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Aliases for SLC9A3 Gene

Aliases for SLC9A3 Gene

  • Solute Carrier Family 9, Subfamily A (NHE3, Cation Proton Antiporter 3), Member 3 2 3
  • NHE3 3 4 6
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Member 3 2 3
  • Solute Carrier Family 9 Member 3 3 4
  • Na(+)/H(+) Exchanger 3 3 4
  • NHE-3 3 4
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Isoform 3 2
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger) 3
  • Sodium/Hydrogen Exchanger 3 3

External Ids for SLC9A3 Gene

Previous Symbols for SLC9A3 Gene

  • NHE3

Summaries for SLC9A3 Gene

GeneCards Summary for SLC9A3 Gene

SLC9A3 (Solute Carrier Family 9, Subfamily A (NHE3, Cation Proton Antiporter 3), Member 3) is a Protein Coding gene. Diseases associated with SLC9A3 include proximal renal tubular acidosis and meconium ileus. Among its related pathways are CREB Pathway and G12-G13 in Cellular Signaling. GO annotations related to this gene include PDZ domain binding and sodium:proton antiporter activity. An important paralog of this gene is SLC9A4.

UniProtKB/Swiss-Prot for SLC9A3 Gene

  • Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction

Gene Wiki entry for SLC9A3 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC9A3 Gene

Genomics for SLC9A3 Gene

Genomic Location for SLC9A3 Gene

473,219 bp from pter
524,434 bp from pter
51,216 bases
Minus strand

Genomic View for SLC9A3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SLC9A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC9A3 Gene

Regulatory Elements for SLC9A3 Gene

Proteins for SLC9A3 Gene

  • Protein details for SLC9A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium/hydrogen exchanger 3
    Protein Accession:
    Secondary Accessions:
    • B7ZKR2
    • E9PF67
    • Q3MIW3

    Protein attributes for SLC9A3 Gene

    834 amino acids
    Molecular mass:
    92855 Da
    Quaternary structure:
    • Binds SLC9A3R1 and SLC9A3R2. Interacts with CHP1, CHP2 and SHANK2. Interacts with PDZK1 (via C-terminal PDZ domain) (By similarity). Interacts with PDZD3 and interactions decrease in response to elevated calcium ion levels.

    Alternative splice isoforms for SLC9A3 Gene


neXtProt entry for SLC9A3 Gene

Proteomics data for SLC9A3 Gene at MOPED

Post-translational modifications for SLC9A3 Gene

  • Phosphorylated by PKA, which inhibits activity. Phosphorylation at Ser-663 by SGK1 is associated with increased abundance at the cell membrane.
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn241 and Asn326

Other Protein References for SLC9A3 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC9A3 Gene

Domains for SLC9A3 Gene

Gene Families for SLC9A3 Gene

Suggested Antigen Peptide Sequences for SLC9A3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family.:
    • P48764
genes like me logo Genes that share domains with SLC9A3: view

Function for SLC9A3 Gene

Molecular function for SLC9A3 Gene

GENATLAS Biochemistry: solute carrier protein family 9 (sodium/hydrogen exchange),member 3,involved in intracellular pH regulation and cell volume,isoform 3B,apical epithelium,expressed in kidney,gastrointestinal tract (amiloride insensitive)
UniProtKB/Swiss-Prot Function: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction

Gene Ontology (GO) - Molecular Function for SLC9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16159897
GO:0015299 solute:proton antiporter activity --
GO:0015385 sodium:proton antiporter activity ISS --
GO:0030165 PDZ domain binding ISS --
genes like me logo Genes that share ontologies with SLC9A3: view
genes like me logo Genes that share phenotypes with SLC9A3: view

Animal Models for SLC9A3 Gene

MGI Knock Outs for SLC9A3:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for SLC9A3 Gene

Localization for SLC9A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC9A3 Gene

Apical cell membrane; Multi-pass membrane protein. Note=In intestinal epithelial cells, localizes to the ileal brush border. Phosphorylation at Ser-663 by SGK1 is associated with increased abundance at the cell membrane.

Subcellular locations from

Jensen Localization Image for SLC9A3 Gene COMPARTMENTS Subcellular localization image for SLC9A3 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1
endosome 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SLC9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005903 brush border ISS --
GO:0009986 cell surface ISS --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with SLC9A3: view

Pathways for SLC9A3 Gene

genes like me logo Genes that share pathways with SLC9A3: view

Gene Ontology (GO) - Biological Process for SLC9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport TAS --
GO:0006812 cation transport --
GO:0006814 sodium ion transport --
GO:0006885 regulation of pH IEA --
GO:0035725 sodium ion transmembrane transport ISS --
genes like me logo Genes that share ontologies with SLC9A3: view

Compounds for SLC9A3 Gene

(1) HMDB Compounds for SLC9A3 Gene

Compound Synonyms Cas Number PubMed IDs
  • Sodium

(60) Novoseek inferred chemical compound relationships for SLC9A3 Gene

Compound -log(P) Hits PubMed IDs
hoe 694 88.3 5
eipa 84.9 12
sulfosuccinimidyl acetate 79 2
glycylsarcosine 73.9 4
hoe-642 71.2 1
genes like me logo Genes that share compounds with SLC9A3: view

Transcripts for SLC9A3 Gene

mRNA/cDNA for SLC9A3 Gene

(6) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC9A3 Gene

Solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SLC9A3 Gene

No ASD Table

Relevant External Links for SLC9A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC9A3 Gene

mRNA expression in normal human tissues for SLC9A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC9A3 Gene

This gene is overexpressed in Colon - Transverse (8.4), Kidney - Cortex (7.2), and Stomach (6.6).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SLC9A3 Gene

SOURCE GeneReport for Unigene cluster for SLC9A3 Gene Hs.658120

genes like me logo Genes that share expressions with SLC9A3: view

No data available for mRNA Expression by UniProt/SwissProt for SLC9A3 Gene

Orthologs for SLC9A3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC9A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC9A3 35
  • 95.25 (n)
  • 94.99 (a)
SLC9A3 36
  • 99 (a)
(Bos Taurus)
Mammalia SLC9A3 35
  • 87.26 (n)
  • 88.1 (a)
SLC9A3 36
  • 88 (a)
(Canis familiaris)
Mammalia SLC9A3 36
  • 68 (a)
(Mus musculus)
Mammalia Slc9a3 35
  • 84.26 (n)
  • 91.56 (a)
Slc9a3 16
Slc9a3 36
  • 90 (a)
(Monodelphis domestica)
Mammalia SLC9A3 36
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia SLC9A3 36
  • 85 (a)
(Rattus norvegicus)
Mammalia Slc9a3 35
  • 85 (n)
  • 91.27 (a)
(Gallus gallus)
Aves SLC9A3 35
  • 71.26 (n)
  • 82.96 (a)
SLC9A3 36
  • 82 (a)
(Anolis carolinensis)
Reptilia SLC9A3 36
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492870 35
  • 66.04 (n)
  • 76.95 (a)
(Danio rerio)
Actinopterygii slc9a3.1 35
  • 61.55 (n)
  • 56.23 (a)
slc9a3.1 36
  • 51 (a)
slc9a3.2 36
  • 46 (a)
(Caenorhabditis elegans)
Secernentea nhx-4 36
  • 24 (a)
pbo-4 36
  • 29 (a)
nhx-9 37
  • 45 (a)
nhx-7 37
  • 32 (a)
nhx-6 37
  • 40 (a)
nhx-3 37
  • 44 (a)
nhx-2 37
  • 39 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHX1 36
  • 22 (a)
Species with no ortholog for SLC9A3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC9A3 Gene

Gene Tree for SLC9A3 (if available)
Gene Tree for SLC9A3 (if available)

Paralogs for SLC9A3 Gene

Paralogs for SLC9A3 Gene

Selected SIMAP similar genes for SLC9A3 Gene using alignment to 3 proteins: Pseudogenes for SLC9A3 Gene

genes like me logo Genes that share paralogs with SLC9A3: view

Variants for SLC9A3 Gene

Sequence variations from dbSNP and Humsavar for SLC9A3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs925693 -- 516,262(-) GGGGA(A/T)CCCAC intron-variant
rs938324 -- 522,867(-) AGGGA(A/G)GTCCA intron-variant
rs1560173 -- 485,711(+) AGGTG(A/G)GACCG intron-variant
rs2278247 -- 483,248(+) CAACC(C/T)GGCCC intron-variant
rs2303734 -- 484,828(+) AGATC(C/G)GGCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC9A3 Gene

Variant ID Type Subtype PubMed ID
dgv1733e1 CNV Complex 17122850
nsv880815 CNV Loss 21882294
nsv830183 CNV Gain+Loss 17160897
esv2752071 CNV Gain 17911159
dgv5880n71 CNV Loss 21882294
nsv881301 CNV Gain 21882294
dgv5881n71 CNV Gain 21882294
dgv5882n71 CNV Loss 21882294
nsv880710 CNV Loss 21882294
nsv881627 CNV Loss 21882294
nsv461889 CNV Gain 19166990
nsv881561 CNV Gain 21882294
nsv461890 CNV Gain 19166990
dgv5883n71 CNV Gain 21882294
dgv5884n71 CNV Gain 21882294
nsv4674 CNV Insertion 18451855
nsv527666 CNV Loss 19592680
dgv5885n71 CNV Loss 21882294
dgv5886n71 CNV Loss 21882294
dgv5887n71 CNV Loss 21882294
nsv881305 CNV Loss 21882294
nsv880308 CNV Loss 21882294
dgv5888n71 CNV Loss 21882294
nsv822926 CNV Gain 20364138
esv22420 CNV Loss 19812545
esv23175 CNV Gain+Loss 19812545
esv1236919 CNV Insertion 17803354
esv1638372 CNV Deletion 17803354
esv1003268 CNV Deletion 20482838
nsv521554 CNV Loss 19592680
nsv880336 CNV Gain 21882294
nsv519778 CNV Loss 19592680
nsv881493 CNV Loss 21882294
nsv822927 CNV Gain 20364138
nsv509042 CNV Insertion 20534489
esv4866 CNV Deletion 18987735
esv990425 CNV Deletion 20482838
esv1337538 CNV Deletion 17803354
esv2577884 CNV Deletion 19546169
esv3198 CNV Deletion 18987735
nsv821281 CNV Deletion 20802225
esv28351 CNV Gain 19812545
nsv513206 CNV Loss 21212237
esv1092347 CNV Deletion 17803354
nsv10648 CNV Gain 18304495
nsv880819 CNV Loss 21882294
nsv328215 CNV Insertion 16902084
esv28621 CNV Gain 19812545
nsv329001 CNV Loss 16902084
nsv10649 CNV Gain 18304495
esv1354613 CNV Deletion 17803354
esv28080 CNV Loss 19812545
nsv881103 CNV Gain 21882294
esv4637 CNV Deletion 18987735
esv2729310 CNV Deletion 23290073
esv2729311 CNV Deletion 23290073
esv2477798 CNV Insertion 19546169
esv1005209 CNV Insertion 20482838
esv1690608 CNV Insertion 17803354
esv2729312 CNV Deletion 23290073
esv1709487 CNV Insertion 17803354
esv1770003 CNV Insertion 17803354
esv2729313 CNV Deletion 23290073
esv2729314 CNV Deletion 23290073
nsv881051 CNV Gain 21882294
esv2729315 CNV Deletion 23290073
esv2729316 CNV Deletion 23290073
nsv881513 CNV Loss 21882294
nsv10651 CNV Gain 18304495

Relevant External Links for SLC9A3 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC9A3 Gene

Disorders for SLC9A3 Gene

(14) Novoseek inferred disease relationships for SLC9A3 Gene

Disease -log(P) Hits PubMed IDs
metabolic acidosis 31 5
cystic fibrosis 26.7 7
acidosis 25.5 2
hypokalemia 20.3 2
adenoma 18.9 6

Relevant External Links for SLC9A3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SLC9A3: view

No data available for UniProtKB/Swiss-Prot for SLC9A3 Gene

Publications for SLC9A3 Gene

  1. Cloning, tissue distribution, and functional analysis of the human Na+/N+ exchanger isoform, NHE3. (PMID: 7631746) Brant S.R. … Tse C.-M. (Am. J. Physiol. 1995) 3 4 23
  2. Physical and genetic mapping of a human apical epithelial Na+/H+ exchanger (NHE3) isoform to chromosome 5p15.3. (PMID: 8096830) Brant S.R. … Tse C.M. (Genomics 1993) 2 3 23
  3. Molecular variants of the sodium/hydrogen exchanger type 3 gene and essential hypertension. (PMID: 15201541) Zhu H. … MacGregor G.A. (J. Hypertens. 2004) 3 23 48
  4. Impact of sodium/proton exchanger 3 gene variants on sudden infant death syndrome. (PMID: 19772970) Poetsch M. … Bajanowski T. (J. Pediatr. 2010) 3 23 48
  5. Functional coupling of the downregulated in adenoma Cl-/base exchanger DRA and the apical Na+/H+ exchangers NHE2 and NHE3. (PMID: 19056765) Musch M.W. … Chang E.B. (Am. J. Physiol. Gastrointest. Liver Physiol. 2009) 3 23

Products for SLC9A3 Gene

Sources for SLC9A3 Gene

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