Human Gene SLC12A9 (ENST00000354161.8) from GENCODE V44
  Description: Homo sapiens solute carrier family 12 member 9 (SLC12A9), transcript variant 1, mRNA. (from RefSeq NM_020246)
Gencode Transcript: ENST00000354161.8
Gencode Gene: ENSG00000146828.18
Transcript (Including UTRs)
   Position: hg38 chr7:100,852,713-100,867,010 Size: 14,298 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chr7:100,854,198-100,866,605 Size: 12,408 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:100,852,713-100,867,010)mRNA (may differ from genome)Protein (914 aa)
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-  Comments and Description Text from UniProtKB
  ID: S12A9_HUMAN
DESCRIPTION: RecName: Full=Solute carrier family 12 member 9; AltName: Full=Cation-chloride cotransporter 6; Short=hCCC6; AltName: Full=Cation-chloride cotransporter-interacting protein 1; Short=CCC-interacting protein 1; Short=hCIP1; AltName: Full=Potassium-chloride transporter 9; AltName: Full=WO3.3;
FUNCTION: May be an inhibitor of SLC12A1. Seems to correspond to a subunit of a multimeric transport system and thus, additional subunits may be required for its function.
SUBUNIT: Interacts with SLC12A1.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Highly expressed in placenta, brain and kidney. Lower expression in lung, liver and heart.
SIMILARITY: Belongs to the SLC12A transporter 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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 58.74 RPKM in Whole Blood
Total median expression: 537.66 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 -68.20165-0.413 Picture PostScript Text
3' UTR -178.00405-0.440 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

Pfam Domains:
PF00324 - Amino acid permease

ModBase Predicted Comparative 3D Structure on Q9BXP2
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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
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Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0015377 cation:chloride symporter activity
GO:0015379 potassium:chloride symporter activity

Biological Process:
GO:0006811 ion transport
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
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK301411 - Homo sapiens cDNA FLJ61603 complete cds, highly similar to Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 9 (SLC12A9), mRNA.
BC000154 - Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 9, mRNA (cDNA clone MGC:5319 IMAGE:2900382), complete cds.
AF284422 - Homo sapiens cation-chloride cotransporter-interacting protein mRNA, complete cds.
AK128873 - Homo sapiens cDNA FLJ46905 fis, clone PLACE6000012.
AB033284 - Homo sapiens hCCC6 mRNA for cation chloride cotransporter 6, complete cds.
AK090458 - Homo sapiens mRNA for FLJ00379 protein.
JD566304 - Sequence 547328 from Patent EP1572962.
JD136777 - Sequence 117801 from Patent EP1572962.
KJ902928 - Synthetic construct Homo sapiens clone ccsbBroadEn_12322 SLC12A9 gene, encodes complete protein.
AK024421 - Homo sapiens mRNA for FLJ00010 protein, partial cds.
AK024420 - Homo sapiens mRNA for FLJ00009 protein, partial cds.
AK024494 - Homo sapiens mRNA for FLJ00100 protein, partial cds.
AK024466 - Homo sapiens mRNA for FLJ00059 protein, partial cds.
JD155196 - Sequence 136220 from Patent EP1572962.
JD191621 - Sequence 172645 from Patent EP1572962.
JD518594 - Sequence 499618 from Patent EP1572962.
JD343804 - Sequence 324828 from Patent EP1572962.
JD453112 - Sequence 434136 from Patent EP1572962.
JD155158 - Sequence 136182 from Patent EP1572962.
JD448110 - Sequence 429134 from Patent EP1572962.
JD351384 - Sequence 332408 from Patent EP1572962.
JD403230 - Sequence 384254 from Patent EP1572962.
AK026624 - Homo sapiens cDNA: FLJ22971 fis, clone KAT10788.
JD481921 - Sequence 462945 from Patent EP1572962.
JD404029 - Sequence 385053 from Patent EP1572962.
JD431361 - Sequence 412385 from Patent EP1572962.
JD109735 - Sequence 90759 from Patent EP1572962.
JD551262 - Sequence 532286 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CCC6, CIP1, D6W5X0, D6W5X2, ENST00000354161.1, ENST00000354161.2, ENST00000354161.3, ENST00000354161.4, ENST00000354161.5, ENST00000354161.6, ENST00000354161.7, NM_020246, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5, S12A9_HUMAN, uc003uwp.1, uc003uwp.2, uc003uwp.3, uc003uwp.4, uc003uwp.5, uc003uwp.6
UCSC ID: ENST00000354161.8
RefSeq Accession: NM_020246
Protein: Q9BXP2 (aka S12A9_HUMAN)
CCDS: CCDS5707.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.