Human Gene PEX6 (ENST00000304611.13_7) from GENCODE V47lift37
  Description: peroxisomal biogenesis factor 6, transcript variant 2 (from RefSeq NM_001316313.2)
Gencode Transcript: ENST00000304611.13_7
Gencode Gene: ENSG00000124587.14_9
Transcript (Including UTRs)
   Position: hg19 chr6:42,931,603-42,946,919 Size: 15,317 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr6:42,932,073-42,946,888 Size: 14,816 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:42,931,603-42,946,919)mRNA (may differ from genome)Protein (980 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PEX6_HUMAN
DESCRIPTION: RecName: Full=Peroxisome assembly factor 2; Short=PAF-2; AltName: Full=Peroxin-6; AltName: Full=Peroxisomal biogenesis factor 6; AltName: Full=Peroxisomal-type ATPase 1;
FUNCTION: Involved in peroxisome biosynthesis. Required for stability of the PTS1 receptor. Anchored by PEX26 to peroxisome membranes, possibly to form heteromeric AAA ATPase complexes required for the import of proteins into peroxisomes.
SUBUNIT: Interacts directly with PEX26 and PEX1. Mediates the indirect interaction between PEX1 and PEX26. Interacts with ZFAND6.
INTERACTION: O43933:PEX1; NbExp=2; IntAct=EBI-988581, EBI-988601;
SUBCELLULAR LOCATION: Cytoplasm. Peroxisome membrane. Note=Associated with peroxisomal membranes.
DISEASE: Defects in PEX6 are the cause of peroxisome biogenesis disorder complementation group 4 (PBD-CG4) [MIM:601498]; also known as PBD-CGC. 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 PEX6 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.
SIMILARITY: Belongs to the AAA ATPase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PEX6";
WEB RESOURCE: Name=dbPEX, PEX Gene Database; URL="http://www.dbpex.org/home.php?select_db=PEX6";

-  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: PEX6
Diseases sorted by gene-association score: peroxisome biogenesis disorder 4a* (1230), heimler syndrome 2* (1230), peroxisome biogenesis disorder 4b* (919), spinocerebellar ataxia, autosomal recessive 3* (247), deafness enamel hypoplasia nail defects* (247), peroxisome biogenesis disorder 1b* (218), neonatal adrenoleukodystrophy* (194), peroxisomal biogenesis disorders* (132), peroxisome biogenesis disorders, zellweger syndrome spectrum* (89), zellweger syndrome (15), refsum disease (9), adrenoleukodystrophy (8), peroxisomal disease (8), ketothiolase deficiency (7), usher syndrome (2), leigh syndrome (1), retinitis pigmentosa (0)
* = 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: 24.81 RPKM in Ovary
Total median expression: 654.14 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 -3.8031-0.123 Picture PostScript Text
3' UTR -186.00470-0.396 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
IPR003593 - AAA+_ATPase
IPR003959 - ATPase_AAA_core
IPR003960 - ATPase_AAA_CS

Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q13608
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008022 protein C-terminus binding
GO:0016887 ATPase activity
GO:0042623 ATPase activity, coupled
GO:0044877 macromolecular complex binding

Biological Process:
GO:0006625 protein targeting to peroxisome
GO:0007031 peroxisome organization
GO:0016561 protein import into peroxisome matrix, translocation
GO:0050821 protein stabilization

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005778 peroxisomal membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0042995 cell projection
GO:0097733 photoreceptor cell cilium


-  Descriptions from all associated GenBank mRNAs
  BC033487 - Homo sapiens peroxisomal biogenesis factor 6, mRNA (cDNA clone IMAGE:5172424).
AB051076 - Homo sapiens PEX6 mRNA for peroxine Pex6p, complete cds.
BC048331 - Homo sapiens peroxisomal biogenesis factor 6, mRNA (cDNA clone MGC:54056 IMAGE:5189685), complete cds.
AB208906 - Homo sapiens mRNA for peroxisomal biogenesis factor 6 variant protein.
JD150997 - Sequence 132021 from Patent EP1572962.
JD525921 - Sequence 506945 from Patent EP1572962.
D83703 - Homo sapiens mRNA for peroxisome assembly factor-2, complete cds.
JD321872 - Sequence 302896 from Patent EP1572962.
JD099532 - Sequence 80556 from Patent EP1572962.
JD219803 - Sequence 200827 from Patent EP1572962.
AB051077 - Homo sapiens PEX6 mRNA for peroxin Pex6p, complete cds, CG6-PEX6(1) sequence.
AB051078 - Homo sapiens PEX6 mRNA for peroxin Pex6p, complete cds, CG6-PEX6(2) sequence.
AK314237 - Homo sapiens cDNA, FLJ94981, highly similar to Homo sapiens peroxisomal biogenesis factor 6 (PEX6), mRNA.
AB590555 - Synthetic construct DNA, clone: pFN21AB8543, Homo sapiens PEX6 gene for peroxisomal biogenesis factor 6, without stop codon, in Flexi system.
AK225704 - Homo sapiens mRNA for peroxisomal biogenesis factor 6 variant, clone: TMS01483.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q13608 (Reactome details) participates in the following event(s):

R-HSA-9033516 Ub:PEX5L (in PEX2:PEX10:PEX12:Ub:PEX5L:PEX7:PEX13:PEX14) binds PEX1:PEX6:PEX26 and ZFAND6
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

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000304611.1, ENST00000304611.10, ENST00000304611.11, ENST00000304611.12, ENST00000304611.2, ENST00000304611.3, ENST00000304611.4, ENST00000304611.5, ENST00000304611.6, ENST00000304611.7, ENST00000304611.8, ENST00000304611.9, NM_001316313, PEX6 , PEX6_HUMAN, PXAAA1 , Q13608, Q5T8W1, Q8WYQ0, Q8WYQ1, Q8WYQ2, Q99476, uc317nlv.1, uc317nlv.2
UCSC ID: ENST00000304611.13_7
RefSeq Accession: NM_000287.4
Protein: Q13608 (aka PEX6_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEX6:
pbd (Zellweger Spectrum Disorder)

-  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.