Human Gene SLCO1C1 (uc010sii.2) Description and Page Index
  Description: Homo sapiens solute carrier organic anion transporter family, member 1C1 (SLCO1C1), transcript variant 1, mRNA.
RefSeq Summary (NM_001145946): This gene encodes a member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of thyroid hormones in brain tissues. This protein has particularly high affinity for the thyroid hormones thyroxine, tri-iodothyronine and reverse tri-iodothyronine. Polymorphisms in the gene encoding this protein may be associated with fatigue and depression in patients suffering from hyperthyroidism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009].
Transcript (Including UTRs)
   Position: hg19 chr12:20,848,289-20,906,320 Size: 58,032 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr12:20,852,511-20,905,413 Size: 52,903 Coding Exon Count: 14 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:20,848,289-20,906,320)mRNA (may differ from genome)Protein (730 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLCO1C1
CDC HuGE Published Literature: SLCO1C1
Positive Disease Associations: Body Height , height , Osteoporosis
Related Studies:
  1. Body Height
    Hana Lango Allen et al. Nature 2010, Hundreds of variants clustered in genomic loci and biological pathways affect human height., Nature. [PubMed 20881960]
  2. height
    Gudbjartsson ,et al. 2008, Many sequence variants affecting diversity of adult human height, Nature genetics 2008 40- 5 : 609-15. [PubMed 18391951]
  3. Osteoporosis
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SLCO1C1
Diseases sorted by gene-association score: allan-herndon-dudley syndrome (12), chronic cholangitis (9), bile duct disease (1), biliary tract disease (1)

-  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: 9.98 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 67.16 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 -113.50355-0.320 Picture PostScript Text
3' UTR -187.60907-0.207 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
IPR002350 - Prot_inh_Kazal

Pfam Domains:
PF00083 - Sugar (and other) transporter
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 Q5JPA4
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 BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  AK308729 - Homo sapiens cDNA, FLJ98770.
AK296236 - Homo sapiens cDNA FLJ56816 complete cds, highly similar to Solute carrier organic anion transporte rfamily member 1C1.
AF205076 - Homo sapiens organic anion transporter polypeptide-related protein 5 (OATPRP5) mRNA, complete cds.
JD168374 - Sequence 149398 from Patent EP1572962.
AK303713 - Homo sapiens cDNA FLJ56833 complete cds, highly similar to Solute carrier organic anion transporter family member 1C1.
JD287936 - Sequence 268960 from Patent EP1572962.
JD198851 - Sequence 179875 from Patent EP1572962.
AL834209 - Homo sapiens mRNA; cDNA DKFZp761B191 (from clone DKFZp761B191).
JD282134 - Sequence 263158 from Patent EP1572962.
JD117475 - Sequence 98499 from Patent EP1572962.
JD043745 - Sequence 24769 from Patent EP1572962.
AK294333 - Homo sapiens cDNA FLJ50133 complete cds, highly similar to Solute carrier organic anion transporter family member 1C1.
BC022461 - Homo sapiens solute carrier organic anion transporter family, member 1C1, mRNA (cDNA clone MGC:26093 IMAGE:4801171), complete cds.
AF260704 - Homo sapiens organic anion transporting polypeptide 14 (SLC21A14) mRNA, complete cds.
KJ904765 - Synthetic construct Homo sapiens clone ccsbBroadEn_14159 SLCO1C1-like gene, encodes complete protein.
EU176210 - Synthetic construct Homo sapiens clone IMAGE:100006616; FLH264075.01X; RZPDo839A01257D solute carrier organic anion transporter family, member 1C1 (SLCO1C1) gene, encodes complete protein.
JD349826 - Sequence 330850 from Patent EP1572962.
JD296125 - Sequence 277149 from Patent EP1572962.
JD449677 - Sequence 430701 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: DKFZp761B191, NM_001145946, NP_001139416, Q5JPA4, Q5JPA4_HUMAN
UCSC ID: uc010sii.2
RefSeq Accession: NM_001145946
Protein: Q5JPA4 CCDS: CCDS8683.1, CCDS53757.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145946.1
exon count: 16CDS single in 3' UTR: no RNA size: 3471
ORF size: 2193CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4377.00frame shift in genome: no % Coverage: 99.54
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.