Human Gene SLC4A10 (uc002ubx.4)
  Description: Homo sapiens solute carrier family 4, sodium bicarbonate transporter, member 10 (SLC4A10), transcript variant 1, mRNA.
RefSeq Summary (NM_001178015): 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 chr2:162,480,845-162,841,786 Size: 360,942 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr2:162,481,029-162,834,244 Size: 353,216 Coding Exon Count: 26 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:162,480,845-162,841,786)mRNA (may differ from genome)Protein (1118 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S4A10_HUMAN
DESCRIPTION: RecName: Full=Sodium-driven chloride bicarbonate exchanger; AltName: Full=Solute carrier family 4 member 10;
FUNCTION: Electrogenic sodium/bicarbonate cotransporter in exchange for intracellular chloride. Plays an important role in regulating intracellular pH (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Note=Localizes to the basolateral membrane (By similarity).
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


-  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 -53.40184-0.290 Picture PostScript Text
3' UTR -458.992124-0.216 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 Q6U841
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
GO:0008510 sodium:bicarbonate symporter activity
GO:0015293 symporter activity
GO:0015297 antiporter activity
GO:0015301 anion:anion antiporter activity

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0006820 anion transport
GO:0006821 chloride transport
GO:0006885 regulation of pH
GO:0007399 nervous system development
GO:0009416 response to light stimulus
GO:0009791 post-embryonic development
GO:0015701 bicarbonate transport
GO:0021860 pyramidal neuron development
GO:0030641 regulation of cellular pH
GO:0035264 multicellular organism growth
GO:0035641 locomotory exploration behavior
GO:0048854 brain morphogenesis
GO:0051453 regulation of intracellular pH
GO:0098656 anion transmembrane transport
GO:1902600 hydrogen ion 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
GO:0043025 neuronal cell body
GO:0097440 apical dendrite
GO:0097441 basilar dendrite
GO:0097442 CA3 pyramidal cell dendrite


-  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.
AL713680 - Homo sapiens mRNA; cDNA DKFZp761J1717 (from clone DKFZp761J1717).
AL832525 - Homo sapiens mRNA; cDNA DKFZp761N0217 (from clone DKFZp761N0217).
JD358556 - Sequence 339580 from Patent EP1572962.
BC036415 - Homo sapiens solute carrier family 4, sodium bicarbonate transporter-like, member 10, mRNA (cDNA clone IMAGE:4795552).
JD289246 - Sequence 270270 from Patent EP1572962.
JD039438 - Sequence 20462 from Patent EP1572962.

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

Protein Q6U841 (Reactome details) participates in the following event(s):

R-HSA-425577 Na+-driven Cl-/HCO3- exchanger transport
R-HSA-425381 Bicarbonate transporters
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZLC5, B9EG69, NCBE, NM_001178015, NP_001171486, Q4ZFX6, Q6U841, Q8TCP2, Q9HCQ6, S4A10_HUMAN
UCSC ID: uc002ubx.4
RefSeq Accession: NM_001178015
Protein: Q6U841 (aka S4A10_HUMAN)
CCDS: CCDS54412.1, CCDS46438.1, CCDS54411.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001178015.1
exon count: 27CDS single in 3' UTR: no RNA size: 5671
ORF size: 3357CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5970.00frame shift in genome: no % Coverage: 99.89
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: 0# 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.