Human Gene SLC7A9 (uc021usa.1)
  Description: Homo sapiens solute carrier family 7 (glycoprotein-associated amino acid transporter light chain, bo,+ system), member 9 (SLC7A9), transcript variant 3, mRNA.
RefSeq Summary (NM_001243036): This gene encodes a protein that belongs to a family of light subunits of amino acid transporters. This protein plays a role in the high-affinity and sodium-independent transport of cystine and neutral and dibasic amino acids, and appears to function in the reabsorption of cystine in the kidney tubule. Mutations in this gene cause non-type I cystinuria, a disease that leads to cystine stones in the urinary system due to impaired transport of cystine and dibasic amino acids. Alternate transcript variants, which encode the same protein, have been found for this gene. [provided by RefSeq, Jul 2011].
Transcript (Including UTRs)
   Position: hg19 chr19:33,321,419-33,360,683 Size: 39,265 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr19:33,321,526-33,359,440 Size: 37,915 Coding Exon Count: 12 

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 (chr19:33,321,419-33,360,683)mRNA (may differ from genome)Protein (487 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BAT1_HUMAN
DESCRIPTION: RecName: Full=B(0,+)-type amino acid transporter 1; Short=B(0,+)AT; AltName: Full=Glycoprotein-associated amino acid transporter b0,+AT1; AltName: Full=Solute carrier family 7 member 9;
FUNCTION: Involved in the high-affinity, sodium-independent transport of cystine and neutral and dibasic amino acids (system b(0,+)-like activity). Thought to be responsible for the high- affinity reabsorption of cystine in the kidney tubule.
SUBUNIT: Disulfide-linked heterodimer with the amino acid transport protein SLC3A1.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Probable).
TISSUE SPECIFICITY: Kidney, small intestine, liver and placenta.
DISEASE: Defects in SLC7A9 are a cause of non-type I cystinuria (CSNU) [MIM:220100]. CSNU arises from impaired transport of cystine and dibasic amino acids through the epithelial cells of the renal tubule and gastrointestinal tract. Three types of cystinuria have been described: type I (fully recessive or silent); type II (high excretor); type III (moderate excretor). Defects in SLC7A9 are associated with type II and type III cystinuria. They also might account for some non-classic type I cystinuria cases.
SIMILARITY: Belongs to the amino acid-polyamine-organocation (APC) superfamily.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SLC7A9";

-  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): SLC7A9
CDC HuGE Published Literature: SLC7A9
Positive Disease Associations: Cystatin C , cystinuria , Metabolism
Related Studies:
  1. Cystatin C
    Anna Kottgen et al. Nature genetics 2010, New loci associated with kidney function and chronic kidney disease., Nature genetics. [PubMed 20383146]
  2. cystinuria
    Schmidt, C. et al. 2003, Genetic variations of the SLC7A9 gene: alleledistribution of 13 polymorphic sites in German cystinuria patients and controls., Clinical nephrology. 2003 May;59(5):353-9. [PubMed 12779097]
    In summary, our results show that cystinuria is a complex disease which is not only caused by mutations in SLC7A9 and SLC3A1, but also influenced by other modifying factors such as variants in SLC7A9.
  3. Metabolism
    Karsten Suhre et al. Nature genetics 2011, A genome-wide association study of metabolic traits in human urine., Nature genetics. [PubMed 21572414]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC7A9
Diseases sorted by gene-association score: cystinuria* (1219), amino acid metabolic disorder (8), aminoaciduria (7), hypotonia-cystinuria syndrome (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 74.94 RPKM in Small Intestine - Terminal Ileum
Total median expression: 102.72 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 -85.10212-0.401 Picture PostScript Text
3' UTR -11.92107-0.111 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
IPR002293 - AA/rel_permease1

Pfam Domains:
PF00324 - Amino acid permease
PF13520 - Amino acid permease

ModBase Predicted Comparative 3D Structure on P82251
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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
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsemblFlyBase SGD
 Protein SequenceProtein SequenceProtein Sequence Protein Sequence
 AlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0015171 amino acid transmembrane transporter activity
GO:0015175 neutral amino acid transmembrane transporter activity
GO:0015184 L-cystine transmembrane transporter activity
GO:0015297 antiporter activity
GO:0022857 transmembrane transporter activity
GO:0042605 peptide antigen binding

Biological Process:
GO:0003333 amino acid transmembrane transport
GO:0006865 amino acid transport
GO:0015804 neutral amino acid transport
GO:0015811 L-cystine transport
GO:0050900 leukocyte migration
GO:0055085 transmembrane transport
GO:0065003 macromolecular complex assembly

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0031526 brush border membrane


-  Descriptions from all associated GenBank mRNAs
  AL365341 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1868615.
AL365340 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 126710.
AJ249199 - Homo sapiens mRNA for glycoprotein-associated amino acid transporter b0,+AT1.
BC029802 - Homo sapiens solute carrier family 7 (cationic amino acid transporter, y+ system), member 9, mRNA (cDNA clone IMAGE:5182360), with apparent retained intron.
AF141289 - Homo sapiens bo,+ amino acid transporter (SLC7A9) mRNA, complete cds.
AB033548 - Homo sapiens mRNA for hBAT1, complete cds.
AK026446 - Homo sapiens cDNA: FLJ22793 fis, clone KAIA2290, highly similar to AF141289 Homo sapiens bo,+ amino acid transporter (SLC7A9) mRNA.
BC017962 - Homo sapiens solute carrier family 7 (cationic amino acid transporter, y+ system), member 9, mRNA (cDNA clone MGC:24085 IMAGE:4608486), complete cds.
AK223147 - Homo sapiens mRNA for solute carrier family 7 (cationic amino acid transporter, y+ system), member 9 variant, clone: KDN05935.
AY170373 - Homo sapiens cationic amino acid transporter y+ system member 9 splice variant (SLC7A9) mRNA, complete sequence, alternatively spliced.
AK313708 - Homo sapiens cDNA, FLJ94301, Homo sapiens solute carrier family 7 (cationic amino acidtransporter, y+ system), member 9 (SLC7A9), mRNA.
DQ892006 - Synthetic construct clone IMAGE:100004636; FLH182247.01X; RZPDo839E03138D solute carrier family 7 (cationic amino acid transporter, y+ system), member 9 (SLC7A9) gene, encodes complete protein.
KJ893231 - Synthetic construct Homo sapiens clone ccsbBroadEn_02625 SLC7A9 gene, encodes complete protein.
KR711201 - Synthetic construct Homo sapiens clone CCSBHm_00021103 SLC7A9 (SLC7A9) mRNA, encodes complete protein.
KR711202 - Synthetic construct Homo sapiens clone CCSBHm_00021118 SLC7A9 (SLC7A9) mRNA, encodes complete protein.
KR711203 - Synthetic construct Homo sapiens clone CCSBHm_00021130 SLC7A9 (SLC7A9) mRNA, encodes complete protein.
KR711204 - Synthetic construct Homo sapiens clone CCSBHm_00021138 SLC7A9 (SLC7A9) mRNA, encodes complete protein.
DQ895195 - Synthetic construct Homo sapiens clone IMAGE:100009655; FLH182243.01L; RZPDo839E03137D solute carrier family 7 (cationic amino acid transporter, y+ system), member 9 (SLC7A9) gene, encodes complete protein.
CU676124 - Synthetic construct Homo sapiens gateway clone IMAGE:100022297 5' read SLC7A9 mRNA.
JD424702 - Sequence 405726 from Patent EP1572962.
JD117608 - Sequence 98632 from Patent EP1572962.
JD464692 - Sequence 445716 from Patent EP1572962.

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

Protein P82251 (Reactome details) participates in the following event(s):

R-HSA-379432 SLC7A9:SLC3A1 exchanges L-Arg, CySS-, L-Lys for L-Leu
R-HSA-375131 Basigin binds CD98 complex
R-HSA-352230 Amino acid transport across the plasma membrane
R-HSA-210991 Basigin interactions
R-HSA-425374 Amino acid and oligopeptide SLC transporters
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-109582 Hemostasis
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9A6, BAT1, BAT1_HUMAN, NM_001243036, NP_055085, P82251
UCSC ID: uc021usa.1
RefSeq Accession: NM_001243036
Protein: P82251 (aka BAT1_HUMAN)
CCDS: CCDS12425.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001243036.1
exon count: 13CDS single in 3' UTR: no RNA size: 1798
ORF size: 1464CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3035.00frame shift in genome: no % Coverage: 99.17
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.