Human Gene SLC10A1 (ENST00000216540.5) from GENCODE V44
  Description: Homo sapiens solute carrier family 10 member 1 (SLC10A1), mRNA. (from RefSeq NM_003049)
RefSeq Summary (NM_003049): The protein encoded by this gene belongs to the sodium/bile acid cotransporter family, which are integral membrane glycoproteins that participate in the enterohepatic circulation of bile acids. Two homologous transporters are involved in the reabsorption of bile acids; the ileal sodium/bile acid cotransporter with an apical cell localization that absorbs bile acids from the intestinal lumen, bile duct and kidney, and the liver-specific sodium/bile acid cotransporter, represented by this protein, that is found in the basolateral membranes of hepatocytes. Bile acids are the catabolic product of cholesterol metabolism, hence this protein is important for cholesterol homeostasis. [provided by RefSeq, Oct 2011].
Gencode Transcript: ENST00000216540.5
Gencode Gene: ENSG00000100652.5
Transcript (Including UTRs)
   Position: hg38 chr14:69,775,416-69,797,241 Size: 21,826 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr14:69,776,282-69,797,155 Size: 20,874 Coding Exon Count: 5 

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 (chr14:69,775,416-69,797,241)mRNA (may differ from genome)Protein (349 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NTCP_HUMAN
DESCRIPTION: RecName: Full=Sodium/bile acid cotransporter; AltName: Full=Cell growth-inhibiting gene 29 protein; AltName: Full=Na(+)/bile acid cotransporter; AltName: Full=Na(+)/taurocholate transport protein; AltName: Full=Sodium/taurocholate cotransporting polypeptide; AltName: Full=Solute carrier family 10 member 1;
FUNCTION: The hepatic sodium/bile acid uptake system exhibits broad substrate specificity and transports various non-bile acid organic compounds as well. It is strictly dependent on the extracellular presence of sodium.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
SIMILARITY: Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family.

-  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: SLC10A1
Diseases sorted by gene-association score: biliary atresia (31), hepatitis b (13), cholestasis (11), bile duct disease (8), pericholangitis (7), biliary tract disease (6), hepatitis (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: 62.26 RPKM in Liver
Total median expression: 64.76 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 -16.8086-0.195 Picture PostScript Text
3' UTR -160.10866-0.185 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
IPR004710 - Bil_ac_transpt
IPR002657 - BilAc/Na_symport

Pfam Domains:
PF01758 - Sodium Bile acid symporter family

ModBase Predicted Comparative 3D Structure on Q14973
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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 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:0001618 virus receptor activity
GO:0008508 bile acid:sodium symporter activity
GO:0015125 bile acid transmembrane transporter activity
GO:0015293 symporter activity

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0015721 bile acid and bile salt transport
GO:0016032 viral process
GO:0046718 viral entry into host cell
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
GO:0016323 basolateral plasma membrane


-  Descriptions from all associated GenBank mRNAs
  L21893 - Human Na/taurocholate cotransporting polypeptide mRNA, complete cds.
BC069822 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1, mRNA (cDNA clone MGC:97348 IMAGE:7262603), complete cds.
BC069799 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1, mRNA (cDNA clone MGC:97357 IMAGE:7262615), complete cds.
JD356832 - Sequence 337856 from Patent EP1572962.
JD113094 - Sequence 94118 from Patent EP1572962.
JD362662 - Sequence 343686 from Patent EP1572962.
JD180814 - Sequence 161838 from Patent EP1572962.
AY544127 - Homo sapiens growth-inhibiting protein 29 mRNA, complete cds.
BC074724 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1, mRNA (cDNA clone MGC:103793 IMAGE:30915174), complete cds.
BC126298 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1, mRNA (cDNA clone MGC:161576 IMAGE:8992014), complete cds.
BC136355 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1, mRNA (cDNA clone MGC:167965 IMAGE:9020342), complete cds.
JD339356 - Sequence 320380 from Patent EP1572962.
HQ258189 - Synthetic construct Homo sapiens clone IMAGE:100072498 solute carrier family 10 (sodium/bile acid cotransporter family), member 1 (SLC10A1) gene, encodes complete protein.
JQ814895 - Homo sapiens Na+-taurocholate cotransporting polypeptide (SLC10A1) mRNA, complete cds.
AK314028 - Homo sapiens cDNA, FLJ94688, highly similar to Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 1 (SLC10A1), mRNA.
HQ447437 - Synthetic construct Homo sapiens clone IMAGE:100070765; CCSB014031_01 solute carrier family 10 (sodium/bile acid cotransporter family), member 1 (SLC10A1) gene, encodes complete protein.
KJ892154 - Synthetic construct Homo sapiens clone ccsbBroadEn_01548 SLC10A1 gene, encodes complete protein.
CU687020 - Synthetic construct Homo sapiens gateway clone IMAGE:100022621 5' read SLC10A1 mRNA.
JD328306 - Sequence 309330 from Patent EP1572962.
JD067214 - Sequence 48238 from Patent EP1572962.
JD062650 - Sequence 43674 from Patent EP1572962.
JD042749 - Sequence 23773 from Patent EP1572962.
JD037816 - Sequence 18840 from Patent EP1572962.

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

Protein Q14973 (Reactome details) participates in the following event(s):

R-HSA-194121 Co-transport (influx) of bile salts and sodium ions by NTCP
R-HSA-159418 Recycling of bile acids and salts
R-HSA-194068 Bile acid and bile salt metabolism
R-HSA-8957322 Metabolism of steroids
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B9EGB6, ENST00000216540.1, ENST00000216540.2, ENST00000216540.3, ENST00000216540.4, GIG29, NM_003049, NTCP, NTCP_HUMAN, Q14973, Q2TU29, uc001xlr.1, uc001xlr.2, uc001xlr.3, uc001xlr.4
UCSC ID: ENST00000216540.5
RefSeq Accession: NM_003049
Protein: Q14973 (aka NTCP_HUMAN)
CCDS: CCDS9797.1

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