Human Gene SLC22A5 (uc003kwx.4)
  Description: Homo sapiens solute carrier family 22 (organic cation/carnitine transporter), member 5 (SLC22A5), mRNA.
RefSeq Summary (NM_003060): 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. The encoded protein is a plasma integral membrane protein which functions both as an organic cation transporter and as a sodium-dependent high affinity carnitine transporter. The encoded protein is involved in the active cellular uptake of carnitine. Mutations in this gene are the cause of systemic primary carnitine deficiency (CDSP), an autosomal recessive disorder manifested early in life by hypoketotic hypoglycemia and acute metabolic decompensation, and later in life by skeletal myopathy or cardiomyopathy. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015].
Transcript (Including UTRs)
   Position: hg19 chr5:131,705,401-131,731,306 Size: 25,906 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr5:131,705,665-131,729,964 Size: 24,300 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:131,705,401-131,731,306)mRNA (may differ from genome)Protein (581 aa)
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OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  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): SLC22A5
CDC HuGE Published Literature: SLC22A5
Positive Disease Associations: Asthma , Crohn Disease , Crohn's disease , Crohn's disease ulcerative colitis , fibrinogen
Related Studies:
  1. Asthma
    Miriam F Moffatt et al. The New England journal of medicine 2010, A large-scale, consortium-based genomewide association study of asthma., The New England journal of medicine. [PubMed 20860503]
    Asthma is genetically heterogeneous. A few common alleles are associated with disease risk at all ages. Implicated genes suggest a role for communication of epithelial damage to the adaptive immune system and activation of airway inflammation. Variants at the ORMDL3/GSDMB locus are associated only with childhood-onset disease. Elevation of total serum IgE levels has a minor role in the development of asthma. (Funded by the European Commission and others.)
  2. Crohn Disease
    Paul R Burton et al. Nature 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls., Nature. [PubMed 17554300]
  3. Crohn's disease
    Peltekova VD 2004, Functional variants of OCTN cation transporter genes are associated with Crohn disease, Nature genetics. 2004 May;36(5):471-5. [PubMed 15107849]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC22A5
Diseases sorted by gene-association score: carnitine deficiency, systemic primary* (1682), visceral steatosis (29), crohn's disease (15), inflammatory bowel disease 5 (13), crohn disease-associated growth failure (8), methylmalonic aciduria and homocystinuria, cblc type (7), cardiomyopathy (5), myopathy (4), amino acid metabolic disorder (2)
* = Manually curated disease association

-  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: 25.65 RPKM in Muscle - Skeletal
Total median expression: 332.58 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 -146.41264-0.555 Picture PostScript Text
3' UTR -387.601342-0.289 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
  Pfam Domains:
PF00083 - Sugar (and other) transporter
PF07690 - Major Facilitator Superfamily

SCOP Domains:
103473 - MFS general substrate transporter

ModBase Predicted Comparative 3D Structure on O76082-3
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AF057164 - Homo sapiens organic cation transporter OCTN2 (OCTN2) mRNA, complete cds.
BC012325 - Homo sapiens solute carrier family 22 (organic cation/carnitine transporter), member 5, mRNA (cDNA clone MGC:20139 IMAGE:4548603), complete cds.
AB015050 - Homo sapiens mRNA for OCTN2, complete cds.
AK313230 - Homo sapiens cDNA, FLJ93734, Homo sapiens solute carrier family 22 (organic cation transporter),member 5 (SLC22A5), mRNA.
KJ897580 - Synthetic construct Homo sapiens clone ccsbBroadEn_06974 SLC22A5 gene, encodes complete protein.
KR710445 - Synthetic construct Homo sapiens clone CCSBHm_00012725 SLC22A5 (SLC22A5) mRNA, encodes complete protein.
DQ895818 - Synthetic construct Homo sapiens clone IMAGE:100010278; FLH187947.01L; RZPDo839E11149D solute carrier family 22 (organic cation transporter), member 5 (SLC22A5) gene, encodes complete protein.
DQ893671 - Synthetic construct clone IMAGE:100006301; FLH187951.01X; RZPDo839E11150D solute carrier family 22 (organic cation transporter), member 5 (SLC22A5) gene, encodes complete protein.
AB291606 - Homo sapiens OCTN2VT mRNA for organic cation transporter 2 splice variant, complete cds.
AB209484 - Homo sapiens mRNA for solute carrier family 22 member 5 variant protein.
AY429569 - Homo sapiens SLC22A5v_2 mRNA sequence; alternatively spliced.
AK128610 - Homo sapiens cDNA FLJ46769 fis, clone TRACH3025346, highly similar to Organic cation/carnitine transporter 2.
JD461559 - Sequence 442583 from Patent EP1572962.
JD237302 - Sequence 218326 from Patent EP1572962.
JD406434 - Sequence 387458 from Patent EP1572962.
JD407364 - Sequence 388388 from Patent EP1572962.
JD075883 - Sequence 56907 from Patent EP1572962.
JD129538 - Sequence 110562 from Patent EP1572962.
CU680286 - Synthetic construct Homo sapiens gateway clone IMAGE:100019864 5' read SLC22A5 mRNA.
JD139236 - Sequence 120260 from Patent EP1572962.
JD273342 - Sequence 254366 from Patent EP1572962.
JD323478 - Sequence 304502 from Patent EP1572962.
JD061790 - Sequence 42814 from Patent EP1572962.
JD080879 - Sequence 61903 from Patent EP1572962.
JD158081 - Sequence 139105 from Patent EP1572962.
JD263621 - Sequence 244645 from Patent EP1572962.
JD513309 - Sequence 494333 from Patent EP1572962.
JD202961 - Sequence 183985 from Patent EP1572962.
JD301683 - Sequence 282707 from Patent EP1572962.
JD114022 - Sequence 95046 from Patent EP1572962.
JD233465 - Sequence 214489 from Patent EP1572962.
JD552422 - Sequence 533446 from Patent EP1572962.

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

Protein O76082 (Reactome details) participates in the following event(s):

R-HSA-165026 OCTN2 / SLC22A5 transports CAR from extracellular space to cytosol
R-HSA-549297 SLC22A4, 5,15,16 cotransport CAR, Na+ from extracellular region to cytosol
R-HSA-200425 Import of palmitoyl-CoA into the mitochondrial matrix
R-HSA-549127 Organic cation transport
R-HSA-8978868 Fatty acid metabolism
R-HSA-549132 Organic cation/anion/zwitterion transport
R-HSA-556833 Metabolism of lipids
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: AB291606, NM_003060, NP_003051, O76082-3, OCTN2
UCSC ID: uc003kwx.4
RefSeq Accession: NM_003060
Protein: O76082-3, splice isoform of O76082 CCDS: CCDS4154.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC22A5:
cdsp (Systemic Primary Carnitine Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB291606.1
exon count: 11CDS single in 3' UTR: no RNA size: 1746
ORF size: 1746CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3689.00frame 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.