PGBD5 Gene (Protein Coding)

PiggyBac Transposable Element Derived 5

GC01M230314
GIFtS:
33
The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived... See more...

Aliases for PGBD5 Gene

Aliases for PGBD5 Gene

  • PiggyBac Transposable Element Derived 5 2 3 5
  • PiggyBac Transposable Element-Derived Protein 5 3 4
  • PiggyBac Transposase 5 3 4
  • PiggyBac Domain Related Protein 5 3
  • PiggyBac Domain-Related Protein 5 4
  • EC 3.1.-.- 4

External Ids for PGBD5 Gene

Previous GeneCards Identifiers for PGBD5 Gene

  • GC01M226185
  • GC01M226930
  • GC01M227492
  • GC01M226764
  • GC01M228524
  • GC01M230457
  • GC01M200945

Summaries for PGBD5 Gene

Entrez Gene Summary for PGBD5 Gene

  • The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families. [provided by RefSeq, May 2010]

GeneCards Summary for PGBD5 Gene

PGBD5 (PiggyBac Transposable Element Derived 5) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for PGBD5 Gene

  • Transposase that mediates sequence-specific genomic rearrangements (PubMed:26406119, PubMed:28504702). Can induce genomic rearrangements that inactivate the HPRT1 gene (PubMed:27491780).

Additional gene information for PGBD5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGBD5 Gene

Genomics for PGBD5 Gene

GeneHancer (GH) Regulatory Elements for PGBD5 Gene

Promoters and enhancers for PGBD5 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
GH01J230424 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 -0.1 -112 4.7 ZBTB40 MIXL1 MYC NFYC ELF1 HLF L3MBTL2 MAX POU5F1 MNT ENSG00000282564 PGBD5 ENSG00000226920 ARV1 COG2
GH01J230310 Enhancer 1.1 Ensembl ENCODE dbSUPER 15.6 +115.6 115618 0.6 FOXK2 ZNF24 CTCF RBPJ CTBP1 CC2D1A RAD21 SP7 ZBTB33 ARID2 PGBD5 ENSG00000224407 ABCB10 lnc-GALNT2-1 HSALNG0011371
GH01J230458 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.4 -32.6 -32569 2.6 ZNF362 SP7 ZSCAN21 PRDM1 IKZF1 PRDM10 ZNF639 BRCA1 IKZF2 ZEB2 C1orf131 PGBD5 NUP133 piR-61240-022 ENSG00000282564
GH01J230366 Enhancer 0.6 dbSUPER 18.6 +58.9 58906 7.9 CTCF RAD21 SOX13 ZNF157 FOXA2 FOXP1 ZNF335 REST RXRA FOXA3 PGBD5 HSALNG0011377 lnc-GALNT2-3
GH01J230327 Enhancer 1.1 Ensembl ENCODE dbSUPER 9.7 +98.4 98431 2.2 RAD21 SP1 CEBPG SMARCA4 ZNF384 CEBPA RFX1 RXRA GATAD2A CEBPB PGBD5 FAM89A LM382375-001 HSALNG0011376
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGBD5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PGBD5 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • FosB
  • Fra-1
  • GR-alpha
  • GR-beta
  • JunB
  • JunD
  • MyoD

Genomic Locations for PGBD5 Gene

Genomic Locations for PGBD5 Gene
chr1:230,314,490-230,426,332
(GRCh38/hg38)
Size:
111,843 bases
Orientation:
Minus strand
chr1:230,457,392-230,561,475
(GRCh37/hg19)
Size:
104,084 bases
Orientation:
Minus strand

Genomic View for PGBD5 Gene

Genes around PGBD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGBD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGBD5 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PGBD5 Gene

Proteins for PGBD5 Gene

Products:

  1. Antibody
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  3. Assay

  • Protein details for PGBD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N414-PGBD5_HUMAN
    Recommended name:
    PiggyBac transposable element-derived protein 5
    Protein Accession:
    Q8N414
    Secondary Accessions:
    • A0A0A0MS21
    • A0PJF3
    • B4DM72
    • B7Z9K3
    • B9EK58
    • Q5SR37
    • Q6PJN2
    • U3REJ1

    Protein attributes for PGBD5 Gene

    Size:
    524 amino acids
    Molecular mass:
    58464 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Has been domesticated very early in vertebrate evolution, approximately 500 million years ago, in the common ancestor of cephalochordates and vertebrates.
    SequenceCaution:
    • Sequence=BAG59784.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAH14339.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for PGBD5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGBD5 Gene

Protein Expression for PGBD5 Gene

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

Post-translational modifications for PGBD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PGBD5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PGBD5 Gene

Domains & Families for PGBD5 Gene

Gene Families for PGBD5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PGBD5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGBD5 Gene

GenScript: Design optimal peptide antigens:
  • PiggyBac transposable element-derived protein 5 (PGBD5_HUMAN)
genes like me logo Genes that share domains with PGBD5: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PGBD5 Gene

Function for PGBD5 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PGBD5 Gene

UniProtKB/Swiss-Prot Function:
Transposase that mediates sequence-specific genomic rearrangements (PubMed:26406119, PubMed:28504702). Can induce genomic rearrangements that inactivate the HPRT1 gene (PubMed:27491780).

Enzyme Numbers (IUBMB) for PGBD5 Gene

Phenotypes From GWAS Catalog for PGBD5 Gene

Gene Ontology (GO) - Molecular Function for PGBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004519 endonuclease activity IEA --
GO:0004803 transposase activity IMP 27491780
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PGBD5: view
genes like me logo Genes that share phenotypes with PGBD5: view

Animal Model Products

CRISPR Products

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  • Addgene plasmids for PGBD5

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PGBD5 Gene

Localization for PGBD5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGBD5 Gene

Nucleus.

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 PGBD5 gene
Compartment Confidence
nucleus 5
cytosol 2
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PGBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,ISS --
genes like me logo Genes that share ontologies with PGBD5: view

Pathways & Interactions for PGBD5 Gene

PathCards logo

SuperPathways for PGBD5 Gene

No Data Available

Interacting Proteins for PGBD5 Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000431404 Q8N414-PGBD5_HUMAN for PGBD5 Gene via STRING IID

GPS-Prot Interaction Network for PGBD5

Gene Ontology (GO) - Biological Process for PGBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032196 transposition IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0098038 non-replicative transposition, DNA-mediated IMP 26406119
genes like me logo Genes that share ontologies with PGBD5: view

No data available for Pathways by source and SIGNOR curated interactions for PGBD5 Gene

Drugs & Compounds for PGBD5 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PGBD5 Gene

Products:

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

mRNA/cDNA for PGBD5 Gene

(2) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(71) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for PGBD5

Alternative Splicing Database (ASD) splice patterns (SP) for PGBD5 Gene

No ASD Table

Relevant External Links for PGBD5 Gene

GeneLoc Exon Structure for
PGBD5
ECgene alternative splicing isoforms for
PGBD5

Expression for PGBD5 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PGBD5 Gene

mRNA expression in normal human tissues for PGBD5 Gene
mRNA expression by BioGPS for PGBD5 GenemRNA expression by GTEx for PGBD5 Gene

mRNA differential expression in normal tissues according to GTEx for PGBD5 Gene

This gene is overexpressed in Brain - Cortex (x5.3), Brain - Frontal Cortex (BA9) (x4.8), Brain - Hippocampus (x4.4), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for PGBD5 Gene

This gene is overexpressed in Heart (43.5), Adipocyte (17.0), and Skin (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PGBD5 Gene



Protein tissue co-expression partners for PGBD5 Gene

NURSA nuclear receptor signaling pathways regulating expression of PGBD5 Gene:

PGBD5

SOURCE GeneReport for Unigene cluster for PGBD5 Gene:

Hs.520463

Evidence on tissue expression from TISSUES for PGBD5 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with PGBD5: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGBD5 Gene

Orthologs for PGBD5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PGBD5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PGBD5 33 32
  • 95.92 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia PGBD5 33 32
  • 91.85 (n)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PGBD5 33
  • 91 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia PGBD5 33 32
  • 89.35 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Pgbd5 32
  • 88.51 (n)
mouse
(Mus musculus)
 Mammalia Pgbd5 17 33 32
  • 88.26 (n)
oppossum
(Monodelphis domestica)
 Mammalia PGBD5 33
  • 86 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PGBD5 33 32
  • 81.58 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia PGBD5 33
  • 67 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia pgbd5 32
  • 74.81 (n)
Str.18969 32
African clawed frog
(Xenopus laevis)
 Amphibia Xl.26300 32
zebrafish
(Danio rerio)
 Actinopterygii pgbd5 33 32
  • 73.85 (n)
 OneToOne
Species where no ortholog for PGBD5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • bread mold (Neurospora crassa)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PGBD5 Gene

ENSEMBL:
Gene Tree for PGBD5 (if available)
TreeFam:
Gene Tree for PGBD5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGBD5: view image

Paralogs for PGBD5 Gene

No data available for Paralogs for PGBD5 Gene

Variants for PGBD5 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PGBD5 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000001701 -- 230,427,541(-) C/A upstream_transcript_variant
rs1000084872 -- 230,341,734(-) A/G intron_variant
rs1000098653 -- 230,422,523(-) A/C intron_variant
rs1000113451 -- 230,391,167(-) G/A intron_variant
rs1000144513 -- 230,390,990(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PGBD5 Gene

Variant ID Type Subtype PubMed ID
dgv291n106 CNV deletion 24896259
dgv55e201 CNV deletion 23290073
esv2296334 CNV deletion 18987734
esv23377 CNV loss 19812545
esv24937 CNV gain 19812545
esv2587431 CNV insertion 19546169
esv2662631 CNV deletion 23128226
esv2667000 CNV deletion 23128226
esv2674758 CNV deletion 23128226
esv2724683 CNV deletion 23290073
esv2724695 CNV deletion 23290073
esv2724706 CNV deletion 23290073
esv2724717 CNV deletion 23290073
esv2741277 CNV deletion 23290073
esv28174 CNV gain 19812545
esv3006323 CNV deletion 24192839
esv3308402 CNV mobile element insertion 20981092
esv3347635 CNV insertion 20981092
esv3427526 CNV insertion 20981092
esv3451220 CNV duplication 20981092
esv3548188 CNV deletion 23714750
nsv1068182 CNV deletion 25765185
nsv1118147 CNV deletion 24896259
nsv952146 CNV deletion 24416366

Variation tolerance for PGBD5 Gene

Gene Damage Index Score: 6.23; 76.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGBD5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGBD5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGBD5 Gene

Disorders for PGBD5 Gene

UniProtKB/Swiss-Prot

PGBD5_HUMAN
  • Note=Induces site-specific DNA rearrangements, including intrachromosomal deletions, as well as inversions, duplications and translocations, in rhabdoid tumors that share developmental origin with cells that normally express PGBD5, even though these tumors may not exhibit apparent widespread genomic instability. This activity recurrently targets regulatory elements and tumor suppressor genes and promotes cell transformation. {ECO:0000269 PubMed:28504702}.

Additional Disease Information for PGBD5

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PGBD5 Gene.

No data available for MalaCards and Genatlas for PGBD5 Gene

Publications for PGBD5 Gene

  1. PGBD5 promotes site-specific oncogenic mutations in human tumors. (PMID: 28504702) Henssen AG … Kentsis A (Nature genetics 2017) 3 4 56
  2. Forward genetic screen of human transposase genomic rearrangements. (PMID: 27491780) Henssen AG … Kentsis A (BMC genomics 2016) 3 4 56
  3. Genomic DNA transposition induced by human PGBD5. (PMID: 26406119) Henssen AG … Kentsis A (eLife 2015) 3 4 56
  4. Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (PMID: 18951430) Anney RJ … Gill M (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 43 56
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56

ExternalLinks

View latest publications for PGBD5 gene in Mastermind

Products for PGBD5 Gene

  • Addgene plasmids for PGBD5

Sources for PGBD5 Gene