Human Gene PEX2 (uc003yay.3) Description and Page Index
  Description: Homo sapiens peroxisomal biogenesis factor 2 (PEX2), transcript variant 2, mRNA.
RefSeq Summary (NM_001079867): This gene encodes an integral peroxisomal membrane protein required for peroxisome biogenesis. The protein is thought to be involved in peroxisomal matrix protein import. Mutations in this gene result in one form of Zellweger syndrome and infantile Refsum disease. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr8:77,892,494-77,912,524 Size: 20,031 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr8:77,895,497-77,896,414 Size: 918 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:77,892,494-77,912,524)mRNA (may differ from genome)Protein (305 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PEX2_HUMAN
DESCRIPTION: RecName: Full=Peroxisome biogenesis factor 2; AltName: Full=35 kDa peroxisomal membrane protein; AltName: Full=Peroxin-2; AltName: Full=Peroxisomal membrane protein 3; AltName: Full=Peroxisome assembly factor 1; Short=PAF-1; AltName: Full=RING finger protein 72;
FUNCTION: Somewhat implicated in the biogenesis of peroxisomes.
SUBCELLULAR LOCATION: Peroxisome membrane; Multi-pass membrane protein.
DISEASE: Defects in PEX2 are the cause of peroxisome biogenesis disorder complementation group 5 (PBD-CG5) [MIM:170993]; also known as PBD-CGF. PBD refers to a group of peroxisomal disorders arising from a failure of protein import into the peroxisomal membrane or matrix. The PBD group is comprised of four disorders: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). ZWS, NALD and IRD are distinct from RCDP and constitute a clinical continuum of overlapping phenotypes known as the Zellweger spectrum. The PBD group is genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies.
DISEASE: Defects in PEX2 are a cause of Zellweger syndrome (ZWS) [MIM:214100]. ZWS is a fatal peroxisome biogenesis disorder characterized by dysmorphic facial features, hepatomegaly, ocular abnormalities, renal cysts, hearing impairment, profound psychomotor retardation, severe hypotonia and neonatal seizures. Death occurs within the first year of life.
DISEASE: Defects in PEX2 are a cause of infantile Refsum disease (IRD) [MIM:266510]. IRD is a mild peroxisome biogenesis disorder (PBD). Clinical features include early onset, mental retardation, minor facial dysmorphism, retinopathy, sensorineural hearing deficit, hepatomegaly, osteoporosis, failure to thrive, and hypocholesterolemia. The biochemical abnormalities include accumulation of phytanic acid, very long chain fatty acids (VLCFA), di- and trihydroxycholestanoic acid and pipecolic acid.
SIMILARITY: Belongs to the pex2/pex10/pex12 family.
SIMILARITY: Contains 1 RING-type zinc finger.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PXMP3";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PEX2
CDC HuGE Published Literature: PEX2
Positive Disease Associations: Body Height , Death, Sudden, Cardiac , Hip , Menarche , Neuroblastoma , Prostatic Neoplasms , Stroke , Waist-Hip Ratio
Related Studies:
  1. Body Height
    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.
  2. Body Height
    Daniel F Gudbjartsson et al. Nature genetics 2008, Many sequence variants affecting diversity of adult human height., Nature genetics. [PubMed 18391951]
  3. Death, Sudden, Cardiac
    Bradley E Aouizerat et al. BMC cardiovascular disorders 2012, GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease., BMC cardiovascular disorders. [PubMed 21658281]
    We demonstrate 11 gene associations for sudden cardiac arrest due to ventricular tachycardia/ventricular fibrillation in patients with coronary artery disease. Validation studies in independent cohorts and functional studies are required to confirm these associations.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PEX2
Diseases sorted by gene-association score: peroxisome biogenesis disorder 5b* (1230), peroxisome biogenesis disorder 5a* (919), peroxisome biogenesis disorder 1b* (164), neonatal adrenoleukodystrophy* (151), peroxisome biogenesis disorders, zellweger syndrome spectrum* (82), zellweger syndrome (40), refsum disease (15), peroxisomal biogenesis disorders (8), ketothiolase deficiency (7), peroxisomal disease (7), peroxisome disorders (6), rhizomelic chondrodysplasia punctata, type 1 (5), bardet-biedl syndrome 2 (4)
* = Manually curated disease association

-  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: 13.70 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 324.04 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 -148.50426-0.349 Picture PostScript Text
3' UTR -867.343003-0.289 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
IPR006845 - Pex_N
IPR018957 - Znf_C3HC4_RING-type
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF04757 - Pex2 / Pex12 amino terminal region

SCOP Domains:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on P28328
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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0000038 very long-chain fatty acid metabolic process
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006625 protein targeting to peroxisome
GO:0006635 fatty acid beta-oxidation
GO:0007031 peroxisome organization
GO:0016558 protein import into peroxisome matrix
GO:0016567 protein ubiquitination
GO:0031648 protein destabilization
GO:0048147 negative regulation of fibroblast proliferation
GO:0050680 negative regulation of epithelial cell proliferation

Cellular Component:
GO:0005777 peroxisome
GO:0005778 peroxisomal membrane
GO:0005779 integral component of peroxisomal membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016593 Cdc73/Paf1 complex


-  Descriptions from all associated GenBank mRNAs
  JD064430 - Sequence 45454 from Patent EP1572962.
HZ480763 - JP 2015535430-A/1269: TERMINALLY MODIFIED RNA.
HZ790694 - JP 2016504050-A/2439: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC513426 - Sequence 3679 from Patent WO2014113089.
LQ071014 - Sequence 1338 from Patent EP2964234.
JD311697 - Sequence 292721 from Patent EP1572962.
JD311696 - Sequence 292720 from Patent EP1572962.
JD420950 - Sequence 401974 from Patent EP1572962.
JD059610 - Sequence 40634 from Patent EP1572962.
JD213187 - Sequence 194211 from Patent EP1572962.
JD256804 - Sequence 237828 from Patent EP1572962.
JD407613 - Sequence 388637 from Patent EP1572962.
JD213185 - Sequence 194209 from Patent EP1572962.
JD213188 - Sequence 194212 from Patent EP1572962.
M85038 - Human 35kD peroxisomal membrane protein mRNA, complete cds.
BC000661 - Homo sapiens peroxisomal membrane protein 3, 35kDa, mRNA (cDNA clone MGC:1658 IMAGE:3347824), complete cds.
M86852 - Homo sapiens peroxisome assembly factor-1 (PAF-1) mRNA, complete cds.
BC093043 - Homo sapiens peroxisomal membrane protein 3, 35kDa, mRNA (cDNA clone MGC:111063 IMAGE:30399827), complete cds.
BC005375 - Homo sapiens peroxisomal membrane protein 3, 35kDa, mRNA (cDNA clone MGC:12491 IMAGE:3934225), complete cds.
JD510420 - Sequence 491444 from Patent EP1572962.
JD350339 - Sequence 331363 from Patent EP1572962.
AK312997 - Homo sapiens cDNA, FLJ93460, highly similar to Homo sapiens peroxisomal membrane protein 3, 35kDa (Zellweger syndrome) (PXMP3), mRNA.
KJ891958 - Synthetic construct Homo sapiens clone ccsbBroadEn_01352 PEX2 gene, encodes complete protein.
KR710162 - Synthetic construct Homo sapiens clone CCSBHm_00010164 PEX2 (PEX2) mRNA, encodes complete protein.
KR710163 - Synthetic construct Homo sapiens clone CCSBHm_00010168 PEX2 (PEX2) mRNA, encodes complete protein.
EU446992 - Synthetic construct Homo sapiens clone IMAGE:100070136; IMAGE:100012201; FLH257522.01L peroxisomal membrane protein 3, 35kDa (Zellweger syndrome) (PXMP3) gene, encodes complete protein.
AB464651 - Synthetic construct DNA, clone: pF1KB9817, Homo sapiens PXMP3 gene for peroxisomal membrane protein 3, 35kDa, without stop codon, in Flexi system.
CU675149 - Synthetic construct Homo sapiens gateway clone IMAGE:100018802 5' read PXMP3 mRNA.
JD062193 - Sequence 43217 from Patent EP1572962.
JD043506 - Sequence 24530 from Patent EP1572962.
JD359950 - Sequence 340974 from Patent EP1572962.
JD042587 - Sequence 23611 from Patent EP1572962.
JD322551 - Sequence 303575 from Patent EP1572962.
AL832262 - Homo sapiens mRNA; cDNA DKFZp667I0317 (from clone DKFZp667I0317).
MA644515 - JP 2017113010-A/2439: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA732399 - JP 2017140048-A/1269: TERMINALLY MODIFIED RNA.
MA801568 - JP 2018183181-A/2439: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04146 - Peroxisome

Reactome (by CSHL, EBI, and GO)

Protein P28328 (Reactome details) participates in the following event(s):

R-HSA-8953917 PEX2:PEX10:PEX12 binds PEX5S,L (in PEX5S:PEX13:PEX14) and Ub:UBE2D1,2,3
R-HSA-9033516 Ub:PEX5L (in PEX2:PEX10:PEX12:Ub:PEX5L:PEX7:PEX13:PEX14) binds PEX1:PEX6:PEX26 and ZFAND6
R-HSA-9033485 PEX2:PEX10:PEX12 monoubiquitinates PEX5L at cysteine-11
R-HSA-9033527 PEX2:PEX10:PEX12 binds PEX5L (in PEX5L:PEX7:PEX13:PEX14:PEX2:PEX10:PEX12) and Ub:UBE2D1,2,3
R-HSA-9033533 Ub:PEX5S,L (in PEX2:PEX10:PEX12:Ub:PEX5S:PEX13:PEX14) binds PEX1:PEX6:PEX26 and ZFAND6
R-HSA-8953946 PEX2:PEX10:PEX12 monoubiquitinates PEX5S,L at cysteine-11
R-HSA-9033236 PEX5S,L:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-9033238 PEX5L:PEX7:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-9033241 Peroxisomal protein import
R-HSA-8852135 Protein ubiquitination
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001079867, NP_001165558, P28328, PAF1, PEX2_HUMAN, PMP3, PMP35, PXMP3, Q567S6, Q9BW41, RNF72
UCSC ID: uc003yay.3
RefSeq Accession: NM_001079867
Protein: P28328 (aka PEX2_HUMAN)
CCDS: CCDS6221.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEX2:
pbd (Zellweger Spectrum Disorder)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001079867.1
exon count: 3CDS single in 3' UTR: no RNA size: 4360
ORF size: 918CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 1713.00frame shift in genome: no % Coverage: 99.70
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: 156# 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.