Mouse Gene Slc4a4 (ENSMUST00000148750.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus solute carrier family 4 (anion exchanger), member 4 (Slc4a4), transcript variant 1, mRNA. (from RefSeq NM_018760)
Gencode Transcript: ENSMUST00000148750.7
Gencode Gene: ENSMUSG00000060961.15
Transcript (Including UTRs)
   Position: mm10 chr5:88,886,818-89,239,653 Size: 352,836 Total Exon Count: 26 Strand: +
Coding Region
   Position: mm10 chr5:88,934,750-89,234,840 Size: 300,091 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:88,886,818-89,239,653)mRNA (may differ from genome)Protein (1079 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: S4A4_MOUSE
DESCRIPTION: RecName: Full=Electrogenic sodium bicarbonate cotransporter 1; Short=Sodium bicarbonate cotransporter; AltName: Full=Na(+)/HCO3(-) cotransporter; AltName: Full=Solute carrier family 4 member 4;
FUNCTION: Electrogenic sodium/bicarbonate cotransporter with a Na(+):HCO3(-) stoichiometry varying from 1:2 to 1:3. May regulate bicarbonate influx/efflux at the basolateral membrane of cells and regulate intracellular pH.
ENZYME REGULATION: Inhibited by stilbene derivatives and regulated by cyclic AMP.
SUBUNIT: Interacts with CA2/carbonic anhydrase 2 and CA4/carbonic anhydrase 4 which may regulate transporter activity.
SUBCELLULAR LOCATION: Basolateral cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Isoform 1 is specifically expressed in pancreatic ducts and acini. Also expressed in parotid acinar cells and in the colonic crypts.
PTM: Phosphorylation of Ser-1026 by PKA increases the binding of CA2 and changes the Na(+):HCO3(-) stoichiometry of the transporter from 3:1 to 2:1 (By similarity).
PTM: N-glycosylated. May not be necessary for the transporter basic functions.
SIMILARITY: Belongs to the anion exchanger (TC 2.A.31) family.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -261.40508-0.515 Picture PostScript Text
3' UTR -1133.804183-0.271 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
IPR011531 - HCO3_transpt_C
IPR013769 - HCO3_transpt_cyt
IPR003020 - HCO3_transpt_euk
IPR003024 - Na/HCO3_transpt
IPR016152 - PTrfase/Anion_transptr

Pfam Domains:
PF00955 - HCO3- transporter family
PF07565 - Band 3 cytoplasmic domain

SCOP Domains:
55804 - Phoshotransferase/anion transport protein

ModBase Predicted Comparative 3D Structure on O88343
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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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005452 inorganic anion exchanger activity
GO:0005515 protein binding
GO:0008509 anion transmembrane transporter activity
GO:0008510 sodium:bicarbonate symporter activity
GO:0015293 symporter activity
GO:0042802 identical protein binding

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0006820 anion transport
GO:0006885 regulation of pH
GO:0015698 inorganic anion transport
GO:0015701 bicarbonate transport
GO:0051453 regulation of intracellular pH
GO:0055085 transmembrane transport
GO:0098656 anion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AK140443 - Mus musculus 10 days neonate medulla oblongata cDNA, RIKEN full-length enriched library, clone:B830021M01 product:solute carrier family 4 (anion exchanger), member 4, full insert sequence.
HQ204220 - Mus musculus strain C57BL/6 electrogenic Na-bicarbonate cotransporter splice variant NBCe1-E (slc4a4) mRNA, complete cds, alternatively spliced.
BC129863 - Mus musculus cDNA clone IMAGE:40110065, containing frame-shift errors.
BC148292 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone MGC:171146 IMAGE:40110074), complete cds.
AF020195 - Mus musculus pancreas sodium bicarbonate cotransporter mRNA, complete cds.
BC129864 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone IMAGE:40110066), partial cds.
BC167254 - Synthetic construct Mus musculus clone IMAGE:100068154, MGC:195771 solute carrier family 4 (anion exchanger), member 4 (Slc4a4) mRNA, encodes complete protein.
HQ285250 - Mus musculus strain C57BL electrogenic sodium bicarbonate cotransporter NBCe1 variant D (Slc4a4) mRNA, complete cds, alternatively spliced.
HQ018820 - Mus musculus sodium bicarbonate cotransporter NBCe1 variant A (Slc4a4) mRNA, complete cds, alternatively spliced.
AF141934 - Mus musculus sodium bicarbonate cotransporter NBC1 mRNA, complete cds.
AK085387 - Mus musculus 0 day neonate kidney cDNA, RIKEN full-length enriched library, clone:D630019H21 product:solute carrier family 4 (anion exchanger), member 4, full insert sequence.
BC026592 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone IMAGE:4973987), partial cds.
AK163619 - Mus musculus 4 days neonate male adipose cDNA, RIKEN full-length enriched library, clone:B430311M19 product:unclassifiable, full insert sequence.
BC031756 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone IMAGE:4222597), with apparent retained intron.
AK165444 - Mus musculus adult male kidney cDNA, RIKEN full-length enriched library, clone:F530003M02 product:unclassifiable, full insert sequence.
BC020415 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone IMAGE:3710145).
BC049236 - Mus musculus solute carrier family 4 (anion exchanger), member 4, mRNA (cDNA clone IMAGE:4235872).
AK134619 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330501O17 product:unclassifiable, full insert sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04964 - Proximal tubule bicarbonate reclamation
mmu04972 - Pancreatic secretion
mmu04976 - Bile secretion

Reactome (by CSHL, EBI, and GO)

Protein O88343 (Reactome details) participates in the following event(s):

R-MMU-8878664 SLC4A4 cotransports Na+ with 3HCO3-
R-MMU-425381 Bicarbonate transporters
R-MMU-425393 Metabolism of nitrogenous molecules
R-MMU-425407 SLC-mediated transmembrane transport
R-MMU-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: Nbc1, Nbce1, NM_018760, O88343, Q3USE4, Q8BUG0, Q8QZR9, Q9R1C4, S4A4_MOUSE, uc008yak.1, uc008yak.2
UCSC ID: uc008yak.2
RefSeq Accession: NM_018760
Protein: O88343 (aka S4A4_MOUSE)
CCDS: CCDS19406.1, CCDS51541.1, CCDS57352.1

-  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.