Human Gene SLC6A12 (ENST00000359674.8) from GENCODE V44
  Description: Homo sapiens solute carrier family 6 member 12 (SLC6A12), transcript variant 2, mRNA. (from RefSeq NM_001122847)
Gencode Transcript: ENST00000359674.8
Gencode Gene: ENSG00000111181.13
Transcript (Including UTRs)
   Position: hg38 chr12:190,077-213,697 Size: 23,621 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg38 chr12:191,068-209,986 Size: 18,919 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:190,077-213,697)mRNA (may differ from genome)Protein (614 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S6A12_HUMAN
DESCRIPTION: RecName: Full=Sodium- and chloride-dependent betaine transporter; AltName: Full=BGT-1; AltName: Full=Na(+)/Cl(-) betaine/GABA transporter; AltName: Full=Solute carrier family 6 member 12;
FUNCTION: Transports betaine and GABA. May have a role in regulation of GABAergic transmission in the brain through the reuptake of GABA into presynaptic terminals, as well as in osmotic regulation.
SUBUNIT: Interacts with LIN7C (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Liver, heart, skeletal muscle, placenta, and a widespread distribution in the brain.
SIMILARITY: Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A12 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


-  MalaCards Disease Associations
  MalaCards Gene Search: SLC6A12
Diseases sorted by gene-association score: traumatic glaucoma (11), spinocerebellar ataxia 11 (6)

-  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: 18.66 RPKM in Kidney - Cortex
Total median expression: 131.38 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 -122.80329-0.373 Picture PostScript Text
3' UTR -353.90991-0.357 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
IPR000175 - Na/ntran_symport
IPR002983 - Na/ntran_symport_betaine

Pfam Domains:
PF00209 - Sodium:neurotransmitter symporter family

ModBase Predicted Comparative 3D Structure on P48065
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0005328 neurotransmitter:sodium symporter activity
GO:0005332 gamma-aminobutyric acid:sodium symporter activity
GO:0005515 protein binding
GO:0015171 amino acid transmembrane transporter activity
GO:0015293 symporter activity

Biological Process:
GO:0003333 amino acid transmembrane transport
GO:0006836 neurotransmitter transport
GO:0006865 amino acid transport
GO:0015812 gamma-aminobutyric acid transport
GO:0055085 transmembrane transport

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


-  Descriptions from all associated GenBank mRNAs
  BC036838 - Homo sapiens cDNA clone IMAGE:5187676, containing frame-shift errors.
AK096046 - Homo sapiens cDNA FLJ38727 fis, clone KIDNE2010419, highly similar to Sodium- and chloride-dependent betaine transporter.
U27699 - Homo sapiens pephBGT-1 betaine-GABA transporter mRNA, complete cds.
BC026339 - Homo sapiens cDNA clone IMAGE:4794351, containing frame-shift errors.
AK125026 - Homo sapiens cDNA FLJ43036 fis, clone BRTHA3002427, highly similar to Sodium- and chloride-dependent betaine transporter.
AK131564 - Homo sapiens cDNA FLJ16816 fis, clone THYMU3046350, highly similar to Sodium- and chloride-dependent betaine transporter.
JD232805 - Sequence 213829 from Patent EP1572962.
JD403561 - Sequence 384585 from Patent EP1572962.
JD323393 - Sequence 304417 from Patent EP1572962.
BC126215 - Homo sapiens solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12, mRNA (cDNA clone MGC:161493 IMAGE:8991931), complete cds.
BC126217 - Homo sapiens solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12, mRNA (cDNA clone MGC:161495 IMAGE:8991933), complete cds.
JD265526 - Sequence 246550 from Patent EP1572962.
JD059464 - Sequence 40488 from Patent EP1572962.
JD142118 - Sequence 123142 from Patent EP1572962.
JD205265 - Sequence 186289 from Patent EP1572962.
JD259937 - Sequence 240961 from Patent EP1572962.
JD325759 - Sequence 306783 from Patent EP1572962.
JD153401 - Sequence 134425 from Patent EP1572962.
JD438129 - Sequence 419153 from Patent EP1572962.
JD242323 - Sequence 223347 from Patent EP1572962.
L42300 - Homo sapiens (clone hS1a) betaine/GABA transporter (BGT-1) mRNA, complete cds.
AK313690 - Homo sapiens cDNA, FLJ94280, highly similar to Homo sapiens solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12 (SLC6A12), mRNA.
HQ258313 - Synthetic construct Homo sapiens clone IMAGE:100072622 solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12 (SLC6A12), transcript variant 2 (SLC6A12) gene, encodes complete protein.
AK307167 - Homo sapiens cDNA, FLJ97115.
JD355102 - Sequence 336126 from Patent EP1572962.
JD200827 - Sequence 181851 from Patent EP1572962.
JD516514 - Sequence 497538 from Patent EP1572962.
JD321490 - Sequence 302514 from Patent EP1572962.
JD097291 - Sequence 78315 from Patent EP1572962.

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

Protein P48065 (Reactome details) participates in the following event(s):

R-HSA-352029 SLC6A12 (BGT-1)-mediated uptake of GABA and betaine
R-HSA-200396 Creatine transport across the plasma membrane
R-HSA-352230 Amino acid transport across the plasma membrane
R-HSA-442660 Na+/Cl- dependent neurotransmitter transporters
R-HSA-888593 Reuptake of GABA
R-HSA-71288 Creatine metabolism
R-HSA-425374 Amino acid and oligopeptide SLC transporters
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds
R-HSA-425428 Amine compound SLC transporters
R-HSA-888590 GABA synthesis, release, reuptake and degradation
R-HSA-351202 Metabolism of polyamines
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-112310 Neurotransmitter release cycle
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-382551 Transport of small molecules
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-1430728 Metabolism
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: A0AV52, B2R992, D3DUN8, ENST00000359674.1, ENST00000359674.2, ENST00000359674.3, ENST00000359674.4, ENST00000359674.5, ENST00000359674.6, ENST00000359674.7, NM_001122847, P48065, S6A12_HUMAN, uc001qia.1, uc001qia.2, uc001qia.3
UCSC ID: ENST00000359674.8
RefSeq Accession: NM_001122847
Protein: P48065 (aka S6A12_HUMAN or S6AC_HUMAN)
CCDS: CCDS8501.1

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