Human Gene SLC5A12 (uc001mra.2)
  Description: Homo sapiens solute carrier family 5 (sodium/glucose cotransporter), member 12 (SLC5A12), mRNA.
RefSeq Summary (NM_178498): Normal blood lactate is maintained at about 1.5 mM, and little filtered lactate is excreted in urine. Reabsorption of lactate is mediated by the low-affinity Na(+)-coupled lactate transporter SLC5A12 in the initial part of the proximal tubule and by the high-affinity Na(+)-coupled lactate transporter SLC5A8 (MIM 608044) in the distal proximal tubule (Gopal et al., 2007 [PubMed 17692818]).[supplied by OMIM, Dec 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr11:26,688,566-26,743,574 Size: 55,009 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr11:26,692,649-26,743,261 Size: 50,613 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:26,688,566-26,743,574)mRNA (may differ from genome)Protein (618 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SC5AC_HUMAN
DESCRIPTION: RecName: Full=Sodium-coupled monocarboxylate transporter 2; AltName: Full=Electroneutral sodium monocarboxylate cotransporter; AltName: Full=Low-affinity sodium-lactate cotransporter; AltName: Full=Solute carrier family 5 member 12;
FUNCTION: Acts as an electroneutral and low-affinity sodium (Na(+))-dependent sodium-coupled solute transporter. Catalyzes the transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, nicotinate, propionate, butyrate and beta-D- hydroxybutyrate. May be responsible for the first step of reabsorption of monocarboxylates from the lumen of the proximal tubule of the kidney and the small intestine. May play also a role in monocarboxylates transport in the retina (By similarity). Mediates electroneutral uptake of lactate, with a stoichiometry of 2 Na(+) for each lactate (By similarity).
ENZYME REGULATION: Cotransport of monocarboxylates and nicotinate strongly inhibited by ibuprofen, fenoprofen and ketoprofen.
SUBCELLULAR LOCATION: Apical cell membrane; Multi-pass membrane protein. Note=Detected at the brush border membrane of the kidney. Colocalizes with viementin in Mueller cells (By similarity).
SIMILARITY: Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) 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): SLC5A12
CDC HuGE Published Literature: SLC5A12
Positive Disease Associations: Asthma , Insulin , Insulin Resistance , Respiratory Function Tests , Stroke
Related Studies:
  1. Asthma
    C Ober et al. American journal of human genetics 2000, A second-generation genomewide screen for asthma-susceptibility alleles in a founder population., American journal of human genetics. [PubMed 11022011]
  2. Insulin
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.
  3. Insulin Resistance
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.
           more ... click here to view the complete list

-  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: 15.10 RPKM in Kidney - Cortex
Total median expression: 32.44 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 -85.63313-0.274 Picture PostScript Text
3' UTR -987.284083-0.242 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
IPR001734 - Na/solute_symporter
IPR019900 - Na/solute_symporter_subgr

Pfam Domains:
PF00474 - Sodium:solute symporter family

ModBase Predicted Comparative 3D Structure on Q1EHB4
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 orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005343 organic acid:sodium symporter activity
GO:0015129 lactate transmembrane transporter activity
GO:0015293 symporter activity
GO:0022857 transmembrane transporter activity

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0035873 lactate transmembrane transport
GO:0055085 transmembrane transport
GO:1903825 organic acid transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC041454 - Homo sapiens solute carrier family 5 (sodium/glucose cotransporter), member 12, mRNA (cDNA clone IMAGE:5187504), partial cds.
AY299482 - Homo sapiens sodium-iodide related cotransporter mRNA, complete cds.
BC049207 - Homo sapiens solute carrier family 5 (sodium/glucose cotransporter), member 12, mRNA (cDNA clone MGC:52019 IMAGE:5188979), complete cds.
KJ903918 - Synthetic construct Homo sapiens clone ccsbBroadEn_13312 SLC5A12 gene, encodes complete protein.
AL049270 - Homo sapiens mRNA; cDNA DKFZp564G223 (from clone DKFZp564G223).
JD020140 - Sequence 1164 from Patent EP1572962.
JD035838 - Sequence 16862 from Patent EP1572962.
JD035762 - Sequence 16786 from Patent EP1572962.
BC029048 - Homo sapiens cDNA clone IMAGE:5184198, partial cds.
JD538986 - Sequence 520010 from Patent EP1572962.
JD162981 - Sequence 144005 from Patent EP1572962.
JD250718 - Sequence 231742 from Patent EP1572962.
JD545404 - Sequence 526428 from Patent EP1572962.
JD053957 - Sequence 34981 from Patent EP1572962.
JD269331 - Sequence 250355 from Patent EP1572962.
JD363693 - Sequence 344717 from Patent EP1572962.

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

Protein Q1EHB4 (Reactome details) participates in the following event(s):

R-HSA-8876312 SLC5A12 cotransports Na+ with LACT, PYR, NCA from extracellular region to cytosol
R-HSA-427601 Multifunctional anion exchangers
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: NM_178498, NP_848593, Q1EHB4, Q86UC7, SC5AC_HUMAN, SMCT2
UCSC ID: uc001mra.2
RefSeq Accession: NM_178498
Protein: Q1EHB4 (aka SC5AC_HUMAN)
CCDS: CCDS7860.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178498.3
exon count: 15CDS single in 3' UTR: no RNA size: 6253
ORF size: 1857CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3909.50frame 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.