Human Gene SLC9A1 (ENST00000263980.8_7) from GENCODE V47lift37
  Description: solute carrier family 9 member A1, transcript variant 2 (from RefSeq NR_046474.2)
Gencode Transcript: ENST00000263980.8_7
Gencode Gene: ENSG00000090020.11_11
Transcript (Including UTRs)
   Position: hg19 chr1:27,425,300-27,481,616 Size: 56,317 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr1:27,426,798-27,480,825 Size: 54,028 Coding Exon Count: 12 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:27,425,300-27,481,616)mRNA (may differ from genome)Protein (815 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SL9A1_HUMAN
DESCRIPTION: RecName: Full=Sodium/hydrogen exchanger 1; AltName: Full=APNH; AltName: Full=Na(+)/H(+) antiporter, amiloride-sensitive; AltName: Full=Na(+)/H(+) exchanger 1; Short=NHE-1; AltName: Full=Solute carrier family 9 member 1;
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.
BIOPHYSICOCHEMICAL PROPERTIES: pH dependence: Fully active at acidic pHs, the antiporter is virtually turned off at neutral pH;
SUBUNIT: Oligomer (By similarity). Interacts with calmodulin and TESC. Interacts (via the juxtamembrane region of the cytoplasmic C-terminus domain) with CHP1; the interaction occurs at the plasma membrane in a calcium-dependent manner. Interacts with CHP2; the interaction occurs in a calcium-dependent manner.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). Cell membrane; Multi-pass membrane protein. Note=Colocalizes with CHP1 at the reticulum endoplasmic (By similarity). Colocalizes with CHP1 and CHP2 at the plasma membrane.
TISSUE SPECIFICITY: Kidney and intestine.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
PTM: O-glycosylated.
PTM: Ubiquitinated, leading to its degradation by the proteasome. Ubiquitination is reduced by CHP1 (By similarity).
MISCELLANEOUS: Inhibited by amiloride and 5-amino-substituted derivatives and activated in a cooperative fashion by intracellular H(+). In quiescent cells upon growth factor stimulation, the apparent affinity for internal H(+) is increased, resulting in a persistent rise in cytoplasmic pH.
SIMILARITY: Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family.
CAUTION: The region between transmembrane regions M4 and M5 and between M6 and M7 (also termed intracellular loops IL2 and IL4, respectively) seem to be localized at least in part in the membrane. The hydrophobic region H10 is proposed to be located within the membrane.
CAUTION: Although PubMed:12809501 report that TESC-binding results in a decrease in activity, studies with rat SLC9A1 show that TESC- binding results in the maturation and accumulation of SLC9A1 at the cell surface.
CAUTION: Although PubMed:12809501 report that CHP1 and TESC bind to SLC9A1 at different sites, studies with rat SLC9A1 show that they bind at the same C-terminal site.

-  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: SLC9A1
Diseases sorted by gene-association score: lichtenstein-knorr syndrome* (1640), myocardial stunning (27), microvillus inclusion disease (8), metabolic acidosis (7), muscle hypertrophy (6), cataract 14, multiple types (6), ventricular fibrillation, familial, 1 (3), hypertension, essential (2)
* = Manually curated disease association

-  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: 19.63 RPKM in Stomach
Total median expression: 438.10 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 -274.10791-0.347 Picture PostScript Text
3' UTR -575.601498-0.384 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
IPR006153 - Cation/H_exchanger
IPR018422 - Cation/H_exchanger_CPA1
IPR001970 - Na/H_exchanger_1
IPR004709 - NaH_exchanger

Pfam Domains:
PF00999 - Sodium/hydrogen exchanger family
PF16644 - Regulatory region of Na+/H+ exchanger NHE binds to calmodulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1Y4E - NMR MuPIT 2BEC - X-ray MuPIT 2E30 - NMR MuPIT 2HTG - NMR 2KBV - NMR 2L0E - NMR 2YGG - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P19634
FrontTopSide
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0015297 antiporter activity
GO:0015299 solute:proton antiporter activity
GO:0015385 sodium:proton antiporter activity
GO:0015386 potassium:proton antiporter activity
GO:0030346 protein phosphatase 2B binding
GO:0030674 protein binding, bridging
GO:0032947 protein complex scaffold
GO:0048306 calcium-dependent protein binding
GO:0086040 sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential

Biological Process:
GO:0002026 regulation of the force of heart contraction
GO:0006811 ion transport
GO:0006812 cation transport
GO:0006814 sodium ion transport
GO:0006883 cellular sodium ion homeostasis
GO:0006885 regulation of pH
GO:0010447 response to acidic pH
GO:0010613 positive regulation of cardiac muscle hypertrophy
GO:0010882 regulation of cardiac muscle contraction by calcium ion signaling
GO:0014070 response to organic cyclic compound
GO:0016477 cell migration
GO:0030011 maintenance of cell polarity
GO:0030154 cell differentiation
GO:0030214 hyaluronan catabolic process
GO:0030307 positive regulation of cell growth
GO:0032869 cellular response to insulin stimulus
GO:0035794 positive regulation of mitochondrial membrane permeability
GO:0035994 response to muscle stretch
GO:0036376 sodium ion export from cell
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0045760 positive regulation of action potential
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051259 protein oligomerization
GO:0051453 regulation of intracellular pH
GO:0051492 regulation of stress fiber assembly
GO:0051893 regulation of focal adhesion assembly
GO:0051930 regulation of sensory perception of pain
GO:0055007 cardiac muscle cell differentiation
GO:0055085 transmembrane transport
GO:0070417 cellular response to cold
GO:0070886 positive regulation of calcineurin-NFAT signaling cascade
GO:0070997 neuron death
GO:0071236 cellular response to antibiotic
GO:0071257 cellular response to electrical stimulus
GO:0071260 cellular response to mechanical stimulus
GO:0071407 cellular response to organic cyclic compound
GO:0071456 cellular response to hypoxia
GO:0071468 cellular response to acidic pH
GO:0071805 potassium ion transmembrane transport
GO:0071872 cellular response to epinephrine stimulus
GO:0086003 cardiac muscle cell contraction
GO:0086036 regulation of cardiac muscle cell membrane potential
GO:0086092 regulation of the force of heart contraction by cardiac conduction
GO:0098719 sodium ion import across plasma membrane
GO:0098735 positive regulation of the force of heart contraction
GO:1902533 positive regulation of intracellular signal transduction
GO:1902600 hydrogen ion transmembrane transport
GO:1903281 positive regulation of calcium:sodium antiporter activity

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0014704 intercalated disc
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane
GO:0016324 apical plasma membrane
GO:0030027 lamellipodium
GO:0030315 T-tubule
GO:0042383 sarcolemma
GO:0045121 membrane raft
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0090533 cation-transporting ATPase complex


-  Descriptions from all associated GenBank mRNAs
  AK124218 - Homo sapiens cDNA FLJ42224 fis, clone THYMU2040114, highly similar to SODIUM/HYDROGEN EXCHANGER 1.
M81768 - Human Na/H antiporter (APNH1) mRNA, complete cds.
M96067 - Human Na+/H+ exchanger mRNA.
S68616 - Na+/H+ exchanger NHE-1 isoform [human, heart, mRNA, 4516 nt].
JD187662 - Sequence 168686 from Patent EP1572962.
JD309961 - Sequence 290985 from Patent EP1572962.
JD294377 - Sequence 275401 from Patent EP1572962.
JD527630 - Sequence 508654 from Patent EP1572962.
JD456548 - Sequence 437572 from Patent EP1572962.
JD386985 - Sequence 368009 from Patent EP1572962.
JD283542 - Sequence 264566 from Patent EP1572962.
JD191663 - Sequence 172687 from Patent EP1572962.
JD217091 - Sequence 198115 from Patent EP1572962.
JD080312 - Sequence 61336 from Patent EP1572962.
JD252174 - Sequence 233198 from Patent EP1572962.
JD428464 - Sequence 409488 from Patent EP1572962.
JD380179 - Sequence 361203 from Patent EP1572962.
JD086693 - Sequence 67717 from Patent EP1572962.
M96066 - Human Na+/H+ exchanger mRNA.
JD055973 - Sequence 36997 from Patent EP1572962.
JD399474 - Sequence 380498 from Patent EP1572962.
JD041626 - Sequence 22650 from Patent EP1572962.
JD159394 - Sequence 140418 from Patent EP1572962.
JD425675 - Sequence 406699 from Patent EP1572962.
JD368041 - Sequence 349065 from Patent EP1572962.
JD548247 - Sequence 529271 from Patent EP1572962.
JD538231 - Sequence 519255 from Patent EP1572962.
JD095223 - Sequence 76247 from Patent EP1572962.
JD398862 - Sequence 379886 from Patent EP1572962.
JD544280 - Sequence 525304 from Patent EP1572962.
JD472778 - Sequence 453802 from Patent EP1572962.
JD338606 - Sequence 319630 from Patent EP1572962.
JD536655 - Sequence 517679 from Patent EP1572962.
JD261008 - Sequence 242032 from Patent EP1572962.
JD419429 - Sequence 400453 from Patent EP1572962.
JD254074 - Sequence 235098 from Patent EP1572962.
JD332089 - Sequence 313113 from Patent EP1572962.
JD218521 - Sequence 199545 from Patent EP1572962.
AK300432 - Homo sapiens cDNA FLJ53198 complete cds, highly similar to Sodium/hydrogen exchanger 1.
JD216478 - Sequence 197502 from Patent EP1572962.
JD254582 - Sequence 235606 from Patent EP1572962.
AF141350 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141351 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141352 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141353 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141354 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141355 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141356 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141357 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141358 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF141359 - Homo sapiens sodium/hydrogen exchanger isoform 1 (APNH) mRNA, complete cds.
AF146430 - Homo sapiens cell-line K562 sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146431 - Homo sapiens cell-line CCRF-CEM sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146432 - Homo sapiens cell-line KG-1a sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146433 - Homo sapiens cell-line MOLT-4 sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146434 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146435 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146436 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146437 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146438 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AF146439 - Homo sapiens sodium/hydrogen exchanger isoform 1 mRNA, complete cds.
AK314190 - Homo sapiens cDNA, FLJ94915, highly similar to Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 1 (antiporter, Na+/H+, amiloride sensitive) (SLC9A1), mRNA.
BC012121 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 1, mRNA (cDNA clone MGC:20164 IMAGE:4652523), complete cds.
JF432248 - Synthetic construct Homo sapiens clone IMAGE:100073416 solute carrier family 9 (sodium/hydrogen exchanger), member 1 (SLC9A1) gene, encodes complete protein.
KJ901744 - Synthetic construct Homo sapiens clone ccsbBroadEn_11138 SLC9A1 gene, encodes complete protein.
CU680226 - Synthetic construct Homo sapiens gateway clone IMAGE:100019858 5' read SLC9A1 mRNA.
JD526659 - Sequence 507683 from Patent EP1572962.
JD461069 - Sequence 442093 from Patent EP1572962.
JD230775 - Sequence 211799 from Patent EP1572962.
JD385049 - Sequence 366073 from Patent EP1572962.
JD487812 - Sequence 468836 from Patent EP1572962.
JD240008 - Sequence 221032 from Patent EP1572962.
JD056044 - Sequence 37068 from Patent EP1572962.
JD528779 - Sequence 509803 from Patent EP1572962.
JD405404 - Sequence 386428 from Patent EP1572962.
JD070307 - Sequence 51331 from Patent EP1572962.
JD184732 - Sequence 165756 from Patent EP1572962.
JD115237 - Sequence 96261 from Patent EP1572962.
JD252027 - Sequence 233051 from Patent EP1572962.
JD255133 - Sequence 236157 from Patent EP1572962.
JD195389 - Sequence 176413 from Patent EP1572962.
JD297819 - Sequence 278843 from Patent EP1572962.
JD402566 - Sequence 383590 from Patent EP1572962.
JD257295 - Sequence 238319 from Patent EP1572962.
JD071184 - Sequence 52208 from Patent EP1572962.
JD414397 - Sequence 395421 from Patent EP1572962.
JD519165 - Sequence 500189 from Patent EP1572962.
JD191515 - Sequence 172539 from Patent EP1572962.
JD439686 - Sequence 420710 from Patent EP1572962.
JD157723 - Sequence 138747 from Patent EP1572962.
JD478320 - Sequence 459344 from Patent EP1572962.

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

Protein P19634 (Reactome details) participates in the following event(s):

R-HSA-2160884 HA:HAR:HYAL2 binds to SLC9A1:p-CHP:Ca2+
R-HSA-425994 Na+/H+ exchanger transport (at cell membrane)
R-HSA-2160916 Hyaluronan uptake and degradation
R-HSA-2142845 Hyaluronan metabolism
R-HSA-425986 Sodium/Proton exchangers
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-71387 Metabolism of carbohydrates
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-1430728 Metabolism
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: APNH1, B1ALD6, D3DPL4, ENST00000263980.1, ENST00000263980.2, ENST00000263980.3, ENST00000263980.4, ENST00000263980.5, ENST00000263980.6, ENST00000263980.7, NHE1 , NR_046474, P19634, Q96EM2, SL9A1_HUMAN, SLC9A1 , uc317hnz.1, uc317hnz.2
UCSC ID: ENST00000263980.8_7
RefSeq Accession: NM_003047.5
Protein: P19634 (aka SL9A1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC9A1:
ataxias (Hereditary Ataxia Overview)

-  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.