Human Gene SLC8A3 (ENST00000534137.5) from GENCODE V38
  Description: Homo sapiens solute carrier family 8 member A3 (SLC8A3), transcript variant b, mRNA. (from RefSeq NM_058240)
RefSeq Summary (NM_058240): This gene encodes a member of the sodium/calcium exchanger integral membrane protein family. Na+/Ca2+ exchange proteins are involved in maintaining Ca2+ homeostasis in a wide variety of cell types. The protein is regulated by intracellular calcium ions and is found in both the plasma membrane and intracellular organellar membranes, where exchange of Na+ for Ca2+ occurs in an electrogenic manner. Alternative splicing has been observed for this gene and multiple variants have been described. [provided by RefSeq, Aug 2013].
Gencode Transcript: ENST00000534137.5
Gencode Gene: ENSG00000100678.19
Transcript (Including UTRs)
   Position: hg38 chr14:70,045,947-70,168,484 Size: 122,538 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr14:70,045,947-70,168,422 Size: 122,476 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr14:70,045,947-70,168,484)mRNA (may differ from genome)Protein (924 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Sodium/calcium exchanger 3; AltName: Full=Na(+)/Ca(2+)-exchange protein 3; 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 (By similarity).
ENZYME REGULATION: By intracellular calcium ions (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Isoform 2 is expressed in brain and skeletal muscle. Isoform 3 is expressed in excitable cells of brain, retina and skeletal muscle. Isoform 4 is expressed in skeletal muscle.
SIMILARITY: Belongs to the sodium/potassium/calcium exchanger family. SLC8 subfamily.
SIMILARITY: Contains 2 Calx-beta domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC8A3
Diseases sorted by gene-association score: corneal dystrophy, schnyder type (11), spastic paraplegia 24, autosomal recessive (10)

-  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: 4.16 RPKM in Muscle - Skeletal
Total median expression: 29.36 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 -17.7062-0.285 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
IPR004836 - Na_Ca_Ex
IPR004837 - NaCa_Exmemb

Pfam Domains:
PF03160 - Calx-beta domain
PF01699 - Sodium/calcium exchanger protein

ModBase Predicted Comparative 3D Structure on P57103
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
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGD EnsemblWormBase 
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005432 calcium:sodium antiporter activity
GO:0005516 calmodulin binding
GO:0015297 antiporter activity
GO:0015368 calcium:cation antiporter activity
GO:0046872 metal ion binding
GO:0099580 ion antiporter activity involved in regulation of postsynaptic membrane potential

Biological Process:
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0006816 calcium ion transport
GO:0006851 mitochondrial calcium ion transport
GO:0006874 cellular calcium ion homeostasis
GO:0007154 cell communication
GO:0007612 learning
GO:0007613 memory
GO:0014819 regulation of skeletal muscle contraction
GO:0021537 telencephalon development
GO:0030001 metal ion transport
GO:0035725 sodium ion transmembrane transport
GO:0042552 myelination
GO:0048709 oligodendrocyte differentiation
GO:0051560 mitochondrial calcium ion homeostasis
GO:0055085 transmembrane transport
GO:0060078 regulation of postsynaptic membrane potential
GO:0060291 long-term synaptic potentiation
GO:0060402 calcium ion transport into cytosol
GO:0070588 calcium ion transmembrane transport
GO:0071320 cellular response to cAMP
GO:0071456 cellular response to hypoxia
GO:0098703 calcium ion import across plasma membrane
GO:1903779 regulation of cardiac conduction
GO:1990034 calcium ion export from cell

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016528 sarcoplasm
GO:0030054 cell junction
GO:0030425 dendrite
GO:0031226 intrinsic component of plasma membrane
GO:0031594 neuromuscular junction
GO:0042383 sarcolemma
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0043204 perikaryon
GO:0048471 perinuclear region of cytoplasm

-  Descriptions from all associated GenBank mRNAs
  AF510501 - Homo sapiens Na+/Ca2+ exchanger isoform 3 splice variant 2 (SLC8A3) mRNA, complete cds; alternatively spliced.
AF510502 - Homo sapiens Na+/Ca2+ exchanger isoform 3 splice variant 3 (SLC8A3) mRNA, complete cds; alternatively spliced.
AF510503 - Homo sapiens Na+/Ca2+ exchanger isoform 3 splice variant 4 (SLC8A3) mRNA, complete cds; alternatively spliced.
AJ508602 - Homo sapiens partial mRNA for Na+/Ca2+ exchanger isoform 4 (NACAIS4 gene).
AJ304852 - Homo sapiens mRNA for sodium/calcium exchanger SCL8A3, alternative splice form A (SCL8A3 gene).
AJ304853 - Homo sapiens mRNA for sodium/calcium exchanger, SCL8A3, alternative splice form B (SCL8A3 gene).
BC160014 - Synthetic construct Homo sapiens clone IMAGE:100063950, MGC:193129 solute carrier family 8 (sodium/calcium exchanger), member 3 (SLC8A3) mRNA, encodes complete protein.
BC150183 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 3, mRNA (cDNA clone IMAGE:40148239), partial cds.
BC150193 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 3, mRNA (cDNA clone IMAGE:40148714), partial cds.
BC036783 - Homo sapiens solute carrier family 8 (sodium-calcium exchanger), member 3, mRNA (cDNA clone IMAGE:5732743).
AK122728 - Homo sapiens cDNA FLJ16234 fis, clone FEBRA2028503, highly similar to SODIUM/CALCIUM EXCHANGER 3 PRECURSOR.
BC142969 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 3, mRNA (cDNA clone IMAGE:8860390), complete cds.
AK096553 - Homo sapiens cDNA FLJ39234 fis, clone OCBBF2007762, highly similar to SODIUM/CALCIUM EXCHANGER 3 PRECURSOR.
AJ745101 - Homo sapiens mRNA for Na+/Ca2+ exchanger 3, variant NCX3-tN.1 (SLC8A3 gene).
AJ745102 - Homo sapiens mRNA for Na+/Ca2+ exchanger 3, variant NCX3-tN.2 (SLC8A3 gene).
KJ897569 - Synthetic construct Homo sapiens clone ccsbBroadEn_06963 SLC8A3 gene, encodes complete protein.
BC023215 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 3, mRNA (cDNA clone IMAGE:4932133), with apparent retained intron.
BC114217 - Homo sapiens solute carrier family 8 (sodium/calcium exchanger), member 3, mRNA (cDNA clone IMAGE:5194668), with apparent retained intron.
BX248763 - human full-length cDNA 5-PRIME end of clone CS0DB006YD18 of Neuroblastoma of Homo sapiens (human).

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04020 - Calcium signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P57103 (Reactome details) participates in the following event(s):

R-HSA-425661 SLC8A1,2,3 exchange 3Na+ for Ca2+
R-HSA-8949703 SLC8A3 (NCX3) exchanges sodium (cytosol) for calcium (mitochondrial intermembrane space)
R-HSA-418359 Reduction of cytosolic Ca++ levels
R-HSA-425561 Sodium/Calcium exchangers
R-HSA-5578775 Ion homeostasis
R-HSA-8949215 Mitochondrial calcium ion transport
R-HSA-418360 Platelet calcium homeostasis
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-5576891 Cardiac conduction
R-HSA-382551 Transport of small molecules
R-HSA-418346 Platelet homeostasis
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-397014 Muscle contraction
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000534137.1, ENST00000534137.2, ENST00000534137.3, ENST00000534137.4, NAC3_HUMAN, NCX3, NM_058240, P57103, Q5K3P6, Q5K3P7, Q8IUE9, Q8IUF0, Q8NFI7, Q96QG1, Q96QG2, uc059cwf.1
UCSC ID: ENST00000534137.5
RefSeq Accession: NM_058240
Protein: P57103 (aka NAC3_HUMAN)
CCDS: CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS53904.1

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