Human Gene SLC12A4 (uc010ceu.2) Description and Page Index
  Description: Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 4 (SLC12A4), transcript variant 4, mRNA.
RefSeq Summary (NM_001145963): This gene encodes a member of the SLC12A transporter family. The encoded protein mediates the coupled movement of potassium and chloride ions across the plasma membrane. This gene is expressed ubiquitously. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2013].
Transcript (Including UTRs)
   Position: hg19 chr16:67,977,377-67,997,968 Size: 20,592 Total Exon Count: 24 Strand: -
Coding Region
   Position: hg19 chr16:67,978,743-67,997,930 Size: 19,188 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:67,977,377-67,997,968)mRNA (may differ from genome)Protein (1079 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: F5H0S9_HUMAN
DESCRIPTION: SubName: Full=Solute carrier family 12 member 4;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC12A4
CDC HuGE Published Literature: SLC12A4

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC12A4
Diseases sorted by gene-association score: agenesis of the corpus callosum with peripheral neuropathy (16), sickle cell disease (9), chronic cervicitis (9), corneal dystrophy, schnyder type (5), cervix disease (5), cervicitis (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C023514 2,6-dinitrotoluene
  • D001464 Barium
  • D019833 Genistein
  • C095651 ((2-n-butyl-6,7-dichloro-2-cyclopentyl-2,3-dihydro-1-oxo-1H-inden-5-yl)oxy)acetic acid
  • D015655 1-Methyl-4-phenylpyridinium
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C016403 2,4-dinitrotoluene
  • D017878 4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid
  • D000082 Acetaminophen
          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: 34.72 RPKM in Artery - Aorta
Total median expression: 825.48 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 -13.4038-0.353 Picture PostScript Text
3' UTR -599.001366-0.439 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
IPR000622 - K/Cl_cotranspt1
IPR018491 - K/Cl_cotranspt_1/3
IPR000076 - KCL_cotranspt
IPR004842 - Na/K/Cl_cotransptS

Pfam Domains:
PF00324 - Amino acid permease
PF03522 - Solute carrier family 12

ModBase Predicted Comparative 3D Structure on F5H0S9
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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
  LF208288 - JP 2014500723-A/15791: Polycomb-Associated Non-Coding RNAs.
M12625 - Human lecithin-cholesterol acyltransferase mRNA, complete cds, with 5' and 3' flanking DNA sequences.
BC014781 - Homo sapiens lecithin-cholesterol acyltransferase, mRNA (cDNA clone MGC:17087 IMAGE:4155094), complete cds.
M26268 - Human lecithin:cholesterol acyltransferase (LCAT) mRNA, 3' end.
X06537 - Human mRNA for lecithin:cholesterol acyltransferase (LCAT); EC 2.3.1.43.
E01185 - DNA encoding lectin-cholesterol acyltransferase.
HM005564 - Homo sapiens clone HTL-S-24 testicular secretory protein Li 24 mRNA, complete cds.
BT009748 - Homo sapiens lecithin-cholesterol acyltransferase mRNA, complete cds.
KM576718 - Homo sapiens clone SLC12A4-LCAT_S26middle-L2 mRNA sequence.
AK310027 - Homo sapiens cDNA, FLJ17069.
BC021193 - Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 4, mRNA (cDNA clone MGC:1455 IMAGE:3349710), complete cds.
AK026911 - Homo sapiens cDNA: FLJ23258 fis, clone COL05740, highly similar to HSKCC Human K-Cl cotransporter (hKCC1) mRNA.
AK097808 - Homo sapiens cDNA FLJ40489 fis, clone TESTI2044194, highly similar to Solute carrier family 12 member 4.
JD193781 - Sequence 174805 from Patent EP1572962.
AK293956 - Homo sapiens cDNA FLJ56476 complete cds, highly similar to Solute carrier family 12 member 4.
JD371845 - Sequence 352869 from Patent EP1572962.
U55054 - Human K-Cl cotransporter (hKCC1) mRNA, complete cds.
JD472839 - Sequence 453863 from Patent EP1572962.
LF374168 - JP 2014500723-A/181671: Polycomb-Associated Non-Coding RNAs.
AK299042 - Homo sapiens cDNA FLJ55911 complete cds, highly similar to Solute carrier family 12 member 4.
AF047338 - Homo sapiens erythroid K:Cl cotransporter (KCC1) mRNA, complete cds.
AF054505 - Homo sapiens erythroid K:Cl cotransporter splicing isoform 1 (KCC1) mRNA, complete cds.
AF054506 - Homo sapiens erythroid K:Cl cotransporter splicing isoform 2 (KCC1) mRNA, complete cds.
AK293906 - Homo sapiens cDNA FLJ60065 complete cds, highly similar to Solute carrier family 12 member 4.
JD174718 - Sequence 155742 from Patent EP1572962.
JD547479 - Sequence 528503 from Patent EP1572962.
AK302790 - Homo sapiens cDNA FLJ53419 complete cds, highly similar to Solute carrier family 12 member 4.
JD360304 - Sequence 341328 from Patent EP1572962.
JD393657 - Sequence 374681 from Patent EP1572962.
JD293850 - Sequence 274874 from Patent EP1572962.
DQ892254 - Synthetic construct clone IMAGE:100004884; FLH184589.01X; RZPDo839H07144D solute carrier family 12 (potassium/chloride transporters), member 4 (SLC12A4) gene, encodes complete protein.
DQ895457 - Synthetic construct Homo sapiens clone IMAGE:100009917; FLH184585.01L; RZPDo839H07143D solute carrier family 12 (potassium/chloride transporters), member 4 (SLC12A4) gene, encodes complete protein.
JD401110 - Sequence 382134 from Patent EP1572962.
AK316415 - Homo sapiens cDNA, FLJ79314 complete cds, highly similar to Solute carrier family 12 member 4.
JD070790 - Sequence 51814 from Patent EP1572962.
KJ897571 - Synthetic construct Homo sapiens clone ccsbBroadEn_06965 SLC12A4 gene, encodes complete protein.
LF374169 - JP 2014500723-A/181672: Polycomb-Associated Non-Coding RNAs.
LF374170 - JP 2014500723-A/181673: Polycomb-Associated Non-Coding RNAs.
LF374171 - JP 2014500723-A/181674: Polycomb-Associated Non-Coding RNAs.
AY026038 - Homo sapiens K-Cl cotransporter (SLC12A4) mRNA, partial cds.
LF374172 - JP 2014500723-A/181675: Polycomb-Associated Non-Coding RNAs.
BC035480 - Homo sapiens solute carrier family 12 (potassium/chloride transporters), member 4, mRNA (cDNA clone IMAGE:4943447).
AF053402 - Homo sapiens erythrocyte K-Cl cotransporter mRNA, partial cds.
AK311073 - Homo sapiens cDNA, FLJ18115.
MA443865 - JP 2018138019-A/15791: Polycomb-Associated Non-Coding RNAs.
MA609745 - JP 2018138019-A/181671: Polycomb-Associated Non-Coding RNAs.
MA609746 - JP 2018138019-A/181672: Polycomb-Associated Non-Coding RNAs.
MA609747 - JP 2018138019-A/181673: Polycomb-Associated Non-Coding RNAs.
MA609748 - JP 2018138019-A/181674: Polycomb-Associated Non-Coding RNAs.
MA609749 - JP 2018138019-A/181675: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: F5H0S9, F5H0S9_HUMAN, NM_001145963, NP_001139435
UCSC ID: uc010ceu.2
RefSeq Accession: NM_001145963
Protein: F5H0S9 CCDS: CCDS10855.1, CCDS54030.1, CCDS54031.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145963.1
exon count: 24CDS single in 3' UTR: no RNA size: 4652
ORF size: 3240CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6668.00frame shift in genome: no % Coverage: 99.83
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.