Human Gene PEX13 (uc002sau.4)
  Description: Homo sapiens peroxisomal biogenesis factor 13 (PEX13), mRNA.
RefSeq Summary (NM_002618): This gene encodes a peroxisomal membrane protein that binds the type 1 peroxisomal targeting signal receptor via a SH3 domain located in the cytoplasm. Mutations and deficiencies in peroxisomal protein importing and peroxisome assembly lead to peroxisomal biogenesis disorders, an example of which is Zellweger syndrome. [provided by RefSeq, Oct 2008]. Sequence Note: The RefSeq transcript and protein were derived from transcript and genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Transcript (Including UTRs)
   Position: hg19 chr2:61,244,812-61,279,125 Size: 34,314 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr2:61,244,895-61,275,905 Size: 31,011 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:61,244,812-61,279,125)mRNA (may differ from genome)Protein (403 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PEX13_HUMAN
DESCRIPTION: RecName: Full=Peroxisomal membrane protein PEX13; AltName: Full=Peroxin-13;
FUNCTION: Component of the peroxisomal translocation machinery with PEX14 and PEX17. Functions as a docking factor for the predominantly cytoplasmic PTS1 receptor (PAS10/PEX5). Involved in the import of PTS1 and PTS2 proteins.
SUBUNIT: Interacts with PEX19.
INTERACTION: P40855:PEX19; NbExp=2; IntAct=EBI-594849, EBI-594747;
SUBCELLULAR LOCATION: Peroxisome membrane; Single-pass membrane protein.
DISEASE: Defects in PEX13 are the cause of peroxisome biogenesis disorder complementation group 13 (PBD-CG13) [MIM:601789]; also known as PBD-CGH. PBD-CG13 is a peroxisomal disorder arising from a failure of protein import into the peroxisomal membrane or matrix. The peroxisome biogenesis disorders (PBD group) are genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies. Include disorders are: 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 (PBD-ZSS).
DISEASE: Defects in PEX13 are a cause of adrenoleukodystrophy neonatal (NALD) [MIM:202370]. NALD is a peroxisome biogenesis disorder (PBD) characterized by the accumulation of very long- chain fatty acids, adrenal insufficiency and mental retardation.
SIMILARITY: Belongs to the peroxin-13 family.
SIMILARITY: Contains 1 SH3 domain.
CAUTION: It is uncertain whether Met-1 or Met-40 is the initiator.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PEX13";

-  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: PEX13
Diseases sorted by gene-association score: peroxisome biogenesis disorder 11b* (1230), peroxisome biogenesis disorder 11a* (919), neonatal adrenoleukodystrophy* (130), peroxisome biogenesis disorder 1b* (129), peroxisome biogenesis disorders, zellweger syndrome spectrum* (63), zellweger syndrome (14), peroxisomal biogenesis disorders (14), peroxisomal disease (6)
* = 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: 6.70 RPKM in Liver
Total median expression: 207.49 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 -26.8083-0.323 Picture PostScript Text
3' UTR -1053.723220-0.327 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
IPR007223 - Peroxin-13_N
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF04088 - Peroxin 13, N-terminal region
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain

ModBase Predicted Comparative 3D Structure on Q92968
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

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

Biological Process:
GO:0001561 fatty acid alpha-oxidation
GO:0001764 neuron migration
GO:0001967 suckling behavior
GO:0006625 protein targeting to peroxisome
GO:0007626 locomotory behavior
GO:0015031 protein transport
GO:0016560 protein import into peroxisome matrix, docking
GO:0016567 protein ubiquitination
GO:0021795 cerebral cortex cell migration
GO:0060152 microtubule-based peroxisome localization

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:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  BC025779 - Homo sapiens, Similar to peroxisome biogenesis factor 13, clone IMAGE:5222848, mRNA.
AK311426 - Homo sapiens cDNA, FLJ18468.
BC032755 - Homo sapiens, Similar to peroxisome biogenesis factor 13, clone IMAGE:5581685, mRNA.
AK315244 - Homo sapiens cDNA, FLJ96246, Homo sapiens peroxisome biogenesis factor 13 (PEX13), mRNA.
AB022192 - Homo sapiens mRNA for PEX13, complete cds.
AF048755 - Homo sapiens HsPex13p (PEX13) mRNA, complete cds.
JD408128 - Sequence 389152 from Patent EP1572962.
BC067090 - Homo sapiens peroxisomal biogenesis factor 13, mRNA (cDNA clone MGC:71242 IMAGE:6285875), complete cds.
JD205815 - Sequence 186839 from Patent EP1572962.
BC020547 - Homo sapiens, Similar to peroxisome biogenesis factor 13, clone IMAGE:4422594, mRNA.
BC040953 - Homo sapiens, clone IMAGE:5724464, mRNA.
BC048804 - Homo sapiens, clone IMAGE:4392514, mRNA.
BC035584 - Homo sapiens, clone IMAGE:5398100, mRNA.
CU688242 - Synthetic construct Homo sapiens gateway clone IMAGE:100022496 5' read PEX13 mRNA.
AB528913 - Synthetic construct DNA, clone: pF1KE0694, Homo sapiens PEX13 gene for peroxisomal biogenesis factor 13, without stop codon, in Flexi system.
HQ448406 - Synthetic construct Homo sapiens clone IMAGE:100071833; CCSB013776_01 peroxisome biogenesis factor 13 (PEX13) gene, encodes complete protein.
KJ891780 - Synthetic construct Homo sapiens clone ccsbBroadEn_01174 PEX13 gene, encodes complete protein.
KR711313 - Synthetic construct Homo sapiens clone CCSBHm_00022788 PEX13 (PEX13) mRNA, encodes complete protein.
KR711314 - Synthetic construct Homo sapiens clone CCSBHm_00022789 PEX13 (PEX13) mRNA, encodes complete protein.
U71374 - Homo sapiens HsPex13p mRNA, complete cds.
AK093866 - Homo sapiens cDNA FLJ36547 fis, clone TRACH2007577.
JD087306 - Sequence 68330 from Patent EP1572962.
JD548136 - Sequence 529160 from Patent EP1572962.
JD376792 - Sequence 357816 from Patent EP1572962.
JD417727 - Sequence 398751 from Patent EP1572962.
JD411998 - Sequence 393022 from Patent EP1572962.
JD321260 - Sequence 302284 from Patent EP1572962.
JD388851 - Sequence 369875 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q92968 (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: B2RCS1, NM_002618, NP_002609, PEX13_HUMAN, Q92968
UCSC ID: uc002sau.4
RefSeq Accession: NM_002618
Protein: Q92968 (aka PEX13_HUMAN or PEXD_HUMAN)
CCDS: CCDS1866.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEX13:
pbd (Zellweger Spectrum Disorder)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002618.3
exon count: 4CDS single in 3' UTR: no RNA size: 4524
ORF size: 1212CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2624.00frame shift in genome: no % Coverage: 99.80
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: 19# 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.