Human Gene TMEM117 (uc001roe.3)
  Description: Homo sapiens transmembrane protein 117 (TMEM117), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:44,229,962-44,783,541 Size: 553,580 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr12:44,238,667-44,782,455 Size: 543,789 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:44,229,962-44,783,541)mRNA (may differ from genome)Protein (410 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: F5H3Q2_HUMAN
DESCRIPTION: SubName: Full=Transmembrane protein 117;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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): TMEM117
CDC HuGE Published Literature: TMEM117
Positive Disease Associations: Blood Pressure , Body Mass Index , Body Weight , Tumor Necrosis Factor-alpha
Related Studies:
  1. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  2. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

-  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: 4.19 RPKM in Nerve - Tibial
Total median expression: 99.93 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 -73.10278-0.263 Picture PostScript Text
3' UTR -267.391086-0.246 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:
PF15113 - TMEM117 protein family

ModBase Predicted Comparative 3D Structure on F5H3Q2
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  BC042192 - Homo sapiens transmembrane protein 117, mRNA (cDNA clone IMAGE:5199664), containing frame-shift errors.
BC060798 - Homo sapiens transmembrane protein 117, mRNA (cDNA clone MGC:71607 IMAGE:30348706), complete cds.
AK057287 - Homo sapiens cDNA FLJ32725 fis, clone TESTI2000970.
BC030284 - Homo sapiens transmembrane protein 117, mRNA (cDNA clone MGC:39862 IMAGE:5240522), complete cds.
AL136855 - Homo sapiens mRNA; cDNA DKFZp434K2435 (from clone DKFZp434K2435).
AB527229 - Synthetic construct DNA, clone: pF1KE0003, Homo sapiens TMEM117 gene for transmembrane protein 117, without stop codon, in Flexi system.
AM393749 - Synthetic construct Homo sapiens clone IMAGE:100001820 for hypothetical protein (TMEM117 gene).
AK097511 - Homo sapiens cDNA FLJ40192 fis, clone TESTI2019336.
BC016819 - Homo sapiens transmembrane protein 117, mRNA (cDNA clone IMAGE:4096369), with apparent retained intron.
JD302156 - Sequence 283180 from Patent EP1572962.
JD510749 - Sequence 491773 from Patent EP1572962.
JD538919 - Sequence 519943 from Patent EP1572962.
JD109434 - Sequence 90458 from Patent EP1572962.
JD185912 - Sequence 166936 from Patent EP1572962.
JD429795 - Sequence 410819 from Patent EP1572962.
JD244588 - Sequence 225612 from Patent EP1572962.
JD357622 - Sequence 338646 from Patent EP1572962.
JD380089 - Sequence 361113 from Patent EP1572962.
JD265605 - Sequence 246629 from Patent EP1572962.
JD488822 - Sequence 469846 from Patent EP1572962.
JD167111 - Sequence 148135 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC030284, F5H3Q2, F5H3Q2_HUMAN
UCSC ID: uc001roe.3
RefSeq Accession: NM_032256
Protein: F5H3Q2 CCDS: CCDS66359.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC030284.1
exon count: 7CDS single in 3' UTR: no RNA size: 2688
ORF size: 1233CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 2454.00frame shift in genome: no % Coverage: 96.61
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.