Human Gene SLCO4A1 (uc002ydb.1)
  Description: Homo sapiens solute carrier organic anion transporter family, member 4A1 (SLCO4A1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:61,273,797-61,303,647 Size: 29,851 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr20:61,287,807-61,303,245 Size: 15,439 Coding Exon Count: 11 

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 (chr20:61,273,797-61,303,647)mRNA (may differ from genome)Protein (722 aa)
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-  Comments and Description Text from UniProtKB
  ID: SO4A1_HUMAN
DESCRIPTION: RecName: Full=Solute carrier organic anion transporter family member 4A1; Short=OATP4A1; AltName: Full=Colon organic anion transporter; AltName: Full=Organic anion transporter polypeptide-related protein 1; Short=OATP-RP1; Short=OATPRP1; Short=POAT; AltName: Full=Organic anion-transporting polypeptide E; Short=OATP-E; AltName: Full=Sodium-independent organic anion transporter E; AltName: Full=Solute carrier family 21 member 12;
FUNCTION: Mediates the Na(+)-independent transport of organic anions such as the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and of estrone-3-sulfate and taurocholate.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Ubiquitous, with the exception of spleen and leukocytes.
SIMILARITY: Belongs to the organo anion transporter (TC 2.A.60) family.
SIMILARITY: Contains 1 Kazal-like domain.
SEQUENCE CAUTION: Sequence=BAA91247.1; 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLCO4A1
CDC HuGE Published Literature: SLCO4A1
Positive Disease Associations: Amyotrophic Lateral Sclerosis
Related Studies:
  1. Amyotrophic Lateral Sclerosis
    Jennifer C Schymick et al. Lancet neurology 2007, Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data., Lancet neurology. [PubMed 17362836]
    We generated publicly available genotype data for sporadic ALS patients and controls. No single locus was definitively associated with increased risk of developing disease, although potentially associated candidate SNPs were identified.

-  MalaCards Disease Associations
  MalaCards Gene Search: SLCO4A1
Diseases sorted by gene-association score: mucinous cystadenocarcinoma (16), aneurysmal bone cysts (8), chronic cholangitis (8), cystadenocarcinoma (7)

-  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: 35.93 RPKM in Lung
Total median expression: 398.74 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 -102.80205-0.501 Picture PostScript Text
3' UTR -142.60402-0.355 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
IPR020846 - MFS_dom
IPR016196 - MFS_dom_general_subst_transpt
IPR004156 - OA_transporter
IPR002350 - Prot_inh_Kazal

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 Q96BD0
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
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0015347 sodium-independent organic anion transmembrane transporter activity
GO:0015349 thyroid hormone transmembrane transporter activity

Biological Process:
GO:0006811 ion transport
GO:0043252 sodium-independent organic anion transport
GO:0055085 transmembrane transport
GO:0070327 thyroid hormone 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
  LF206060 - JP 2014500723-A/13563: Polycomb-Associated Non-Coding RNAs.
BC015727 - Homo sapiens solute carrier organic anion transporter family, member 4A1, mRNA (cDNA clone MGC:22943 IMAGE:4908245), complete cds.
AK023410 - Homo sapiens cDNA FLJ13348 fis, clone OVARC1002127, weakly similar to SODIUM-INDEPENDENT ORGANIC ANION TRANSPORTER 2.
AF205072 - Homo sapiens organic anion transporter polypeptide-related protein 1 (OATPRP1) mRNA, complete cds.
AF104334 - Homo sapiens putative organic anion transporter mRNA, complete cds.
JD319196 - Sequence 300220 from Patent EP1572962.
AB031051 - Homo sapiens mRNA for organic anion transporter OATP-E, complete cds.
JD331532 - Sequence 312556 from Patent EP1572962.
JD367837 - Sequence 348861 from Patent EP1572962.
JD196530 - Sequence 177554 from Patent EP1572962.
JD154993 - Sequence 136017 from Patent EP1572962.
JD446305 - Sequence 427329 from Patent EP1572962.
CU677405 - Synthetic construct Homo sapiens gateway clone IMAGE:100020039 5' read SLCO4A1 mRNA.
DQ892857 - Synthetic construct clone IMAGE:100005487; FLH190345.01X; RZPDo839H0375D solute carrier organic anion transporter family, member 4A1 (SLCO4A1) gene, encodes complete protein.
DQ896104 - Synthetic construct Homo sapiens clone IMAGE:100010564; FLH190341.01L; RZPDo839H0365D solute carrier organic anion transporter family, member 4A1 (SLCO4A1) gene, encodes complete protein.
AF187817 - Homo sapiens colon organic anion transporter mRNA, complete cds.
KJ898696 - Synthetic construct Homo sapiens clone ccsbBroadEn_08090 SLCO4A1 gene, encodes complete protein.
JD021984 - Sequence 3008 from Patent EP1572962.
JD033797 - Sequence 14821 from Patent EP1572962.
AK000551 - Homo sapiens cDNA FLJ20544 fis, clone KAT11437.
AK095985 - Homo sapiens cDNA FLJ38666 fis, clone HLUNG2004416.
JD371450 - Sequence 352474 from Patent EP1572962.
JD414272 - Sequence 395296 from Patent EP1572962.
JD304039 - Sequence 285063 from Patent EP1572962.
JD252213 - Sequence 233237 from Patent EP1572962.
MA441637 - JP 2018138019-A/13563: Polycomb-Associated Non-Coding RNAs.

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

Protein Q96BD0 (Reactome details) participates in the following event(s):

R-HSA-879575 SLCOs, SLC16A2 transport T3,T4 from extracellular region to cytosol
R-HSA-879518 Transport of organic anions
R-HSA-425397 Transport of vitamins, nucleosides, and related molecules
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: NM_016354, NP_057438, OATP1, OATP4A1, OATPE, Q96BD0, Q9H4T7, Q9H4T8, Q9H8P2, Q9NWX8, Q9UI35, Q9UIG7, SLC21A12, SO4A1_HUMAN
UCSC ID: uc002ydb.1
RefSeq Accession: NM_016354
Protein: Q96BD0 (aka SO4A1_HUMAN or SO41_HUMAN)
CCDS: CCDS13501.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016354.3
exon count: 12CDS single in 3' UTR: no RNA size: 2796
ORF size: 2169CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4436.00frame shift in genome: no % Coverage: 99.28
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.