Human Gene SLCO6A1 (ENST00000506729.6_9) from GENCODE V47lift37
  Description: solute carrier organic anion transporter family member 6A1, transcript variant 1 (from RefSeq NM_173488.5)
Gencode Transcript: ENST00000506729.6_9
Gencode Gene: ENSG00000205359.10_12
Transcript (Including UTRs)
   Position: hg19 chr5:101,707,478-101,834,705 Size: 127,228 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr5:101,709,056-101,834,548 Size: 125,493 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:101,707,478-101,834,705)mRNA (may differ from genome)Protein (719 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SO6A1_HUMAN
DESCRIPTION: RecName: Full=Solute carrier organic anion transporter family member 6A1; AltName: Full=Cancer/testis antigen 48; Short=CT48; AltName: Full=Gonad-specific transporter; Short=GST; AltName: Full=Organic anion-transporting polypeptide 6A1; AltName: Full=Organic anion-transporting polypeptide I; Short=OATP-I; AltName: Full=Solute carrier family 21 member 19;
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Strongly expressed in testis. Weakly expressed in spleen, brain, fetal brain and placenta. Detected in lung tumors.
SIMILARITY: Belongs to the organo anion transporter (TC 2.A.60) family.
SIMILARITY: Contains 1 Kazal-like domain.

-  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

+  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: 18.90 RPKM in Testis
Total median expression: 18.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -84.20157-0.536 Picture PostScript Text
3' UTR -77.50365-0.212 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
IPR011497 - Kazal-type_dom
IPR016196 - MFS_dom_general_subst_transpt
IPR004156 - OA_transporter

Pfam Domains:
PF03137 - Organic Anion Transporter Polypeptide (OATP) family
PF07648 - Kazal-type serine protease inhibitor domain
PF07690 - Major Facilitator Superfamily

SCOP Domains:
103473 - MFS general substrate transporter
100895 - Kazal-type serine protease inhibitors

ModBase Predicted Comparative 3D Structure on Q86UG4
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0015347 sodium-independent organic anion transmembrane transporter activity

Biological Process:
GO:0043252 sodium-independent organic anion 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
  AY273897 - Homo sapiens OATP-I mRNA, complete cds.
BC034976 - Homo sapiens solute carrier organic anion transporter family, member 6A1, mRNA (cDNA clone MGC:26949 IMAGE:4820512), complete cds.
AK131445 - Homo sapiens cDNA FLJ16580 fis, clone TESTI2050780.
AF505657 - Homo sapiens organic anion transporter mRNA, complete cds.
HM005487 - Homo sapiens clone HTL-T-174 testicular tissue protein Li 174 mRNA, complete cds.
DQ893559 - Synthetic construct clone IMAGE:100006189; FLH166810.01X; RZPDo839D0788D solute carrier organic anion transporter family, member 6A1 (SLCO6A1) gene, encodes complete protein.
KJ903782 - Synthetic construct Homo sapiens clone ccsbBroadEn_13176 SLCO6A1 gene, encodes complete protein.
DQ894042 - Synthetic construct Homo sapiens clone IMAGE:100008502; FLH166806.01L; RZPDo839D0787D solute carrier organic anion transporter family, member 6A1 (SLCO6A1) gene, encodes complete protein.
JD221680 - Sequence 202704 from Patent EP1572962.
JD036517 - Sequence 17541 from Patent EP1572962.
CU690004 - Synthetic construct Homo sapiens gateway clone IMAGE:100018394 5' read SLCO6A1 mRNA.
JD188914 - Sequence 169938 from Patent EP1572962.
JD383944 - Sequence 364968 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHC1, ENST00000506729.1, ENST00000506729.2, ENST00000506729.3, ENST00000506729.4, ENST00000506729.5, NM_173488, OATP6A1, Q6ZMY5, Q86UG4, Q86UV2, Q8IYU5, SLC21A19, SO6A1_HUMAN, uc323bmf.1, uc323bmf.2
UCSC ID: ENST00000506729.6_9
RefSeq Accession: NM_173488.5
Protein: Q86UG4 (aka SO6A1_HUMAN)

-  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.