Human Gene SLC32A1 (ENST00000217420.2) from GENCODE V44
  Description: Homo sapiens solute carrier family 32 member 1 (SLC32A1), mRNA. (from RefSeq NM_080552)
RefSeq Summary (NM_080552): The protein encoded by this gene is an integral membrane protein involved in gamma-aminobutyric acid (GABA) and glycine uptake into synaptic vesicles. The encoded protein is a member of amino acid/polyamine transporter family II. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000217420.2
Gencode Gene: ENSG00000101438.4
Transcript (Including UTRs)
   Position: hg38 chr20:38,724,486-38,729,372 Size: 4,887 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr20:38,724,725-38,728,639 Size: 3,915 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:38,724,486-38,729,372)mRNA (may differ from genome)Protein (525 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VIAAT_HUMAN
DESCRIPTION: RecName: Full=Vesicular inhibitory amino acid transporter; AltName: Full=GABA and glycine transporter; AltName: Full=Solute carrier family 32 member 1; AltName: Full=Vesicular GABA transporter; Short=hVIAAT;
FUNCTION: Involved in the uptake of GABA and glycine into the synaptic vesicles.
SUBCELLULAR LOCATION: Cytoplasmic vesicle membrane; Multi-pass membrane protein (By similarity).
TISSUE SPECIFICITY: Retina. Expressed throughout the horizontal cells or more specifically at the terminals.
SIMILARITY: Belongs to the amino acid/polyamine transporter 2 family.
SEQUENCE CAUTION: Sequence=AAH36458.2; Type=Erroneous initiation;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.03 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 115.69 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 -72.30239-0.303 Picture PostScript Text
3' UTR -285.50733-0.389 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
IPR013057 - AA_transpt_TM

Pfam Domains:
PF01490 - Transmembrane amino acid transporter protein

ModBase Predicted Comparative 3D Structure on Q9H598
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0015171 amino acid transmembrane transporter activity
GO:0015187 glycine transmembrane transporter activity
GO:0015495 gamma-aminobutyric acid:proton symporter activity

Biological Process:
GO:0003333 amino acid transmembrane transport
GO:0006811 ion transport
GO:0006836 neurotransmitter transport
GO:0007269 neurotransmitter secretion
GO:0007568 aging
GO:0015812 gamma-aminobutyric acid transport
GO:0015816 glycine transport
GO:0021766 hippocampus development
GO:0098700 neurotransmitter loading into synaptic vesicle

Cellular Component:
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030285 integral component of synaptic vesicle membrane
GO:0030425 dendrite
GO:0030659 cytoplasmic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0043005 neuron projection
GO:0043229 intracellular organelle
GO:0044292 dendrite terminus
GO:0044306 neuron projection terminus
GO:0044316 cone cell pedicle
GO:0045202 synapse
GO:0048786 presynaptic active zone
GO:0051286 cell tip
GO:0060077 inhibitory synapse
GO:0061202 clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane


-  Descriptions from all associated GenBank mRNAs
  AF064848 - Homo sapiens map 20q12; 3.87cR from WI-7121 repeat region, complete sequence.
AK055051 - Homo sapiens cDNA FLJ30489 fis, clone BRAWH2000142, highly similar to Rattus norvegicus vesicular GABA transporter (VGAT) mRNA.
JD189293 - Sequence 170317 from Patent EP1572962.
JD318715 - Sequence 299739 from Patent EP1572962.
JD458533 - Sequence 439557 from Patent EP1572962.
JD129011 - Sequence 110035 from Patent EP1572962.
BC053582 - Homo sapiens solute carrier family 32 (GABA vesicular transporter), member 1, mRNA (cDNA clone MGC:61677 IMAGE:5180816), complete cds.
JD431537 - Sequence 412561 from Patent EP1572962.
AY044836 - Homo sapiens vesicular inhibitory amino acid transporter mRNA, complete cds.
KJ895547 - Synthetic construct Homo sapiens clone ccsbBroadEn_04941 SLC32A1 gene, encodes complete protein.
BC036458 - Homo sapiens solute carrier family 32 (GABA vesicular transporter), member 1, mRNA (cDNA clone IMAGE:4813726), partial cds.
AK091079 - Homo sapiens cDNA FLJ33760 fis, clone BRCOC2000004, highly similar to Vesicular inhibitory amino acid transporter.
JD423175 - Sequence 404199 from Patent EP1572962.
JD319186 - Sequence 300210 from Patent EP1572962.
JD458699 - Sequence 439723 from Patent EP1572962.
JD471786 - Sequence 452810 from Patent EP1572962.
JD427366 - Sequence 408390 from Patent EP1572962.
JD484275 - Sequence 465299 from Patent EP1572962.
JD521454 - Sequence 502478 from Patent EP1572962.
JD384969 - Sequence 365993 from Patent EP1572962.
JD276830 - Sequence 257854 from Patent EP1572962.
JD165564 - Sequence 146588 from Patent EP1572962.
JD204804 - Sequence 185828 from Patent EP1572962.
JD156258 - Sequence 137282 from Patent EP1572962.
JD300994 - Sequence 282018 from Patent EP1572962.
JD305017 - Sequence 286041 from Patent EP1572962.

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

Protein Q9H598 (Reactome details) participates in the following event(s):

R-HSA-888589 Release of GABA at the synapse
R-HSA-917744 GABA loaded synaptic vesicle Docking and Priming
R-HSA-888592 Loading of GABA into clathrin sculpted GABA transport vesicle lumen
R-HSA-428625 Vesicular inhibitory amino acid transport
R-HSA-888590 GABA synthesis, release, reuptake and degradation
R-HSA-112310 Neurotransmitter release cycle
R-HSA-425374 Amino acid and oligopeptide SLC transporters
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-112316 Neuronal System
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000217420.1, NM_080552, Q8N489, Q9H598, uc002xjc.1, uc002xjc.2, uc002xjc.3, uc002xjc.4, VGAT, VIAAT, VIAAT_HUMAN
UCSC ID: ENST00000217420.2
RefSeq Accession: NM_080552
Protein: Q9H598 (aka VIAAT_HUMAN or VIAA_HUMAN)
CCDS: CCDS13307.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.