Human Gene SLC22A12 (uc009ypr.1)
  Description: Homo sapiens solute carrier family 22 (organic anion/urate transporter), member 12 (SLC22A12), transcript variant 1, mRNA.
RefSeq Summary (NM_144585): The protein encoded by this gene is a member of the organic anion transporter (OAT) family, and it acts as a urate transporter to regulate urate levels in blood. This protein is an integral membrane protein primarily found in epithelial cells of the proximal tubule of the kidney. An elevated level of serum urate, hyperuricemia, is associated with increased incidences of gout, and mutations in this gene cause renal hypouricemia type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013].
Transcript (Including UTRs)
   Position: hg19 chr11:64,358,282-64,366,395 Size: 8,114 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr11:64,359,029-64,366,393 Size: 7,365 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:64,358,282-64,366,395)mRNA (may differ from genome)Protein (381 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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-  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): SLC22A12
CDC HuGE Published Literature: SLC22A12
Positive Disease Associations: , gout , hyperuricemia; uric acid , kidney disease , serum uric acid , uric acid
Related Studies:

  1. Hung-Pin Tu , et al. Annals of the rheumatic diseases 2009 Sep, SLC22A12 Gene is Associated with Gout in Han Chinese and Solomon Islanders., Annals of the rheumatic diseases 2009 Sep. [PubMed 19762362]
  2. gout
    Vazquez-Mellado, J. et al. 2006, Molecular analysis of the SLC22A12 (URAT1) gene in patients with primary gout, Rheumatology (Oxford) 2006. [PubMed 16837472]
    We found several mutations in SLC22A12 gene associated with primary gout, the definite role of these mutations in URAT1 activity needs to be further studied.
  3. Gout
    Adrienne Tin et al. Human molecular genetics 2011, Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele., Human molecular genetics. [PubMed 21768215]
    , we identified and replicated one novel locus in association with serum urate levels and experimentally characterize the novel G65W variant in URAT1 as a functional allele.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC22A12
Diseases sorted by gene-association score: hypouricemia, renal* (1691), hyperuricemia (33), gout (27), acute kidney failure (13), hemopericardium (11), nephrolithiasis (10), hyperuricemic nephropathy, familial juvenile 1 (8), neurotic disorder (8), xanthinuria (4)
* = 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: 48.16 RPKM in Kidney - Cortex
Total median expression: 48.43 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 -324.60747-0.435 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
IPR016196 - MFS_dom_general_subst_transpt
IPR005828 - Sub_transporter

Pfam Domains:
PF00083 - Sugar (and other) transporter

SCOP Domains:
103473 - MFS general substrate transporter

ModBase Predicted Comparative 3D Structure on Q05CF4
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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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0022857 transmembrane transporter activity

Biological Process:
GO:0055085 transmembrane transport

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  DQ655911 - Homo sapiens clone Affy08242C05, mRNA sequence.
DQ655912 - Homo sapiens clone Affy08242A06, mRNA sequence.
JD114977 - Sequence 96001 from Patent EP1572962.
AB050269 - Homo sapiens OAT4L mRNA for organic anion transporter 4 like protein, complete cds.
JD374144 - Sequence 355168 from Patent EP1572962.
JD471717 - Sequence 452741 from Patent EP1572962.
JD373010 - Sequence 354034 from Patent EP1572962.
JD075336 - Sequence 56360 from Patent EP1572962.
JD317584 - Sequence 298608 from Patent EP1572962.
JD404786 - Sequence 385810 from Patent EP1572962.
JD109050 - Sequence 90074 from Patent EP1572962.
JD264286 - Sequence 245310 from Patent EP1572962.
JD205544 - Sequence 186568 from Patent EP1572962.
JD098303 - Sequence 79327 from Patent EP1572962.
JD401070 - Sequence 382094 from Patent EP1572962.
JD210251 - Sequence 191275 from Patent EP1572962.
JD210252 - Sequence 191276 from Patent EP1572962.
JD123061 - Sequence 104085 from Patent EP1572962.
JD155706 - Sequence 136730 from Patent EP1572962.
BC026291 - Homo sapiens solute carrier family 22 (organic anion/urate transporter), member 12, mRNA (cDNA clone IMAGE:4608353), partial cds.
AK055737 - Homo sapiens cDNA FLJ31175 fis, clone KIDNE2000167, highly similar to Homo sapiens solute carrier family 22 (organic anion/cation transporter), member 12 (SLC22A12), transcript variant 2, mRNA.
AK122599 - Homo sapiens cDNA FLJ16006 fis, clone KIDNE1000064, highly similar to Homo sapiens solute carrier family 22 (organic anion/cation transporter), member 12 (SLC22A12), transcript variant 1, mRNA.
AK315061 - Homo sapiens cDNA, FLJ96013.
BC053348 - Homo sapiens solute carrier family 22 (organic anion/urate transporter), member 12, mRNA (cDNA clone MGC:61679 IMAGE:5183650), complete cds.
AY358183 - Homo sapiens clone DNA190931 SLC22A12 (UNQ6453) mRNA, complete cds.
JD078822 - Sequence 59846 from Patent EP1572962.
JD205522 - Sequence 186546 from Patent EP1572962.
JD422701 - Sequence 403725 from Patent EP1572962.
JD531285 - Sequence 512309 from Patent EP1572962.
JD319129 - Sequence 300153 from Patent EP1572962.
JD370639 - Sequence 351663 from Patent EP1572962.
AB071863 - Homo sapiens SLC22A12 mRNA for URAT1, complete cds.
JD394454 - Sequence 375478 from Patent EP1572962.
JD440505 - Sequence 421529 from Patent EP1572962.
JD234274 - Sequence 215298 from Patent EP1572962.
JD271124 - Sequence 252148 from Patent EP1572962.
CU690958 - Synthetic construct Homo sapiens gateway clone IMAGE:100021754 5' read SLC22A12 mRNA.
KJ900034 - Synthetic construct Homo sapiens clone ccsbBroadEn_09428 SLC22A12 gene, encodes complete protein.
KR711089 - Synthetic construct Homo sapiens clone CCSBHm_00020150 SLC22A12 (SLC22A12) mRNA, encodes complete protein.
KR711090 - Synthetic construct Homo sapiens clone CCSBHm_00020155 SLC22A12 (SLC22A12) mRNA, encodes complete protein.
KR711091 - Synthetic construct Homo sapiens clone CCSBHm_00020159 SLC22A12 (SLC22A12) mRNA, encodes complete protein.
KR711092 - Synthetic construct Homo sapiens clone CCSBHm_00020165 SLC22A12 (SLC22A12) mRNA, encodes complete protein.
JD213525 - Sequence 194549 from Patent EP1572962.
JD146968 - Sequence 127992 from Patent EP1572962.
AK309588 - Homo sapiens cDNA, FLJ99629.

-  Other Names for This Gene
  Alternate Gene Symbols: BC026291, NM_144585, NP_653186, Q05CF4, Q05CF4_HUMAN
UCSC ID: uc009ypr.1
RefSeq Accession: NM_144585
Protein: Q05CF4

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC026291.1
exon count: 5CDS single in 3' UTR: no RNA size: 1659
ORF size: 1143CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2050.50frame shift in genome: no % Coverage: 83.24
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 849# 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.