Human Gene PPARA (ENST00000407236.6_3) from GENCODE V47lift37
  Description: peroxisome proliferator activated receptor alpha, transcript variant 5 (from RefSeq NM_005036.6)
Gencode Transcript: ENST00000407236.6_3
Gencode Gene: ENSG00000186951.17_10
Transcript (Including UTRs)
   Position: hg19 chr22:46,546,429-46,639,652 Size: 93,224 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr22:46,594,281-46,631,277 Size: 36,997 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:46,546,429-46,639,652)mRNA (may differ from genome)Protein (468 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PPARA_HUMAN
DESCRIPTION: RecName: Full=Peroxisome proliferator-activated receptor alpha; Short=PPAR-alpha; AltName: Full=Nuclear receptor subfamily 1 group C member 1;
FUNCTION: Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl- 2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.
SUBUNIT: Heterodimer; with RXRA. This heterodimerization is required for DNA binding and transactivation activity. Interacts with AKAP13, LPIN1 and PRDM16. Also interacts with PPARBP coactivator in vitro. Interacts with CITED2; the interaction stimulates its transcriptional activity (By similarity). Interacts with NCOA3 and NCOA6 coactivators. Interacts with ASXL1 AND ASXL2.
INTERACTION: Q3L8U1-3:CHD9; NbExp=2; IntAct=EBI-78615, EBI-960730;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Skeletal muscle, liver, heart and kidney.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
WEB RESOURCE: Name=Wikipedia; Note=Peroxisome proliferator- activated receptor entry; URL="http://en.wikipedia.org/wiki/Peroxisome_proliferator-activated_receptor";
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ppara/";

-  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: PPARA
Diseases sorted by gene-association score: fatty liver disease (24), alcoholic cardiomyopathy (22), lipid metabolism disorder (11), tularemia (10), nonalcoholic steatohepatitis (10), hepatoblastoma (8), citrullinemia (7), familial hyperlipidemia (6), 3-hydroxyacyl-coa dehydrogenase deficiency (6), fatty acid oxidation disorders (6), idiopathic edema (6), liver disease (6), cardiovascular disease risk factor ) (6), peroxisomal acyl-coa oxidase deficiency (5), diabetes mellitus, noninsulin-dependent (5), epileptic encephalopathy, childhood-onset (4), hypoalphalipoproteinemia (3), obesity (3), arteriosclerosis (2), heart disease (2), glucose metabolism disease (1), acquired metabolic 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: 12.39 RPKM in Liver
Total median expression: 172.60 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 -151.20336-0.450 Picture PostScript Text
3' UTR -2661.508375-0.318 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
IPR003074 - 1Cnucl_rcpt
IPR003076 - 1Cnucl_rcpt_A
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1I7G - X-ray MuPIT 1K7L - X-ray MuPIT 1KKQ - X-ray MuPIT 2NPA - X-ray MuPIT 2P54 - X-ray MuPIT 2REW - X-ray MuPIT 2ZNN - X-ray MuPIT 3ET1 - X-ray MuPIT 3FEI - X-ray MuPIT 3G8I - X-ray MuPIT 3KDT - X-ray MuPIT 3KDU - X-ray MuPIT 3SP6 - X-ray MuPIT 3VI8 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q07869
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001103 RNA polymerase II repressing transcription factor binding
GO:0001190 transcriptional activator activity, RNA polymerase II transcription factor binding
GO:0001223 transcription coactivator binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0008144 drug binding
GO:0008270 zinc ion binding
GO:0008289 lipid binding
GO:0019902 phosphatase binding
GO:0019904 protein domain specific binding
GO:0031624 ubiquitin conjugating enzyme binding
GO:0038023 signaling receptor activity
GO:0043565 sequence-specific DNA binding
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding
GO:0051525 NFAT protein binding
GO:0097371 MDM2/MDM4 family protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001666 response to hypoxia
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0007165 signal transduction
GO:0007507 heart development
GO:0008544 epidermis development
GO:0010468 regulation of gene expression
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0010871 negative regulation of receptor biosynthetic process
GO:0010887 negative regulation of cholesterol storage
GO:0010891 negative regulation of sequestering of triglyceride
GO:0015908 fatty acid transport
GO:0019216 regulation of lipid metabolic process
GO:0019217 regulation of fatty acid metabolic process
GO:0030522 intracellular receptor signaling pathway
GO:0032000 positive regulation of fatty acid beta-oxidation
GO:0032091 negative regulation of protein binding
GO:0032099 negative regulation of appetite
GO:0032868 response to insulin
GO:0032922 circadian regulation of gene expression
GO:0035095 behavioral response to nicotine
GO:0042060 wound healing
GO:0042157 lipoprotein metabolic process
GO:0042752 regulation of circadian rhythm
GO:0043401 steroid hormone mediated signaling pathway
GO:0045722 positive regulation of gluconeogenesis
GO:0045776 negative regulation of blood pressure
GO:0045820 negative regulation of glycolytic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046321 positive regulation of fatty acid oxidation
GO:0048511 rhythmic process
GO:0050728 negative regulation of inflammatory response
GO:0070166 enamel mineralization
GO:0072363 regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter
GO:0072366 regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter
GO:0072369 regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter
GO:1901215 negative regulation of neuron death
GO:1902894 negative regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1903038 negative regulation of leukocyte cell-cell adhesion
GO:2000678 negative regulation of transcription regulatory region DNA binding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  CU013435 - Homo sapiens PPARA, mRNA (cDNA clone IMAGE:100000404), complete cds, without stop codon, in Gateway system.
CU013147 - Homo sapiens PPARA, mRNA (cDNA clone IMAGE:100000500), complete cds, with stop codon, in Gateway system.
AY258330 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 5 and partial cds.
AY258328 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 3 and partial cds.
AK289821 - Homo sapiens cDNA FLJ76337 complete cds, highly similar to Homo sapiens peroxisome proliferative activated receptor, alpha(PPARA), transcript variant 3, mRNA.
AF270490 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5' untranslated region.
JD210057 - Sequence 191081 from Patent EP1572962.
L02932 - Human peroxisome proliferator activated receptor mRNA, complete cds.
JD337836 - Sequence 318860 from Patent EP1572962.
AY258329 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 4 and partial cds.
AY258331 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 6 and partial cds.
CR456547 - Homo sapiens PPARA full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.PPARA).
AY258327 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 2 and partial cds.
S74349 - hPPAR alpha =peroxisome proliferator activated receptor alpha [human, liver, mRNA, 1731 nt].
JD469366 - Sequence 450390 from Patent EP1572962.
BC000052 - Homo sapiens peroxisome proliferator-activated receptor alpha, mRNA (cDNA clone IMAGE:3505209).
JD096307 - Sequence 77331 from Patent EP1572962.
JD493038 - Sequence 474062 from Patent EP1572962.
JD177963 - Sequence 158987 from Patent EP1572962.
AY258326 - Homo sapiens peroxisome proliferator-activated receptor alpha (PPARA) mRNA, 5'UTR variant 1 and partial cds.
AB463164 - Synthetic construct DNA, clone: pF1KB9549, Homo sapiens PPARA gene for peroxisome proliferator-activated receptor alpha, without stop codon, in Flexi system.
CU674014 - Synthetic construct Homo sapiens gateway clone IMAGE:100018064 5' read PPARA mRNA.
KJ901654 - Synthetic construct Homo sapiens clone ccsbBroadEn_11048 PPARA gene, encodes complete protein.
KR709797 - Synthetic construct Homo sapiens clone CCSBHm_00006146 PPARA (PPARA) mRNA, encodes complete protein.
KR709798 - Synthetic construct Homo sapiens clone CCSBHm_00006147 PPARA (PPARA) mRNA, encodes complete protein.
KR709799 - Synthetic construct Homo sapiens clone CCSBHm_00006148 PPARA (PPARA) mRNA, encodes complete protein.
CR457435 - Homo sapiens full open reading frame cDNA clone RZPDo834B076D for gene PPARA, peroxisome proliferative activated receptor, alpha; complete cds, incl. stopcodon.
AB307690 - Homo sapiens NR1C1 mRNA for peroxisome proliferator activated receptor alpha, complete cds.
EU395809 - Homo sapiens peroxisome proliferator-activated receptor alpha splice variant (PPARA) mRNA, complete cds, alternatively spliced.
EU650667 - Homo sapiens cell-line HepG2 peroxisome proliferator-activated receptor alpha mRNA, complete cds.
HQ692862 - Homo sapiens peroxisome proliferator-activated nuclear receptor alpha variant 3 (NR1C1) mRNA, complete cds.
Y07619 - H.sapiens mRNA for peroxisome proliferator-activated receptor alpha.
DQ572747 - Homo sapiens piRNA piR-40859, complete sequence.
Y16186 - Homo sapiens mRNA for peroxisome proliferator-activated receptor alpha, partial.
JD411292 - Sequence 392316 from Patent EP1572962.
JD060879 - Sequence 41903 from Patent EP1572962.
JD097715 - Sequence 78739 from Patent EP1572962.
JD404141 - Sequence 385165 from Patent EP1572962.
JD173626 - Sequence 154650 from Patent EP1572962.
AF018254 - Homo sapiens critical myeloma-associated breakpoint region sequence.
JD135812 - Sequence 116836 from Patent EP1572962.
JD047629 - Sequence 28653 from Patent EP1572962.
JD047631 - Sequence 28655 from Patent EP1572962.
JD047630 - Sequence 28654 from Patent EP1572962.
JD457021 - Sequence 438045 from Patent EP1572962.
JD117523 - Sequence 98547 from Patent EP1572962.
JD219919 - Sequence 200943 from Patent EP1572962.
AK024738 - Homo sapiens cDNA: FLJ21085 fis, clone CAS03203.
BC004162 - Homo sapiens cDNA clone IMAGE:2961235.
JD408349 - Sequence 389373 from Patent EP1572962.
JD493911 - Sequence 474935 from Patent EP1572962.
JD554311 - Sequence 535335 from Patent EP1572962.
JD114286 - Sequence 95310 from Patent EP1572962.
JD049567 - Sequence 30591 from Patent EP1572962.
JD308845 - Sequence 289869 from Patent EP1572962.
JD071566 - Sequence 52590 from Patent EP1572962.
JD460612 - Sequence 441636 from Patent EP1572962.
JD137670 - Sequence 118694 from Patent EP1572962.
JD438738 - Sequence 419762 from Patent EP1572962.
JD283938 - Sequence 264962 from Patent EP1572962.
JD401218 - Sequence 382242 from Patent EP1572962.
JD407219 - Sequence 388243 from Patent EP1572962.
JD111556 - Sequence 92580 from Patent EP1572962.
JD151140 - Sequence 132164 from Patent EP1572962.
DQ583767 - Homo sapiens piRNA piR-50879, complete sequence.
JD049574 - Sequence 30598 from Patent EP1572962.
JD407855 - Sequence 388879 from Patent EP1572962.
JD427202 - Sequence 408226 from Patent EP1572962.
JD060681 - Sequence 41705 from Patent EP1572962.
JD563380 - Sequence 544404 from Patent EP1572962.
JD214205 - Sequence 195229 from Patent EP1572962.
JD255448 - Sequence 236472 from Patent EP1572962.
JD470840 - Sequence 451864 from Patent EP1572962.
JD096201 - Sequence 77225 from Patent EP1572962.
JD197686 - Sequence 178710 from Patent EP1572962.
JD355078 - Sequence 336102 from Patent EP1572962.
JD355148 - Sequence 336172 from Patent EP1572962.
JD402915 - Sequence 383939 from Patent EP1572962.
JD303876 - Sequence 284900 from Patent EP1572962.
DQ589189 - Homo sapiens piRNA piR-56301, complete sequence.
JD405703 - Sequence 386727 from Patent EP1572962.
JD067692 - Sequence 48716 from Patent EP1572962.
JD525873 - Sequence 506897 from Patent EP1572962.
JD521281 - Sequence 502305 from Patent EP1572962.
JD332878 - Sequence 313902 from Patent EP1572962.
JD056259 - Sequence 37283 from Patent EP1572962.
AK311946 - Homo sapiens cDNA, FLJ92214.
JD488415 - Sequence 469439 from Patent EP1572962.
JD099903 - Sequence 80927 from Patent EP1572962.
AB073605 - Homo sapiens primary hepatoblastoma cDNA, clone:HMFT1488, full insert sequence.
JD236165 - Sequence 217189 from Patent EP1572962.
JD301014 - Sequence 282038 from Patent EP1572962.
BC071932 - Homo sapiens peroxisome proliferator-activated receptor alpha, mRNA (cDNA clone IMAGE:6259713).
JD559588 - Sequence 540612 from Patent EP1572962.
JD429882 - Sequence 410906 from Patent EP1572962.
AK091885 - Homo sapiens cDNA FLJ34566 fis, clone KIDNE2007910.
JD118659 - Sequence 99683 from Patent EP1572962.
JD409597 - Sequence 390621 from Patent EP1572962.
JD101753 - Sequence 82777 from Patent EP1572962.
JD116250 - Sequence 97274 from Patent EP1572962.
JD135466 - Sequence 116490 from Patent EP1572962.
JD403518 - Sequence 384542 from Patent EP1572962.
JD547380 - Sequence 528404 from Patent EP1572962.
JD339630 - Sequence 320654 from Patent EP1572962.
JD205066 - Sequence 186090 from Patent EP1572962.
JD442494 - Sequence 423518 from Patent EP1572962.
JD436199 - Sequence 417223 from Patent EP1572962.
JD170045 - Sequence 151069 from Patent EP1572962.
JD278652 - Sequence 259676 from Patent EP1572962.
JD551978 - Sequence 533002 from Patent EP1572962.
JD106322 - Sequence 87346 from Patent EP1572962.
JD139436 - Sequence 120460 from Patent EP1572962.
JD310170 - Sequence 291194 from Patent EP1572962.
JD329929 - Sequence 310953 from Patent EP1572962.
JD268215 - Sequence 249239 from Patent EP1572962.
JD208223 - Sequence 189247 from Patent EP1572962.
JD244716 - Sequence 225740 from Patent EP1572962.
JD224691 - Sequence 205715 from Patent EP1572962.
JD195437 - Sequence 176461 from Patent EP1572962.
JD265440 - Sequence 246464 from Patent EP1572962.
AK027101 - Homo sapiens cDNA: FLJ23448 fis, clone HSI05222.
BC009069 - Homo sapiens peroxisome proliferative activated receptor, alpha, mRNA (cDNA clone IMAGE:3867243).

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_pgc1aPathway - Regulation of PGC-1a
h_pparaPathway - Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)
h_bArrestinPathway - �-arrestins in GPCR Desensitization
h_tollPathway - Toll-Like Receptor Pathway
h_pparPathway - Basic mechanism of action of PPARa, PPARb(d) and PPARg and effects on gene expression
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity

Reactome (by CSHL, EBI, and GO)

Protein Q07869 (Reactome details) participates in the following event(s):

R-HSA-400204 PPARA binds RXRA forming PPARA:RXRA heterodimer at promoter of target gene
R-HSA-400183 PPARA:RXRA heterodimer recruits corepressors
R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-1368108 BMAL1:CLOCK,NPAS2 activates circadian gene expression
R-HSA-1989781 PPARA activates gene expression
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-556833 Metabolism of lipids
R-HSA-400253 Circadian Clock
R-HSA-212436 Generic Transcription Pathway
R-HSA-1430728 Metabolism
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B0G0X3, ENST00000407236.1, ENST00000407236.2, ENST00000407236.3, ENST00000407236.4, ENST00000407236.5, NM_005036, NR1C1, PPAR, PPARA_HUMAN, Q07869, Q16241, Q6I9S0, Q92486, Q92689, Q9Y3N1, uc319dur.1, uc319dur.2
UCSC ID: ENST00000407236.6_3
RefSeq Accession: NM_005036.6
Protein: Q07869 (aka PPARA_HUMAN)

-  Gene Model Information
  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.