Human Gene SLC1A4 (ENST00000234256.4) from GENCODE V44
  Description: Homo sapiens solute carrier family 1 member 4 (SLC1A4), transcript variant 1, mRNA. (from RefSeq NM_003038)
RefSeq Summary (NM_003038): The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability. [provided by RefSeq, Jan 2017].
Gencode Transcript: ENST00000234256.4
Gencode Gene: ENSG00000115902.11
Transcript (Including UTRs)
   Position: hg38 chr2:64,989,399-65,023,865 Size: 34,467 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr2:64,989,644-65,021,146 Size: 31,503 Coding Exon Count: 8 

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 (chr2:64,989,399-65,023,865)mRNA (may differ from genome)Protein (532 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SATT_HUMAN
DESCRIPTION: RecName: Full=Neutral amino acid transporter A; AltName: Full=Alanine/serine/cysteine/threonine transporter 1; Short=ASCT-1; AltName: Full=SATT; AltName: Full=Solute carrier family 1 member 4;
FUNCTION: Transporter for alanine, serine, cysteine, and threonine. Exhibits sodium dependence.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
TISSUE SPECIFICITY: Expressed mostly in brain, muscle, and pancreas but detected in all tissues examined.
SIMILARITY: Belongs to the sodium:dicarboxylate (SDF) symporter (TC 2.A.23) family. SLC1A4 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: SLC1A4
Diseases sorted by gene-association score: spastic tetraplegia, thin corpus callosum, and progressive microcephaly* (1681), microcephaly (10), hartnup disorder (9), spasticity (9), serine deficiency (8), intellectual disability (6), cystinuria (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D004390 Chlorpyrifos
  • C006253 pirinixic acid
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C014024 2,4,5,2',4',5'-hexachlorobiphenyl
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • C103505 AM 251
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.39 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 476.52 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 -94.20245-0.384 Picture PostScript Text
3' UTR -888.302719-0.327 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

ModBase Predicted Comparative 3D Structure on P43007
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005254 chloride channel activity
GO:0015171 amino acid transmembrane transporter activity
GO:0015175 neutral amino acid transmembrane transporter activity
GO:0015180 L-alanine transmembrane transporter activity
GO:0015184 L-cystine transmembrane transporter activity
GO:0015186 L-glutamine transmembrane transporter activity
GO:0015193 L-proline transmembrane transporter activity
GO:0015194 L-serine transmembrane transporter activity
GO:0015195 L-threonine transmembrane transporter activity
GO:0015293 symporter activity
GO:0034590 L-hydroxyproline transmembrane transporter activity

Biological Process:
GO:0003333 amino acid transmembrane transport
GO:0006865 amino acid transport
GO:0006868 glutamine transport
GO:0015808 L-alanine transport
GO:0015811 L-cystine transport
GO:0015824 proline transport
GO:0015825 L-serine transport
GO:0015826 threonine transport
GO:0034589 hydroxyproline transport
GO:0035249 synaptic transmission, glutamatergic
GO:0035524 proline transmembrane transport
GO:0050890 cognition
GO:0055085 transmembrane transport
GO:1902476 chloride transmembrane transport

Cellular Component:
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005882 intermediate filament
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030425 dendrite
GO:0042470 melanosome
GO:0043025 neuronal cell body
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK295687 - Homo sapiens cDNA FLJ52500 complete cds, highly similar to Neutral amino acid transporter A.
AK298472 - Homo sapiens cDNA FLJ53154 complete cds, highly similar to Neutral amino acid transporter A.
AK315986 - Homo sapiens cDNA, FLJ78885 complete cds, highly similar to Neutral amino acid transporter A.
AK313052 - Homo sapiens cDNA, FLJ93528, highly similar to Homo sapiens solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 (SLC1A4), mRNA.
AK223486 - Homo sapiens mRNA for solute carrier family 1, member 4 variant, clone: FCC119F11.
BC072423 - Homo sapiens solute carrier family 1 (glutamate/neutral amino acid transporter), member 4, mRNA (cDNA clone MGC:90209 IMAGE:6186177), complete cds.
L14595 - Human alanine/serine/cysteine/threonine transporter (ASCT1) mRNA, complete cds.
BC026216 - Homo sapiens solute carrier family 1 (glutamate/neutral amino acid transporter), member 4, mRNA (cDNA clone MGC:21344 IMAGE:4420405), complete cds.
L19444 - Homo sapiens neutral amino acid transporter (SATT) mRNA, complete cds.
AB026689 - Homo sapiens mRNA for hASCT1, complete cds.
DQ891127 - Synthetic construct clone IMAGE:100003757; FLH169550.01X; RZPDo839D0796D solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 (SLC1A4) gene, encodes complete protein.
DQ894306 - Synthetic construct Homo sapiens clone IMAGE:100008766; FLH169546.01L; RZPDo839D0795D solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 (SLC1A4) gene, encodes complete protein.
AK126636 - Homo sapiens cDNA FLJ44678 fis, clone BRACE3009392, highly similar to Neutral amino acid transporter A.
JD254180 - Sequence 235204 from Patent EP1572962.
JD439622 - Sequence 420646 from Patent EP1572962.
JD101006 - Sequence 82030 from Patent EP1572962.
JD280667 - Sequence 261691 from Patent EP1572962.
AL833067 - Homo sapiens mRNA; cDNA DKFZp451L0215 (from clone DKFZp451L0215).
JD233241 - Sequence 214265 from Patent EP1572962.
JD383672 - Sequence 364696 from Patent EP1572962.
JD474141 - Sequence 455165 from Patent EP1572962.
JD390154 - Sequence 371178 from Patent EP1572962.
JD126010 - Sequence 107034 from Patent EP1572962.
JD490130 - Sequence 471154 from Patent EP1572962.
JD161496 - Sequence 142520 from Patent EP1572962.
JD086164 - Sequence 67188 from Patent EP1572962.
JD313513 - Sequence 294537 from Patent EP1572962.
JD220818 - Sequence 201842 from Patent EP1572962.
JD082520 - Sequence 63544 from Patent EP1572962.
BC007350 - Homo sapiens solute carrier family 1 (glutamate/neutral amino acid transporter), member 4, mRNA (cDNA clone IMAGE:3614401), partial cds.
JD562058 - Sequence 543082 from Patent EP1572962.
JD370951 - Sequence 351975 from Patent EP1572962.
JD377312 - Sequence 358336 from Patent EP1572962.
JD550984 - Sequence 532008 from Patent EP1572962.
JD235730 - Sequence 216754 from Patent EP1572962.
JD338015 - Sequence 319039 from Patent EP1572962.
JD287482 - Sequence 268506 from Patent EP1572962.
JD207478 - Sequence 188502 from Patent EP1572962.
JD283545 - Sequence 264569 from Patent EP1572962.
JD042639 - Sequence 23663 from Patent EP1572962.
JD525984 - Sequence 507008 from Patent EP1572962.
JD511955 - Sequence 492979 from Patent EP1572962.
JD288748 - Sequence 269772 from Patent EP1572962.
JD097173 - Sequence 78197 from Patent EP1572962.
JD524073 - Sequence 505097 from Patent EP1572962.
JD232572 - Sequence 213596 from Patent EP1572962.
JD535963 - Sequence 516987 from Patent EP1572962.
JD560235 - Sequence 541259 from Patent EP1572962.

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

Protein P43007 (Reactome details) participates in the following event(s):

R-HSA-352347 SLC1A4-mediated exchange of extracellular serine for cytosolic alanine, threonine, or cysteine
R-HSA-352354 SLC1A4-mediated exchange of extracellular cysteine for cytosolic alanine, serine, or threonine
R-HSA-352364 SLC1A4-mediated exchange of extracellular alanine for cytosolic serine, threonine, or cysteine
R-HSA-352371 SLC1A4-mediated exchange of extracellular threonine for cytosolic alanine, serine, or cysteine
R-HSA-352230 Amino acid transport across the plasma membrane
R-HSA-425374 Amino acid and oligopeptide SLC 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: ASCT1, B7Z3C0, D6W5F0, ENST00000234256.1, ENST00000234256.2, ENST00000234256.3, NM_003038, P43007, SATT, SATT_HUMAN, uc010yqa.1, uc010yqa.2, uc010yqa.3, uc010yqa.4
UCSC ID: ENST00000234256.4
RefSeq Accession: NM_003038
Protein: P43007 (aka SATT_HUMAN)
CCDS: CCDS1879.1

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