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PEX16 Gene(Protein Coding)

Peroxisomal Biogenesis Factor 16

GCID:
GC11M054225
GIFtS:
48
Genes Participants
UDN Logo

Aliases for PEX16 Gene

Aliases for PEX16 Gene

  • Peroxisomal Biogenesis Factor 16 2 3 4 5
  • Peroxisomal Membrane Protein PEX16 3
  • Peroxisome Biogenesis Factor 16 3
  • Peroxin 16 3
  • Peroxin-16 4
  • PBD8A 3
  • PBD8B 3

External Ids for PEX16 Gene

Previous GeneCards Identifiers for PEX16 Gene

  • GC11M047715
  • GC11M046620
  • GC11M045962
  • GC11M045895
  • GC11M045887
  • GC11M045931
  • GC11M045638
  • GC11M047070
  • GC11M047917
  • GC11M050774
  • GC11M051569
  • GC11M052231
  • GC11M052891
  • GC11M053559

Summaries for PEX16 Gene

Entrez Gene Summary for PEX16 Gene

  • The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for PEX16 Gene

PEX16 (Peroxisomal Biogenesis Factor 16) is a Protein Coding gene. Diseases associated with PEX16 include Peroxisome Biogenesis Disorder 8B and Peroxisome Biogenesis Disorder 8A. Among its related pathways are Peroxisome. Gene Ontology (GO) annotations related to this gene include protein C-terminus binding.

UniProtKB/Swiss-Prot for PEX16 Gene

  • Required for peroxisome membrane biogenesis. May play a role in early stages of peroxisome assembly. Can recruit other peroxisomal proteins, such as PEX3 and PMP34, to de novo peroxisomes derived from the endoplasmic reticulum (ER). May function as receptor for PEX3.

Gene Wiki entry for PEX16 Gene

Additional gene information for PEX16 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PEX16 Gene

Genomics for PEX16 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PEX16 Gene

Promoters and enhancers for PEX16 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11I045916 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 550.8 0.0 -38 3.9 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A YY1 POLR2B ZNF766 E2F8 PEX16 RPS10P19 ZNF408 LARGE2
GH11I045879 Enhancer 1.1 ENCODE dbSUPER 13 +37.7 37678 3.1 ATF1 PKNOX1 TCF12 FOS ATF7 NCOA1 REST TSHZ1 ATF4 GMEB1 C11orf94 ENSG00000255498 LARGE2 PEX16 MAPK8IP1 DKFZp779M0652 CRY2
GH11I045854 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.5 +60.7 60710 6.2 MXI1 CLOCK USF1 KLF17 MAX SIN3A ZIC2 RAD21 YY1 ZFHX2 MAPK8IP1 ENSG00000255498 C11orf94 LARGE2 PEX16 DKFZp779M0652 SLC35C1 CRY2
GH11I045941 Enhancer 0.4 dbSUPER 13 -23.4 -23383 2.3 ATF4 ATF7 ATF2 LARGE2 PEX16 C11orf94 ENSG00000255498 PHF21A ENSG00000254653
GH11I045944 Enhancer 0.4 ENCODE 12.5 -26.8 -26837 2.2 NFIC IKZF1 CBFA2T3 LARGE2 PEX16 C11orf94 ENSG00000255498 SLC35C1 PHF21A ENSG00000254653
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PEX16 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PEX16 gene promoter:

Genomic Locations for PEX16 Gene

Genomic Locations for PEX16 Gene
chr11:45,909,669-45,918,812
(GRCh38/hg38)
Size:
9,144 bases
Orientation:
Minus strand
chr11:45,931,220-45,940,363
(GRCh37/hg19)

Genomic View for PEX16 Gene

Genes around PEX16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PEX16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PEX16 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PEX16 Gene

Proteins for PEX16 Gene

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  • Protein details for PEX16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5Y5-PEX16_HUMAN
    Recommended name:
    Peroxisomal membrane protein PEX16
    Protein Accession:
    Q9Y5Y5
    Secondary Accessions:
    • Q9BWB9

    Protein attributes for PEX16 Gene

    Size:
    336 amino acids
    Molecular mass:
    38629 Da
    Quaternary structure:
    • Interacts with PEX19.

    Alternative splice isoforms for PEX16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PEX16 Gene

Protein Expression for PEX16 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PEX16 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PEX16 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PEX16 Gene

Domains & Families for PEX16 Gene

Gene Families for PEX16 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for PEX16 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PEX16 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5Y5

UniProtKB/Swiss-Prot:

PEX16_HUMAN :
  • Belongs to the peroxin-16 family.
Family:
  • Belongs to the peroxin-16 family.
genes like me logo Genes that share domains with PEX16: view

Function for PEX16 Gene

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Molecular function for PEX16 Gene

UniProtKB/Swiss-Prot Function:
Required for peroxisome membrane biogenesis. May play a role in early stages of peroxisome assembly. Can recruit other peroxisomal proteins, such as PEX3 and PMP34, to de novo peroxisomes derived from the endoplasmic reticulum (ER). May function as receptor for PEX3.

Gene Ontology (GO) - Molecular Function for PEX16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12096124
GO:0008022 protein C-terminus binding IPI 15713480
genes like me logo Genes that share ontologies with PEX16: view
genes like me logo Genes that share phenotypes with PEX16: view

Human Phenotype Ontology for PEX16 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for PEX16 Gene

Localization for PEX16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PEX16 Gene

Peroxisome membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PEX16 gene
Compartment Confidence
peroxisome 5
endoplasmic reticulum 5
cytosol 2
plasma membrane 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for PEX16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005777 peroxisome IDA,IEA 9837814
GO:0005778 peroxisomal membrane HDA,IEA 21525035
GO:0005779 integral component of peroxisomal membrane IMP 9922452
GO:0005783 endoplasmic reticulum IDA,IEA 19479899
GO:0005789 endoplasmic reticulum membrane IDA,IEA 16717127
genes like me logo Genes that share ontologies with PEX16: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PEX16 Gene

Pathways & Interactions for PEX16 Gene

SuperPathways for PEX16 Gene

PathCards logo More details on SuperPathways for PEX16
SuperPathway Contained pathways
1 Peroxisome
Peroxisome
-
genes like me logo Genes that share pathways with PEX16: view

Pathways by source for PEX16 Gene

1 KEGG pathway for PEX16 Gene

Gene Ontology (GO) - Biological Process for PEX16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006625 protein targeting to peroxisome IMP 9837814
GO:0007031 peroxisome organization IMP 15813749
GO:0016557 peroxisome membrane biogenesis IMP 9837814
GO:0016558 protein import into peroxisome matrix IMP 9922452
GO:0022615 protein to membrane docking IDA 19114594
genes like me logo Genes that share ontologies with PEX16: view

No data available for SIGNOR curated interactions for PEX16 Gene

Drugs & Compounds for PEX16 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for PEX16 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PEX16 Gene

(3) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(129) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PEX16 Gene

Peroxisomal biogenesis factor 16:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PEX16 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c
SP1: -
SP2: - -
SP3: -
SP4: -

Relevant External Links for PEX16 Gene

GeneLoc Exon Structure for
PEX16
ECgene alternative splicing isoforms for
PEX16

Expression for PEX16 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PEX16 Gene

mRNA expression in normal human tissues for PEX16 Gene
mRNA expression by BioGPS for PEX16 GenemRNA expression by GTEx for PEX16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PEX16 Gene

This gene is overexpressed in Bone (44.3) and Lung (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PEX16 Gene



Protein tissue co-expression partners for PEX16 Gene

NURSA nuclear receptor signaling pathways regulating expression of PEX16 Gene:

PEX16

SOURCE GeneReport for Unigene cluster for PEX16 Gene:

Hs.100915

Evidence on tissue expression from TISSUES for PEX16 Gene

  • Lung(4.2)
  • Nervous system(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PEX16 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • scalp
  • skull
  • tongue
Thorax:
  • bronchus
  • chest wall
  • clavicle
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • thymus
Abdomen:
  • abdominal wall
  • adrenal gland
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • ovary
  • pelvis
  • penis
  • testicle
  • ureter
  • urethra
  • uterus
  • vagina
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with PEX16: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PEX16 Gene

Orthologs for PEX16 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PEX16 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PEX16 33 34
  • 99.5 (n)
cow
(Bos Taurus)
 Mammalia PEX16 33 34
  • 91.17 (n)
dog
(Canis familiaris)
 Mammalia PEX16 33 34
  • 91.07 (n)
mouse
(Mus musculus)
 Mammalia Pex16 33 16 34
  • 86.9 (n)
rat
(Rattus norvegicus)
 Mammalia Pex16 33
  • 83.82 (n)
oppossum
(Monodelphis domestica)
 Mammalia PEX16 34
  • 79 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PEX16 34
  • 74 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PEX16 33 34
  • 71.69 (n)
lizard
(Anolis carolinensis)
 Reptilia PEX16 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia pex16 33
  • 61.86 (n)
Str.8967 33
zebrafish
(Danio rerio)
 Actinopterygii pex16 33 34
  • 67.76 (n)
Dr.16594 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002283 33
  • 50.37 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Pex16 33 34
  • 50.2 (n)
CG3947 35
  • 36 (a)
bread mold
(Neurospora crassa)
 Ascomycetes NCU01850 33
  • 41.61 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.4212 34
  • 30 (a)
 OneToOne
Species where no ortholog for PEX16 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PEX16 Gene

ENSEMBL:
Gene Tree for PEX16 (if available)
TreeFam:
Gene Tree for PEX16 (if available)

Paralogs for PEX16 Gene

No data available for Paralogs for PEX16 Gene

Variants for PEX16 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PEX16 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs10838529 benign, Zellweger syndrome 45,909,951(-) G/A 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs1132349 benign, not specified, Zellweger syndrome 45,913,833(-) A/C/G/T coding_sequence_variant, stop_gained, synonymous_variant
rs143868125 likely-benign, uncertain-significance, Zellweger syndrome 45,909,878(-) C/G/T 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs144897515 uncertain-significance, not specified, Zellweger syndrome 45,910,263(-) A/G coding_sequence_variant, intron_variant, synonymous_variant
rs149348130 conflicting-interpretations-of-pathogenicity, uncertain-significance, not specified, Zellweger syndrome 45,916,248(-) C/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PEX16 Gene

Variant ID Type Subtype PubMed ID
nsv516442 CNV loss 19592680

Variation tolerance for PEX16 Gene

Residual Variation Intolerance Score: 59.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.44; 54.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PEX16 Gene

Human Gene Mutation Database (HGMD)
PEX16
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PEX16

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PEX16 Gene

Disorders for PEX16 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PEX16 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
peroxisome biogenesis disorder 8b
  • pbd8b
peroxisome biogenesis disorder 8a
  • pbd8a
peroxisome biogenesis disorder 1b
  • pbd1b
neonatal adrenoleukodystrophy
  • adrenoleukodystrophy autosomal neonatal form
zellweger spectrum disorder
  • cerebrohepatorenal syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PEX16 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PEX16_HUMAN
  • Peroxisome biogenesis disorder 8A (PBD8A) [MIM:614876]: A fatal peroxisome biogenesis disorder belonging to the Zellweger disease spectrum and clinically characterized by severe neurologic dysfunction with profound psychomotor retardation, severe hypotonia and neonatal seizures, craniofacial abnormalities, liver dysfunction, and biochemically by the absence of peroxisomes. Additional features include cardiovascular and skeletal defects, renal cysts, ocular abnormalities, and hearing impairment. Most severely affected individuals with the classic form of the disease (classic Zellweger syndrome) die within the first year of life. {ECO:0000269 PubMed:9837814}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Peroxisome biogenesis disorder 8B (PBD8B) [MIM:614877]: A relatively mild peroxisome biogenesis disorder. Affected individuals manifest lower limb spasticity and ataxia resulting in wheelchair dependence. Other features include optic atrophy, cataracts, dysarthria, dysphagia, constipation, and a peripheral demyelinating motor and sensory neuropathy. Cognition is relatively preserved. Biochemical abnormalities are mild and include increased very-long-chain fatty acids (VLCFA), increased bile acid intermediates, and increased branched chain fatty acids. Phytanic acid alpha-oxidation, pristanic acid beta-oxidation, and red cell plasmalogen are normal. {ECO:0000269 PubMed:20647552}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Peroxisome biogenesis disorder complementation group 9 (PBD-CG9) [MIM:614876]: 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). {ECO:0000269 PubMed:9837814}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PEX16

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PEX16: view

No data available for Genatlas for PEX16 Gene

Publications for PEX16 Gene

  1. Peroxisome synthesis in the absence of preexisting peroxisomes. (PMID: 9922452) South ST … Gould SJ (The Journal of cell biology 1999) 2 3 4 58
  2. Mutation in PEX16 is causal in the peroxisome-deficient Zellweger syndrome of complementation group D. (PMID: 9837814) Honsho M … Fujiki Y (American journal of human genetics 1998) 3 4 22 58
  3. Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene. (PMID: 20647552) Ebberink MS … Ferdinandusse S (Journal of medical genetics 2010) 3 4 58
  4. The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER. (PMID: 16717127) Kim PK … Lippincott-Schwartz J (The Journal of cell biology 2006) 3 4 58
  5. PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins. (PMID: 14709540) Jones JM … Gould SJ (The Journal of cell biology 2004) 3 4 58

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