Human Gene SLC10A7 (uc003ikr.2) Description and Page Index
  Description: Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7 (SLC10A7), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:147,175,137-147,443,123 Size: 267,987 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr4:147,177,643-147,442,869 Size: 265,227 Coding Exon Count: 12 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:147,175,137-147,443,123)mRNA (may differ from genome)Protein (340 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC10A7
CDC HuGE Published Literature: SLC10A7
Positive Disease Associations: Cholesterol, LDL , Echocardiography
Related Studies:
  1. Cholesterol, LDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.

-  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: 3.15 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 64.00 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 -64.20254-0.253 Picture PostScript Text
3' UTR -566.762506-0.226 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
  Pfam Domains:
PF01758 - Sodium Bile acid symporter family
PF13593 - SBF-like CPA transporter family (DUF4137)

ModBase Predicted Comparative 3D Structure on Q0GE19-2
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 BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  EU831740 - Synthetic construct Homo sapiens clone HAIB:100066769; DKFZo003G0820 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 protein (SLC10A7) gene, encodes complete protein.
EU831744 - Synthetic construct Homo sapiens clone HAIB:100066773; DKFZo003H0220 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 protein (SLC10A7) gene, encodes complete protein.
AK075364 - Homo sapiens cDNA PSEC0051 fis, clone NT2RP2000168.
CR933647 - Homo sapiens mRNA; cDNA DKFZp313H0531 (from clone DKFZp313H0531).
BC150308 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone MGC:167104 IMAGE:8860437), complete cds.
AK126000 - Homo sapiens cDNA FLJ44012 fis, clone TESTI4024874, highly similar to Rattus norvegicus solute carrier family 10 (sodium/bile acid cotransporter family), member 7 (Slc10a7), mRNA.
CR936751 - Homo sapiens mRNA; cDNA DKFZp779O2438 (from clone DKFZp779O2438).
AK172727 - Homo sapiens cDNA PSEC0026 fis, clone: NT2RP1000434.
AY346324 - Homo sapiens SBF-domain containing protein mRNA, complete cds.
AK291046 - Homo sapiens cDNA FLJ77110 complete cds.
EU831657 - Synthetic construct Homo sapiens clone HAIB:100066686; DKFZo007G0819 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 protein (SLC10A7) gene, encodes complete protein.
EU831663 - Synthetic construct Homo sapiens clone HAIB:100066692; DKFZo007H0219 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 protein (SLC10A7) gene, encodes complete protein.
DQ122860 - Homo sapiens P7 isoform a (P7) mRNA, complete cds.
DQ122861 - Homo sapiens P7 isoform b (P7) mRNA, complete cds.
DQ871036 - Homo sapiens P7 isoform c (P7) mRNA, complete cds.
KJ903379 - Synthetic construct Homo sapiens clone ccsbBroadEn_12773 SLC10A7 gene, encodes complete protein.
BC063471 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:5210212), complete cds.
AL136728 - Homo sapiens mRNA; cDNA DKFZp566M114 (from clone DKFZp566M114).
BC148252 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:40115393), complete cds.
BC120970 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:40115389), complete cds.
BC120971 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:40115390), complete cds.
BC127626 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:40115391), complete cds.
BC127627 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:40115392), complete cds.
CU687734 - Synthetic construct Homo sapiens gateway clone IMAGE:100021619 5' read SLC10A7 mRNA.
KJ906356 - Synthetic construct Homo sapiens clone ccsbBroadEn_16026 SLC10A7 gene, encodes complete protein.
AM392861 - Synthetic construct Homo sapiens clone IMAGE:100001804 for hypothetical protein (C4orf13 gene).
BC146684 - Synthetic construct Homo sapiens clone IMAGE:100001804, MGC:165120 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 (SLC10A7) mRNA, encodes complete protein.
BC023288 - Homo sapiens solute carrier family 10 (sodium/bile acid cotransporter family), member 7, mRNA (cDNA clone IMAGE:4475169), complete cds.
KJ903378 - Synthetic construct Homo sapiens clone ccsbBroadEn_12772 SLC10A7 gene, encodes complete protein.
JD251078 - Sequence 232102 from Patent EP1572962.
JD423925 - Sequence 404949 from Patent EP1572962.
JD363195 - Sequence 344219 from Patent EP1572962.
JD205388 - Sequence 186412 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C4orf13, NM_001029998, NP_001025169, P7, PSEC0051, Q0GE19-2
UCSC ID: uc003ikr.2
RefSeq Accession: NM_001029998
Protein: Q0GE19-2, splice isoform of Q0GE19 CCDS: CCDS34073.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001029998.3
exon count: 12CDS single in 3' UTR: no RNA size: 3783
ORF size: 1023CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2085.50frame shift in genome: no % Coverage: 100.00
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.