Format

Send to:

Choose Destination

SLC8A3 solute carrier family 8 member A3 [ Homo sapiens (human) ]

Gene ID: 6547, updated on 3-Feb-2021

Summary

Official Symbol
SLC8A3provided by HGNC
Official Full Name
solute carrier family 8 member A3provided by HGNC
Primary source
HGNC:HGNC:11070
See related
Ensembl:ENSG00000100678 MIM:607991
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NCX3
Summary
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]
Expression
Biased expression in brain (RPKM 2.0), adrenal (RPKM 0.3) and 4 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SLC8A3 in Genome Data Viewer
Location:
14q24.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (70044215..70189626, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (70510932..70655668, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene SPARC related modular calcium binding 1 Neighboring gene small nucleolar RNA, C/D box 169 Neighboring gene Sharpr-MPRA regulatory region 14883 Neighboring gene ADAM metallopeptidase domain 20 pseudogene Neighboring gene uncharacterized LOC107984686 Neighboring gene histone deacetylase complex subunit SAP25 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genetic variants near PDGFRA are associated with corneal curvature in Australians.
GeneReviews: Not available
Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2.
GeneReviews: Not available
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
 
calcium:sodium antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium:sodium antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
cation:cation antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ion antiporter activity involved in regulation of postsynaptic membrane potential IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
calcium ion export across plasma membrane IEA
Inferred from Electronic Annotation
more info
 
calcium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
 
cell communication IEA
Inferred from Electronic Annotation
more info
 
cellular calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to cAMP IEA
Inferred from Electronic Annotation
more info
 
cellular response to hypoxia ISS
Inferred from Sequence or Structural Similarity
more info
 
hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
ion transport TAS
Traceable Author Statement
more info
 
learning ISS
Inferred from Sequence or Structural Similarity
more info
 
learning or memory ISS
Inferred from Sequence or Structural Similarity
more info
 
long-term synaptic potentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
memory ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
mitochondrial calcium ion transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
 
modulation of excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
myelination ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of protein serine/threonine kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
oligodendrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cardiac conduction TAS
Traceable Author Statement
more info
 
regulation of postsynaptic cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
 
regulation of skeletal muscle contraction ISS
Inferred from Sequence or Structural Similarity
more info
 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse organization ISS
Inferred from Sequence or Structural Similarity
more info
 
telencephalon development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
axon terminus ISS
Inferred from Sequence or Structural Similarity
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
intrinsic component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
microtubule IEA
Inferred from Electronic Annotation
more info
 
mitochondrial outer membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
neuromuscular junction ISS
Inferred from Sequence or Structural Similarity
more info
 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
perikaryon IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
sarcolemma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sarcolemma ISS
Inferred from Sequence or Structural Similarity
more info
 
sarcoplasm IEA
Inferred from Electronic Annotation
more info
 
synapse IDA
Inferred from Direct Assay
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
sodium/calcium exchanger 3
Names
Na(+)/Ca(2+)-exchange protein 3
sodium/calcium exchanger SLC8A3
solute carrier family 8 (sodium/calcium exchanger), member 3

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047080.1 RefSeqGene

    Range
    39662..184398
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130417.3NP_001123889.1  sodium/calcium exchanger 3 isoform G

    See identical proteins and their annotated locations for NP_001123889.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (g, also known as NCX3-tN.2) differs in the presence and absence of exons at its 5' end, compared to variant c. These differences result in a distinct 5' UTR and translation initiation at a downstream start codon, and an isoform (G) that is shorter than isoform C.
    Source sequence(s)
    AF510501, AL135747, BC142969, BX098112, DA351808
    Consensus CDS
    CCDS45131.1
    UniProtKB/Swiss-Prot
    P57103
    Related
    ENSP00000216568.7, ENST00000216568.11
    Conserved Domains (1) summary
    cl02522
    Location:10298
    Calx-beta; Calx-beta domain
  2. NM_033262.5NP_150287.1  sodium/calcium exchanger 3 isoform A precursor

    See identical proteins and their annotated locations for NP_150287.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) includes an alternate in-frame exon, lacks another alternate in-frame exon and uses an alternate in-frame splice site in the mid coding region, compared to variant c. The encoded isoform (A) is shorter than isoform C.
    Source sequence(s)
    AF510501, AJ304852, AL135747, BX098112
    Consensus CDS
    CCDS9799.1
    UniProtKB/Swiss-Prot
    P57103
    Related
    ENSP00000350560.3, ENST00000357887.7
    Conserved Domains (1) summary
    TIGR00845
    Location:1925
    caca; sodium/calcium exchanger 1
  3. NM_058240.4NP_489479.1  sodium/calcium exchanger 3 isoform B precursor

    See identical proteins and their annotated locations for NP_489479.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) uses an alternate in-frame splice site in the mid coding region, compared to variant c. The encoded isoform (B) is shorter than isoform C.
    Source sequence(s)
    AF510502, AJ304853, AL135747, BX098112
    Consensus CDS
    CCDS53904.1
    UniProtKB/Swiss-Prot
    P57103
    Related
    ENSP00000436688.1, ENST00000534137.5
    Conserved Domains (1) summary
    TIGR00845
    Location:1924
    caca; sodium/calcium exchanger 1
  4. NM_182932.3NP_891977.1  sodium/calcium exchanger 3 isoform D precursor

    See identical proteins and their annotated locations for NP_891977.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d, also known as NCX3.2), lacks an alternate in-frame exon in the mid coding region, compared to variant c. The encoded isoform (D) is shorter than isoform C.
    Source sequence(s)
    AF510501, AL135747, BX098112
    Consensus CDS
    CCDS9800.1
    UniProtKB/Swiss-Prot
    P57103
    Related
    ENSP00000349392.2, ENST00000356921.6
    Conserved Domains (1) summary
    TIGR00845
    Location:1921
    caca; sodium/calcium exchanger 1
  5. NM_182936.3NP_891981.1  sodium/calcium exchanger 3 isoform F

    See identical proteins and their annotated locations for NP_891981.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (f, also known as NCX3-tN.1) differs in the presence and absence of exons at its 5' end, compared to variant c. These differences result in a distinct 5' UTR and translation initiation at a downstream start codon, and an isoform (F) that is shorter than isoform C.
    Source sequence(s)
    AF510501, AK096553, AL135747, BX098112, DA351808
    Consensus CDS
    CCDS41967.1
    UniProtKB/Swiss-Prot
    P57103
    UniProtKB/TrEMBL
    B3KU59
    Related
    ENSP00000377863.2, ENST00000394330.6
    Conserved Domains (1) summary
    TIGR00845
    Location:1284
    caca; sodium/calcium exchanger 1
  6. NM_183002.3NP_892114.1  sodium/calcium exchanger 3 isoform C precursor

    See identical proteins and their annotated locations for NP_892114.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c, also known as NCX3.3), encodes the longest isoform (C).
    Source sequence(s)
    AF510502, AL135747, BX098112
    Consensus CDS
    CCDS35498.1
    UniProtKB/Swiss-Prot
    P57103
    Related
    ENSP00000370669.2, ENST00000381269.6
    Conserved Domains (1) summary
    TIGR00845
    Location:1927
    caca; sodium/calcium exchanger 1

RNA

  1. NR_104122.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (h) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant c, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF510503, AL135747, BX098112
    Related
    ENST00000494208.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    70044215..70189626 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021608.1XP_016877097.1  sodium/calcium exchanger 3 isoform X3

    UniProtKB/Swiss-Prot
    P57103
    Conserved Domains (1) summary
    TIGR00845
    Location:1921
    caca; sodium/calcium exchanger 1
  2. XM_017021606.1XP_016877095.1  sodium/calcium exchanger 3 isoform X1

    UniProtKB/Swiss-Prot
    P57103
    Conserved Domains (1) summary
    TIGR00845
    Location:1927
    caca; sodium/calcium exchanger 1
  3. XM_017021609.1XP_016877098.1  sodium/calcium exchanger 3 isoform X4

    Conserved Domains (4) summary
    TIGR00845
    Location:1920
    caca; sodium/calcium exchanger 1
    pfam01699
    Location:746911
    Na_Ca_ex; Sodium/calcium exchanger protein
    pfam03160
    Location:395485
    Calx-beta; Calx-beta domain
    pfam16494
    Location:253374
    Na_Ca_ex_C; C-terminal extension of sodium/calcium exchanger domain
  4. XM_017021607.1XP_016877096.1  sodium/calcium exchanger 3 isoform X2

    Conserved Domains (4) summary
    TIGR00845
    Location:1926
    caca; sodium/calcium exchanger 1
    pfam01699
    Location:752917
    Na_Ca_ex; Sodium/calcium exchanger protein
    pfam03160
    Location:395485
    Calx-beta; Calx-beta domain
    pfam16494
    Location:253374
    Na_Ca_ex_C; C-terminal extension of sodium/calcium exchanger domain
  5. XM_006720240.3XP_006720303.1  sodium/calcium exchanger 3 isoform X7

    See identical proteins and their annotated locations for XP_006720303.1

    Conserved Domains (1) summary
    pfam01699
    Location:130295
    Na_Ca_ex; Sodium/calcium exchanger protein
  6. XM_017021611.1XP_016877100.1  sodium/calcium exchanger 3 isoform X6

  7. XM_017021610.1XP_016877099.1  sodium/calcium exchanger 3 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_182933.1: Suppressed sequence

    Description
    NM_182933.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center