from Patent EP1572962.
JD088928 - Sequence 69952 from Patent EP1572962.
JD468526 - Sequence 449550 from Patent EP1572962.
JD204428 - Sequence 185452 from Patent EP1572962.
JD078894 - Sequence 59918 from Patent EP1572962.
AK096980 - Homo sapiens cDNA FLJ39661 fis, clone SMINT2007101.
JD053127 - Sequence 34151 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75751 (Reactome details) participates in the following event(s):

R-HSA-549304 OCT3 mediates renal clearance of organic cations
R-HSA-561072 OCT3 mediates renal uptake of organic cations
R-HSA-2161500 abacavir [extracellular] => abacavir [cytosol]
R-HSA-549127 Organic cation transport
R-HSA-2161517 Abacavir transmembrane transport
R-HSA-549132 Organic cation/anion/zwitterion transport
R-HSA-2161522 Abacavir transport and metabolism
R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds
R-HSA-1430728 Metabolism
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: EMTH, NM_021977, NP_068812, O75751, OCT3, Q5SYN6, Q9UP02, S22A3_HUMAN, uc003qti.3
UCSC ID: uc003qti.4
RefSeq Accession: NM_021977
Protein: O75751 (aka S22A3_HUMAN)
CCDS: CCDS5277.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_021977.3
exon count: 11CDS single in 3' UTR: no RNA size: 3245
ORF size: 1671CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3423.00frame shift in genome: no % Coverage: 99.88
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.