Human Gene SLC8A1 (ENST00000332839.9_11) from GENCODE V47lift37
  Description: solute carrier family 8 member A1, transcript variant A (from RefSeq NM_021097.5)
Gencode Transcript: ENST00000332839.9_11
Gencode Gene: ENSG00000183023.19_19
Transcript (Including UTRs)
   Position: hg19 chr2:40,324,410-40,679,230 Size: 354,821 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr2:40,342,393-40,657,420 Size: 315,028 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:40,324,410-40,679,230)mRNA (may differ from genome)Protein (973 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NAC1_HUMAN
DESCRIPTION: RecName: Full=Sodium/calcium exchanger 1; AltName: Full=Na(+)/Ca(2+)-exchange protein 1; Flags: Precursor;
FUNCTION: Rapidly transports Ca(2+) during excitation-contraction coupling. Ca(2+) is extruded from the cell during relaxation so as to prevent overloading of intracellular stores.
ENZYME REGULATION: By ATP.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in cardiac sarcolemma, brain, kidney, liver, pancreas, skeletal muscle, placenta and lung.
SIMILARITY: Belongs to the sodium/potassium/calcium exchanger family. SLC8 subfamily.
SIMILARITY: Contains 2 Calx-beta domains.

-  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: SLC8A1
Diseases sorted by gene-association score: long qt syndrome 9 (7), corneal dystrophy, schnyder type (6), aromatase deficiency (5), heart disease (3), cardiomyopathy (2), arrhythmogenic right ventricular cardiomyopathy (2), hypertension, essential (1), long qt syndrome 1 (1)

-  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: 9.89 RPKM in Heart - Left Ventricle
Total median expression: 80.75 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 -77.50211-0.367 Picture PostScript Text
3' UTR -4348.3917983-0.242 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
IPR003644 - Calx_beta
IPR001623 - DnaJ_N
IPR004836 - Na_Ca_Ex
IPR002987 - NaCa_exhngr1
IPR004837 - NaCa_Exmemb

Pfam Domains:
PF01699 - Sodium/calcium exchanger protein
PF03160 - Calx-beta domain
PF16494 - C-terminal extension of sodium/calcium exchanger domain

SCOP Domains:
141072 - CalX-like

ModBase Predicted Comparative 3D Structure on P32418
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005432 calcium:sodium antiporter activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0008092 cytoskeletal protein binding
GO:0015297 antiporter activity
GO:0030506 ankyrin binding
GO:0044325 ion channel binding
GO:0046872 metal ion binding
GO:0099580 ion antiporter activity involved in regulation of postsynaptic membrane potential

Biological Process:
GO:0001666 response to hypoxia
GO:0002026 regulation of the force of heart contraction
GO:0002027 regulation of heart rate
GO:0002028 regulation of sodium ion transport
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0006816 calcium ion transport
GO:0006874 cellular calcium ion homeostasis
GO:0006883 cellular sodium ion homeostasis
GO:0006936 muscle contraction
GO:0007154 cell communication
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007584 response to nutrient
GO:0009749 response to glucose
GO:0010649 regulation of cell communication by electrical coupling
GO:0010763 positive regulation of fibroblast migration
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
GO:0010882 regulation of cardiac muscle contraction by calcium ion signaling
GO:0014829 vascular smooth muscle contraction
GO:0021537 telencephalon development
GO:0030501 positive regulation of bone mineralization
GO:0033198 response to ATP
GO:0034614 cellular response to reactive oxygen species
GO:0035725 sodium ion transmembrane transport
GO:0035902 response to immobilization stress
GO:0035994 response to muscle stretch
GO:0036376 sodium ion export from cell
GO:0042493 response to drug
GO:0042542 response to hydrogen peroxide
GO:0044557 relaxation of smooth muscle
GO:0051481 negative regulation of cytosolic calcium ion concentration
GO:0051924 regulation of calcium ion transport
GO:0055013 cardiac muscle cell development
GO:0055074 calcium ion homeostasis
GO:0055085 transmembrane transport
GO:0055119 relaxation of cardiac muscle
GO:0060048 cardiac muscle contraction
GO:0060078 regulation of postsynaptic membrane potential
GO:0060401 cytosolic calcium ion transport
GO:0060402 calcium ion transport into cytosol
GO:0070509 calcium ion import
GO:0070588 calcium ion transmembrane transport
GO:0071313 cellular response to caffeine
GO:0071320 cellular response to cAMP
GO:0071456 cellular response to hypoxia
GO:0086012 membrane depolarization during cardiac muscle cell action potential
GO:0086064 cell communication by electrical coupling involved in cardiac conduction
GO:0098719 sodium ion import across plasma membrane
GO:0098735 positive regulation of the force of heart contraction
GO:1901660 calcium ion export
GO:1903779 regulation of cardiac conduction

Cellular Component:
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0014704 intercalated disc
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030018 Z disc
GO:0030315 T-tubule
GO:0042383 sarcolemma
GO:0042995 cell projection
GO:0043197 dendritic spine
GO:0043198 dendritic shaft
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  BX537482 - Homo sapiens mRNA; cDNA DKFZp779F0871 (from clone DKFZp779F0871).
BX648299 - Homo sapiens mRNA; cDNA DKFZp686J04125 (from clone DKFZp686J04125).
M91368 - Human Na+/Ca+ exchanger (CNC) mRNA, complete cds.
M96368 - Homo sapiens Na+/Ca+ exchanger mRNA sequence.
BC098285 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 1, mRNA (cDNA clone IMAGE:40008516), partial cds.
BC098308 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 1, mRNA (cDNA clone IMAGE:40008518), complete cds.
BC098345 - Homo sapiens cDNA clone IMAGE:40008513, with apparent retained intron.
AK291696 - Homo sapiens cDNA FLJ77463 complete cds.
AF128524 - Homo sapiens sodium-calcium exchanger isoform NCX1.7 precursor (SLC8A1) mRNA, complete cds.
AB209075 - Homo sapiens mRNA for solute carrier family 8 (sodium/calcium exchanger), member 1 variant protein.
AF108388 - Homo sapiens sodium/calcium exchanger isoform NaCa7 (NCX1) mRNA, complete cds.
AF108389 - Homo sapiens sodium/calcium exchanger isoform NaCa3 (NCX1) mRNA, complete cds.
BC172488 - Synthetic construct Homo sapiens clone IMAGE:100069182, MGC:199193 solute carrier family 8 (sodium/calcium exchanger), member 1 (SLC8A1) mRNA, encodes complete protein.
BC156359 - Synthetic construct Homo sapiens clone IMAGE:100061840, MGC:190113 solute carrier family 8 (sodium/calcium exchanger), member 1 (SLC8A1) mRNA, encodes complete protein.
AF115505 - Homo sapiens sodium/calcium exchanger 1 splice variant NaCa10 (SLC8A1) mRNA, partial cds.
AK095013 - Homo sapiens cDNA FLJ37694 fis, clone BRHIP2015224.
AK125406 - Homo sapiens cDNA FLJ43417 fis, clone OCBBF2026025.
JD120605 - Sequence 101629 from Patent EP1572962.
JD379770 - Sequence 360794 from Patent EP1572962.
JD120604 - Sequence 101628 from Patent EP1572962.
X91221 - H.sapiens mRNA for NCX1 protein 3'UTR.
JD499603 - Sequence 480627 from Patent EP1572962.
JD378896 - Sequence 359920 from Patent EP1572962.
Y13033 - Homo sapiens NCX1 mRNA alternative 5'end, exon 1c and 2.
Y12878 - Homo sapiens NCX1 mRNA alternative 5'end, exon 1d, 1c and 2.
Y13032 - Homo sapiens NCX1 mRNA alternative 5'end, exon 1a, 1e and 2.
Y12885 - Homo sapiens NCX1 mRNA alternative 5'end, exon 1d and 2.
JD234492 - Sequence 215516 from Patent EP1572962.

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

Protein P32418 (Reactome details) participates in the following event(s):

R-HSA-425661 SLC8A1,2,3 exchange 3Na+ for Ca2+
R-HSA-418359 Reduction of cytosolic Ca++ levels
R-HSA-425561 Sodium/Calcium exchangers
R-HSA-5578775 Ion homeostasis
R-HSA-418360 Platelet calcium homeostasis
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-5576891 Cardiac conduction
R-HSA-418346 Platelet homeostasis
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-397014 Muscle contraction
R-HSA-109582 Hemostasis
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6N1, CNC, D6W595, ENST00000332839.1, ENST00000332839.2, ENST00000332839.3, ENST00000332839.4, ENST00000332839.5, ENST00000332839.6, ENST00000332839.7, ENST00000332839.8, NAC1_HUMAN, NCX1 , NM_021097, O95849, P32418, Q4QQG6, Q587I6, Q59GN4, Q9UBL8, Q9UD55, Q9UDN1, Q9UDN2, Q9UKX6, uc317tnn.1, uc317tnn.2
UCSC ID: ENST00000332839.9_11
RefSeq Accession: NM_021097.5
Protein: P32418 (aka NAC1_HUMAN)

-  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.