Human Gene FTO (uc002ehs.3)
  Description: Homo sapiens fat mass and obesity associated (FTO), mRNA.
RefSeq Summary (NM_001080432): This gene is a nuclear protein of the AlkB related non-haem iron and 2-oxoglutarate-dependent oxygenase superfamily but the exact physiological function of this gene is not known. Other non-heme iron enzymes function to reverse alkylated DNA and RNA damage by oxidative demethylation. Studies in mice and humans indicate a role in nervous and cardiovascular systems and a strong association with body mass index, obesity risk, and type 2 diabetes. [provided by RefSeq, Jul 2011].
Transcript (Including UTRs)
   Position: hg19 chr16:53,967,897-54,148,379 Size: 180,483 Total Exon Count: 3 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:53,967,897-54,148,379)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerGeneNetworkH-INVHGNC
LynxMalacardsPubMedWikipedia

-  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): FTO
CDC HuGE Published Literature: FTO
Positive Disease Associations: , Adiposity , adiposity and blood pressure , Biomedical quantitative traits , Birth Weight|Cardiovascular Diseases , BMI , body mass index , Body Weight , C-reactive protein blood levels , Cell Adhesion Molecules , Coronary Disease , Diabetes Mellitus, Type 2 , Diabetes Mellitus, Type 2|Obesity , diabetes, type 2 , Menarche , Metabolic Syndrome X , obesity , obesity (early onset extreme) , obesity (extreme) , obesity-related traits , Potassium , type 2 diabetes , waist circumference , Waist-Hip Ratio , weight
Related Studies:

  1. Tuomo Rankinen , et al. Obesity 2010 18(2):322-6, FTO genotype is associated with exercise training-induced changes in body composition., Obesity 2010 18(2):322-6. [PubMed 19543202]
  2. Adiposity
    Tuomas O Kilpelainen et al. Nature genetics 2011, Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile., Nature genetics. [PubMed 21706003]
  3. adiposity and blood pressure
    Zdenka Pausova , et al. Circulation 2009 2(3):260-9, A common variant of the FTO gene is associated with not only increased adiposity but also elevated blood pressure in French Canadians., Circulation 2009 2(3):260-9. [PubMed 20031594]
    These results suggest that, in a French Canadian founder population, FTO may increase not only risk for obesity, as demonstrated in other populations, but also for hypertension.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: FTO
Diseases sorted by gene-association score: growth retardation, developmental delay, facial dysmorphism* (1550), obesity bmiq14* (550), growth retardation, developmental delay, coarse facies, and early death* (500), obesity (19), overnutrition (15), morbid obesity (6), suppression amblyopia (4), cranioectodermal dysplasia 1 (3), acquired metabolic disease (1)
* = Manually curated disease association

-  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: 8.93 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 241.76 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.

-  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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF384420 - JP 2014500723-A/191923: Polycomb-Associated Non-Coding RNAs.
AK096554 - Homo sapiens cDNA FLJ39235 fis, clone OCBBF2007829, highly similar to Mus musculus mRNA for fatso protein.
AB051539 - Homo sapiens KIAA1752 mRNA for KIAA1752 protein.
AK295196 - Homo sapiens cDNA FLJ61116 complete cds.
BC148442 - Synthetic construct Homo sapiens clone IMAGE:100015377, MGC:183011 fat mass and obesity associated (FTO) mRNA, encodes complete protein.
BC153032 - Synthetic construct Homo sapiens clone IMAGE:100016381, MGC:184272 fat mass and obesity associated (FTO) mRNA, encodes complete protein.
BC132892 - Homo sapiens fat mass and obesity associated, mRNA (cDNA clone IMAGE:40146914), complete cds.
BC137091 - Homo sapiens fat mass and obesity associated, mRNA (cDNA clone IMAGE:9021088), complete cds.
BC030798 - Homo sapiens fat mass and obesity associated, mRNA (cDNA clone IMAGE:3457322), complete cds.
BC003583 - Homo sapiens fat mass and obesity associated, mRNA (cDNA clone IMAGE:3353414), complete cds.
KJ906309 - Synthetic construct Homo sapiens clone ccsbBroadEn_15979 FTO gene, encodes complete protein.
MA619997 - JP 2018138019-A/191923: Polycomb-Associated Non-Coding RNAs.
JD362624 - Sequence 343648 from Patent EP1572962.
JD456260 - Sequence 437284 from Patent EP1572962.
JD121082 - Sequence 102106 from Patent EP1572962.
JD299810 - Sequence 280834 from Patent EP1572962.
JD438552 - Sequence 419576 from Patent EP1572962.
JD540233 - Sequence 521257 from Patent EP1572962.
U79260 - Human clone 23745 mRNA, complete cds.
BC001284 - Homo sapiens fat mass and obesity associated, mRNA (cDNA clone IMAGE:3453653).
JD225060 - Sequence 206084 from Patent EP1572962.
JD439667 - Sequence 420691 from Patent EP1572962.
JD264815 - Sequence 245839 from Patent EP1572962.
JD389386 - Sequence 370410 from Patent EP1572962.
JD550475 - Sequence 531499 from Patent EP1572962.
JD225895 - Sequence 206919 from Patent EP1572962.
JD502509 - Sequence 483533 from Patent EP1572962.
JD262750 - Sequence 243774 from Patent EP1572962.
JD134629 - Sequence 115653 from Patent EP1572962.
JD174238 - Sequence 155262 from Patent EP1572962.
JD414077 - Sequence 395101 from Patent EP1572962.
JD302076 - Sequence 283100 from Patent EP1572962.
JD170934 - Sequence 151958 from Patent EP1572962.
JD311406 - Sequence 292430 from Patent EP1572962.
JD080706 - Sequence 61730 from Patent EP1572962.
JD484380 - Sequence 465404 from Patent EP1572962.
JD399369 - Sequence 380393 from Patent EP1572962.
JD566814 - Sequence 547838 from Patent EP1572962.
JD384796 - Sequence 365820 from Patent EP1572962.
JD374550 - Sequence 355574 from Patent EP1572962.
JD409296 - Sequence 390320 from Patent EP1572962.
JD489176 - Sequence 470200 from Patent EP1572962.
JD489177 - Sequence 470201 from Patent EP1572962.
JD567027 - Sequence 548051 from Patent EP1572962.
JD567026 - Sequence 548050 from Patent EP1572962.
JD551149 - Sequence 532173 from Patent EP1572962.
JD566085 - Sequence 547109 from Patent EP1572962.
JD566084 - Sequence 547108 from Patent EP1572962.
JD508036 - Sequence 489060 from Patent EP1572962.
JD064538 - Sequence 45562 from Patent EP1572962.
JD064537 - Sequence 45561 from Patent EP1572962.
JD333258 - Sequence 314282 from Patent EP1572962.
JD296855 - Sequence 277879 from Patent EP1572962.
JD488167 - Sequence 469191 from Patent EP1572962.
JD524309 - Sequence 505333 from Patent EP1572962.
JD257308 - Sequence 238332 from Patent EP1572962.
JD488093 - Sequence 469117 from Patent EP1572962.
JD414695 - Sequence 395719 from Patent EP1572962.
JD306793 - Sequence 287817 from Patent EP1572962.
JD414697 - Sequence 395721 from Patent EP1572962.
JD505787 - Sequence 486811 from Patent EP1572962.
JD107542 - Sequence 88566 from Patent EP1572962.
JD186683 - Sequence 167707 from Patent EP1572962.
JD475678 - Sequence 456702 from Patent EP1572962.
JD271885 - Sequence 252909 from Patent EP1572962.
JD465191 - Sequence 446215 from Patent EP1572962.
JD418279 - Sequence 399303 from Patent EP1572962.
JD390687 - Sequence 371711 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC003583
UCSC ID: uc002ehs.3
RefSeq Accession: NM_001080432

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: no RNA accession: BC003583.1
exon count: 3CDS single in 3' UTR: no RNA size: 2833
ORF size: 0CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 528.50frame shift in genome: no % Coverage: 98.59
has start codon: no stop codon in genome: no # of Alignments: 1
has end codon: no 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.