Human Gene PEX5 (uc010sgc.2)
  Description: Homo sapiens peroxisomal biogenesis factor 5 (PEX5), transcript variant 1, mRNA.
RefSeq Summary (NM_001131023): The product of this gene binds to the C-terminal PTS1-type tripeptide peroxisomal targeting signal (SKL-type) and plays an essential role in peroxisomal protein import. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. The peroxisomal biogenesis disorders are a heterogeneous group with at least 14 complementation groups and with more than 1 phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause of neonatal adrenoleukodystrophy (NALD), a cause of Zellweger syndrome (ZWS) as well as may be a cause of infantile Refsum disease (IRD). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:7,342,282-7,364,079 Size: 21,798 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr12:7,342,974-7,362,819 Size: 19,846 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:7,342,282-7,364,079)mRNA (may differ from genome)Protein (654 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  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: PEX5
Diseases sorted by gene-association score: rhizomelic chondrodysplasia punctata, type 5* (1366), peroxisome biogenesis disorder 2b* (1230), peroxisome biogenesis disorder 2a* (919), neonatal adrenoleukodystrophy* (789), rhizomelic chondrodysplasia punctata* (439), peroxisome biogenesis disorder 1b* (185), peroxisome biogenesis disorders, zellweger syndrome spectrum* (100), zellweger syndrome (26), refsum disease (19), peroxisomal biogenesis disorders (16), adrenoleukodystrophy (13), mulibrey nanism (12), peroxisomal disease (11), peroxisomal acyl-coa oxidase deficiency (10), primary hyperoxaluria (9), rhizomelic chondrodysplasia punctata, type 3 (8), peroxisome disorders (7), chondrodysplasia punctata syndrome (7), d-bifunctional protein deficiency (6), rhizomelic chondrodysplasia punctata, type 2 (6), hyperlysinemia (6), x-linked chondrodysplasia punctata (6), cerebral degeneration (5), rhizomelic chondrodysplasia punctata, type 1 (4), inherited metabolic disorder (1)
* = 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: 35.38 RPKM in Testis
Total median expression: 680.21 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 -28.1081-0.347 Picture PostScript Text
3' UTR -454.001260-0.360 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:
PF13176 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat
PF13374 - Tetratricopeptide repeat
PF13432 - Tetratricopeptide repeat

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on P50542-4
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK292256 - Homo sapiens cDNA FLJ78290 complete cds, highly similar to H.sapiens mRNA for peroxisomal C-terminal targeting signal import receptor.
Z48054 - H.sapiens mRNA for peroxisomal targeting signal 1 (SKL type) receptor.
AK299105 - Homo sapiens cDNA FLJ51948 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
AK302742 - Homo sapiens cDNA FLJ52372 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
AK312317 - Homo sapiens cDNA, FLJ92625.
AK316250 - Homo sapiens cDNA, FLJ79149 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
AK225126 - Homo sapiens mRNA for Peroxisomal targeting signal 1 receptor variant, clone: CBL05087.
AK303515 - Homo sapiens cDNA FLJ56404 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
X84899 - H.sapiens mRNA for peroxisomal C-terminal targeting signal import receptor.
BC010621 - Homo sapiens peroxisomal biogenesis factor 5, mRNA (cDNA clone MGC:9180 IMAGE:3872822), complete cds.
U19721 - Human peroxisomal targeting signal receptor 1 (PXR1) mRNA, complete cds.
JD466178 - Sequence 447202 from Patent EP1572962.
AB527550 - Synthetic construct DNA, clone: pF1KB6136, Homo sapiens PEX5 gene for peroxisomal biogenesis factor 5, without stop codon, in Flexi system.
DQ891142 - Synthetic construct clone IMAGE:100003772; FLH169688.01X; RZPDo839F0196D peroxisomal biogenesis factor 5 (PEX5) gene, encodes complete protein.
DQ894321 - Synthetic construct Homo sapiens clone IMAGE:100008781; FLH169684.01L; RZPDo839F0195D peroxisomal biogenesis factor 5 (PEX5) gene, encodes complete protein.
CU679763 - Synthetic construct Homo sapiens gateway clone IMAGE:100019966 5' read PEX5 mRNA.
KJ897433 - Synthetic construct Homo sapiens clone ccsbBroadEn_06827 PEX5 gene, encodes complete protein.
KU178292 - Homo sapiens peroxisomal biogenesis factor 5 isoform 1 (PEX5) mRNA, partial cds.
KU178293 - Homo sapiens peroxisomal biogenesis factor 5 isoform 2 (PEX5) mRNA, partial cds.
KU178294 - Homo sapiens peroxisomal biogenesis factor 5 isoform 3 (PEX5) mRNA, partial cds.
KU178295 - Homo sapiens peroxisomal biogenesis factor 5 isoform 4 (PEX5) mRNA, complete cds, alternatively spliced.
KU178296 - Homo sapiens peroxisomal biogenesis factor 5 isoform 5 (PEX5) mRNA, complete cds, alternatively spliced.
AK301700 - Homo sapiens cDNA FLJ50721 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
AK299534 - Homo sapiens cDNA FLJ50634 complete cds, highly similar to Peroxisomal targeting signal 1 receptor.
DQ596687 - Homo sapiens piRNA piR-34753, complete sequence.
DQ600153 - Homo sapiens piRNA piR-38219, complete sequence.
JD244308 - Sequence 225332 from Patent EP1572962.
JD086011 - Sequence 67035 from Patent EP1572962.
JD090369 - Sequence 71393 from Patent EP1572962.
JD339937 - Sequence 320961 from Patent EP1572962.
JD362181 - Sequence 343205 from Patent EP1572962.
JD218540 - Sequence 199564 from Patent EP1572962.
JD218541 - Sequence 199565 from Patent EP1572962.
JD196929 - Sequence 177953 from Patent EP1572962.
JD406356 - Sequence 387380 from Patent EP1572962.
JD550177 - Sequence 531201 from Patent EP1572962.
JD199751 - Sequence 180775 from Patent EP1572962.
JD501594 - Sequence 482618 from Patent EP1572962.
JD048695 - Sequence 29719 from Patent EP1572962.
JD343008 - Sequence 324032 from Patent EP1572962.
JD234807 - Sequence 215831 from Patent EP1572962.
JD162112 - Sequence 143136 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein P50542 (Reactome details) participates in the following event(s):

R-HSA-9033478 USP9X hydrolyzes Ub:PEX5S yielding PEX5S and Ubiquitin
R-HSA-9033233 PEX5S,L binds cargo proteins containing PTS1
R-HSA-9033526 USP9X binds Ub:PEX5S
R-HSA-8953917 PEX2:PEX10:PEX12 binds PEX5S,L (in PEX5S:PEX13:PEX14) and Ub:UBE2D1,2,3
R-HSA-9033236 PEX5S,L:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-8953946 PEX2:PEX10:PEX12 monoubiquitinates PEX5S,L at cysteine-11
R-HSA-9033533 Ub:PEX5S,L (in PEX2:PEX10:PEX12:Ub:PEX5S:PEX13:PEX14) binds PEX1:PEX6:PEX26 and ZFAND6
R-HSA-9033241 Peroxisomal protein import
R-HSA-392499 Metabolism of proteins
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-8852135 Protein ubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-9033240 PEX5L binds PEX7:Cargo protein
R-HSA-9033491 USP9X hydrolyzes Ub:PEX5L yielding PEX5L and Ubiquitin
R-HSA-9033238 PEX5L:PEX7:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-9033233 PEX5S,L binds cargo proteins containing PTS1
R-HSA-9033527 PEX2:PEX10:PEX12 binds PEX5L (in PEX5L:PEX7:PEX13:PEX14:PEX2:PEX10:PEX12) and Ub:UBE2D1,2,3
R-HSA-9033509 USP9X binds Ub:PEX5L
R-HSA-9033236 PEX5S,L:Cargo binds PEX13:PEX14 of PEX13:PEX14:PEX2:PEX10:PEX12 (Docking and Translocation Complex)
R-HSA-9033485 PEX2:PEX10:PEX12 monoubiquitinates PEX5L at cysteine-11
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-8953946 PEX2:PEX10:PEX12 monoubiquitinates PEX5S,L at cysteine-11
R-HSA-9033533 Ub:PEX5S,L (in PEX2:PEX10:PEX12:Ub:PEX5S:PEX13:PEX14) binds PEX1:PEX6:PEX26 and ZFAND6
R-HSA-9033241 Peroxisomal protein import
R-HSA-392499 Metabolism of proteins
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-8852135 Protein ubiquitination
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001131023, NP_001124495, P50542-4, PXR1
UCSC ID: uc010sgc.2
RefSeq Accession: NM_001131023
Protein: P50542-4, splice isoform of P50542 CCDS: CCDS8576.1, CCDS44822.1, CCDS44823.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEX5:
pbd (Zellweger Spectrum Disorder)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001131023.1
exon count: 16CDS single in 3' UTR: no RNA size: 3324
ORF size: 1965CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3836.00frame shift in genome: no % Coverage: 99.46
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: 1241# 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.