Human Gene SLC4A10 (uc010fpa.1)
  Description: Homo sapiens solute carrier family 4, sodium bicarbonate transporter, member 10 (SLC4A10), transcript variant 3, mRNA.
RefSeq Summary (NM_001178016): This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010].
Transcript (Including UTRs)
   Position: hg19 chr2:162,480,845-162,757,670 Size: 276,826 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr2:162,567,178-162,757,606 Size: 190,429 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:162,480,845-162,757,670)mRNA (may differ from genome)Protein (520 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F8WDX9_HUMAN
DESCRIPTION: SubName: Full=Sodium-driven chloride bicarbonate exchanger;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC4A10
CDC HuGE Published Literature: SLC4A10

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC4A10
Diseases sorted by gene-association score: complex partial epilepsy (24)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 16.45 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 86.81 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 -147.40545-0.270 Picture PostScript Text
3' UTR -6.4064-0.100 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
IPR013769 - HCO3_transpt_cyt
IPR003020 - HCO3_transpt_euk
IPR003024 - Na/HCO3_transpt
IPR016152 - PTrfase/Anion_transptr

Pfam Domains:
PF07565 - Band 3 cytoplasmic domain

SCOP Domains:
55804 - Phoshotransferase/anion transport protein

ModBase Predicted Comparative 3D Structure on F8WDX9
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005452 inorganic anion exchanger activity
GO:0008509 anion transmembrane transporter activity

Biological Process:
GO:0006820 anion transport
GO:0015698 inorganic anion transport
GO:0098656 anion transmembrane transport

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC051190 - Homo sapiens cDNA clone IMAGE:5259366, containing frame-shift errors.
AK294767 - Homo sapiens cDNA FLJ53785 complete cds, highly similar to Sodium-driven chloride bicarbonate exchanger.
AK308529 - Homo sapiens cDNA, FLJ98570.
AK309839 - Homo sapiens cDNA, FLJ99880.
BC038298 - Homo sapiens cDNA clone IMAGE:5265156, containing frame-shift errors.
AK293793 - Homo sapiens cDNA FLJ58098 complete cds, highly similar to Sodium-driven chloride bicarbonate exchanger.
AB040457 - Homo sapiens SLC4A10 mRNA for NCBE, complete cds.
BC136269 - Homo sapiens solute carrier family 4, sodium bicarbonate transporter, member 10, mRNA (cDNA clone MGC:167879 IMAGE:9020256), complete cds.
BC143714 - Homo sapiens solute carrier family 4, sodium bicarbonate transporter, member 10, mRNA (cDNA clone MGC:177245 IMAGE:9052228), complete cds.
AY376402 - Homo sapiens solute carrier family 4 sodium bicarbonate cotransporter-like member 10 (SLC4A10) mRNA, complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: AK308529, F8WDX9, F8WDX9_HUMAN, NM_001178016, NP_001171487
UCSC ID: uc010fpa.1
RefSeq Accession: NM_001178016
Protein: F8WDX9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK308529.1
exon count: 15CDS single in 3' UTR: no RNA size: 2107
ORF size: 1563CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2393.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 149# strange splices: 0
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.