Mouse Gene Slc1a6 (ENSMUST00000005490.9) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 (Slc1a6), mRNA. (from RefSeq NM_009200)
Gencode Transcript: ENSMUST00000005490.9
Gencode Gene: ENSMUSG00000005357.9
Transcript (Including UTRs)
   Position: mm10 chr10:78,780,496-78,814,765 Size: 34,270 Total Exon Count: 10 Strand: +
Coding Region
   Position: mm10 chr10:78,787,769-78,814,615 Size: 26,847 Coding Exon Count: 9 

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 (chr10:78,780,496-78,814,765)mRNA (may differ from genome)Protein (561 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: EAA4_MOUSE
DESCRIPTION: RecName: Full=Excitatory amino acid transporter 4; AltName: Full=High-affinity neuronal glutamate transporter; AltName: Full=Sodium-dependent glutamate/aspartate transporter; AltName: Full=Solute carrier family 1 member 6;
FUNCTION: Transports L-glutamate and also L- and D-aspartate. Seems to act as a symport by cotransporting sodium (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Brain specific.
SIMILARITY: Belongs to the sodium:dicarboxylate (SDF) symporter (TC 2.A.23) family. SLC1A6 subfamily.

-  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 -82.80193-0.429 Picture PostScript Text
3' UTR -48.90150-0.326 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
IPR001991 - Na-dicarboxylate_symporter
IPR018107 - Na-dicarboxylate_symporter_CS

Pfam Domains:
PF00375 - Sodium:dicarboxylate symporter family

SCOP Domains:
118215 - Proton glutamate symport protein

ModBase Predicted Comparative 3D Structure on O35544
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD Ensembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005313 L-glutamate transmembrane transporter activity
GO:0005314 high-affinity glutamate transmembrane transporter activity
GO:0008509 anion transmembrane transporter activity
GO:0015293 symporter activity
GO:0046872 metal ion binding

Biological Process:
GO:0006865 amino acid transport
GO:0015813 L-glutamate transport
GO:0042391 regulation of membrane potential
GO:0098712 L-glutamate import across plasma membrane

Cellular Component:
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0045111 intermediate filament cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AK159197 - Mus musculus osteoclast-like cell cDNA, RIKEN full-length enriched library, clone:I420008D08 product:solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6, full insert sequence.
D83262 - Mus musculus mRNA for neuronal glutamate transporter EAAT4, complete cds.
BC138120 - Mus musculus solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6, mRNA (cDNA clone MGC:169744 IMAGE:8861139), complete cds.
BC138140 - Mus musculus solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6, mRNA (cDNA clone MGC:169764 IMAGE:8861159), complete cds.

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

Protein O35544 (Reactome details) participates in the following event(s):

R-MMU-210404 SLC1A1-3,6,7 exchange L-Glu, H+ and 3Na+ for K+
R-MMU-428015 SLC1A1,2,3,6,7 cotransport L-Glu,L-Asp,D-Asp,H+,3Na+ from extracellular region to cytosol
R-MMU-210500 Glutamate Neurotransmitter Release Cycle
R-MMU-425374 Amino acid and oligopeptide SLC transporters
R-MMU-425393 Metabolism of nitrogenous molecules
R-MMU-112310 Neurotransmitter release cycle
R-MMU-425407 SLC-mediated transmembrane transport
R-MMU-112315 Transmission across Chemical Synapses
R-MMU-382551 Transport of small molecules
R-MMU-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: EAA4_MOUSE, Eaat4, NM_009200, O35544, uc007fyg.1, uc007fyg.2, uc007fyg.3
UCSC ID: uc007fyg.3
RefSeq Accession: NM_009200
Protein: O35544 (aka EAA4_MOUSE)
CCDS: CCDS23970.1

-  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.