Human Gene SLC12A2 (ENST00000262461.7_8) from GENCODE V47lift37
  Description: solute carrier family 12 member 2, transcript variant 3 (from RefSeq NR_046207.2)
Gencode Transcript: ENST00000262461.7_8
Gencode Gene: ENSG00000064651.14_12
Transcript (Including UTRs)
   Position: hg19 chr5:127,419,458-127,525,369 Size: 105,912 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr5:127,419,647-127,522,323 Size: 102,677 Coding Exon Count: 27 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:127,419,458-127,525,369)mRNA (may differ from genome)Protein (1212 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: SLC12A2
Diseases sorted by gene-association score: basosquamous carcinoma (19), metatypical basal cell carcinoma (17), baylisascariasis (11), arachnoid cysts (10), bartter disease (7), agenesis of the corpus callosum with peripheral neuropathy (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: 18.52 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 330.06 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 -103.80189-0.549 Picture PostScript Text
3' UTR -721.803046-0.237 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
IPR004841 - AA-permease_dom
IPR013612 - AA_permease_N
IPR002443 - Na/K/Cl_cotranspt
IPR002444 - Na/K/Cl_cotranspt1
IPR004842 - Na/K/Cl_cotransptS

Pfam Domains:
PF00324 - Amino acid permease
PF03522 - Solute carrier family 12
PF08403 - Amino acid permease N-terminal
PF13520 - Amino acid permease

SCOP Domains:
56300 - Metallo-dependent phosphatases

ModBase Predicted Comparative 3D Structure on Q53ZR1
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0008511 sodium:potassium:chloride symporter activity
GO:0015377 cation:chloride symporter activity

Biological Process:
GO:0006811 ion transport
GO:0006813 potassium ion transport
GO:0006814 sodium ion transport
GO:0006821 chloride transport
GO:0006972 hyperosmotic response
GO:0007214 gamma-aminobutyric acid signaling pathway
GO:0007568 aging
GO:0045795 positive regulation of cell volume
GO:0055085 transmembrane transport
GO:0071805 potassium ion transmembrane transport
GO:1902476 chloride transmembrane transport

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


-  Descriptions from all associated GenBank mRNAs
  AY280459 - Homo sapiens bumetanide-sensitive Na-K-Cl cotransporter (SLC12A2) mRNA, complete cds.
U30246 - Human bumetanide-sensitive Na-K-Cl cotransporter (NKCC1) mRNA, complete cds.
BC033003 - Homo sapiens solute carrier family 12 (sodium/potassium/chloride transporters), member 2, mRNA (cDNA clone IMAGE:4824556), with apparent retained intron.
BC144221 - Homo sapiens solute carrier family 12 (sodium/potassium/chloride transporters), member 2, mRNA (cDNA clone MGC:177758 IMAGE:9052741), complete cds.
BC146839 - Homo sapiens solute carrier family 12 (sodium/potassium/chloride transporters), member 2, mRNA (cDNA clone MGC:181942 IMAGE:9056767), complete cds.
JD524483 - Sequence 505507 from Patent EP1572962.
JD323181 - Sequence 304205 from Patent EP1572962.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
AF439152 - Homo sapiens sodium-potassium-chloride cotransporter (SLC12A2) mRNA, partial cds, alternatively spliced.
AB209192 - Homo sapiens mRNA for solute carrier family 12 (sodium/potassium/chloride transporters), member 2 variant protein.
Z36839 - H.sapiens (xs81) mRNA, 289bp.
JD300153 - Sequence 281177 from Patent EP1572962.
AK025062 - Homo sapiens cDNA: FLJ21409 fis, clone COL03924.
JD337750 - Sequence 318774 from Patent EP1572962.
JD337752 - Sequence 318776 from Patent EP1572962.
JD463311 - Sequence 444335 from Patent EP1572962.
JD463312 - Sequence 444336 from Patent EP1572962.
M18217 - Human DNA of undetermined origin found 5' to NCA mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000262461.1, ENST00000262461.2, ENST00000262461.3, ENST00000262461.4, ENST00000262461.5, ENST00000262461.6, hCG_27034 , NR_046207, Q53ZR1, Q53ZR1_HUMAN, SLC12A2 , uc317haq.1, uc317haq.2
UCSC ID: ENST00000262461.7_8
RefSeq Accession: NM_001046.3
Protein: Q53ZR1

-  Gene Model Information
  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.