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SLC9A3 solute carrier family 9 member A3 [ Homo sapiens (human) ]

Gene ID: 6550, updated on 4-Jun-2020

Summary

Official Symbol
SLC9A3provided by HGNC
Official Full Name
solute carrier family 9 member A3provided by HGNC
Primary source
HGNC:HGNC:11073
See related
Ensembl:ENSG00000066230 MIM:182307
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
NHE3; DIAR8; NHE-3
Summary
The protein encoded by this gene is an epithelial brush border Na/H exchanger that uses an inward sodium ion gradient to expel acids from the cell. Defects in this gene are a cause of congenital secretory sodium diarrhea. Pseudogenes of this gene exist on chromosomes 10 and 22. [provided by RefSeq, Mar 2016]
Expression
Biased expression in colon (RPKM 56.4), kidney (RPKM 51.3) and 9 other tissues See more
Orthologs

Genomic context

See SLC9A3 in Genome Data Viewer
Location:
5p15.33
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (470456..524449, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (473298..524549, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene EXOC3 antisense RNA 1 Neighboring gene exocyst complex component 3 Neighboring gene SLC9A3 antisense RNA 1 Neighboring gene uncharacterized LOC25845 Neighboring gene uncharacterized LOC107986395 Neighboring gene microRNA 4456

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
Diarrhea 8, secretory sodium, congenital
MedGen: CN515063 OMIM: 616868 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of solute carrier family 9 (sodium/hydrogen exchanger), member 3 (SLC9A3) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef EIPA, a potent and specific inhibitor of Na+/H+ exchanger activity, significantly inhibits the Nef internalization into M2-macrophages, indicating that Nef is imported by Na+/H+ exchanger (solute carrier family 9, subfamily A) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC126718, MGC126720

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding ISS
Inferred from Sequence or Structural Similarity
more info
 
potassium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sodium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium:proton antiporter activity IDA
Inferred from Direct Assay
more info
PubMed 
sodium:proton antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
anion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
ion transport TAS
Traceable Author Statement
more info
 
potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion import across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
apical plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
brush border ISS
Inferred from Sequence or Structural Similarity
more info
 
brush border membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
cell surface ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium/hydrogen exchanger 3
Names
Na(+)/H(+) exchanger 3
solute carrier family 9 (sodium/hydrogen exchanger), isoform 3
solute carrier family 9 (sodium/hydrogen exchanger), member 3
solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3

NCBI Reference Sequences (RefSeq)

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_046804.1 RefSeqGene

    Range
    50980..104973
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001284351.3NP_001271280.1  sodium/hydrogen exchanger 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the mid-coding region compared to variant 1. The resulting shorter isoform (2) lacks a 9 aa protein segment compared to isoform 1.
    Source sequence(s)
    AC010442, AC106772, BC011555, BC101669, BC143328, BP270851
    Consensus CDS
    CCDS64116.1
    UniProtKB/Swiss-Prot
    P48764
    Related
    ENSP00000422983.1, ENST00000514375.1
    Conserved Domains (3) summary
    TIGR00840
    Location:48637
    b_cpa1; sodium/hydrogen exchanger 3
    pfam00999
    Location:105457
    Na_H_Exchanger; Sodium/hydrogen exchanger family
    pfam16644
    Location:595667
    NEXCaM_BD; Regulatory region of Na+/H+ exchanger NHE binds to calmodulin
  2. NM_004174.4NP_004165.2  sodium/hydrogen exchanger 3 isoform 1

    See identical proteins and their annotated locations for NP_004165.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC010442, AC106772, BC011555, BC101669, BP270851
    Consensus CDS
    CCDS3855.1
    UniProtKB/Swiss-Prot
    P48764
    Related
    ENSP00000264938.3, ENST00000264938.8
    Conserved Domains (3) summary
    TIGR00840
    Location:48646
    b_cpa1; sodium/hydrogen exchanger 3
    pfam00999
    Location:105462
    Na_H_Exchanger; Sodium/hydrogen exchanger family
    pfam16644
    Location:604676
    NEXCaM_BD; Regulatory region of Na+/H+ exchanger NHE binds to calmodulin

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    470456..524449 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187550.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    104122..104460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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