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Aliases for PGBD3 Gene

Aliases for PGBD3 Gene

  • PiggyBac Transposable Element Derived 3 2 3
  • ERCC Excision Repair 6, Chromatin Remodeling Factor 5
  • ERCC6 5

External Ids for PGBD3 Gene

Previous GeneCards Identifiers for PGBD3 Gene

  • GC10U900015
  • GC10M050560
  • GC10M050012
  • GC10M050015
  • GC10M050337
  • GC10M050393
  • GC10M050723
  • GC10M044987

Summaries for PGBD3 Gene

Entrez Gene Summary for PGBD3 Gene

  • This gene is a member of a small family of genes derived from piggyBac transposable elements. The encoded protein contains a zinc-ribbon domain characteristic of transposon-derived proteins and may function as a regulator of transcription. Alternative splicing occurs between a splice site from exon 5 of the adjacent upstream gene 'excision repair cross-complementation group 6' (ERCC6, GeneID: 2074) and the 3' splice site upstream of the open reading frame (ORF) of this gene, which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. Pseudogenes for this gene are defined on chromosomes 4, 5 and 12. [provided by RefSeq, Mar 2016]

GeneCards Summary for PGBD3 Gene

PGBD3 (PiggyBac Transposable Element Derived 3) is a Protein Coding gene. Diseases associated with PGBD3 include Cockayne Syndrome and Uv-Sensitive Syndrome. An important paralog of this gene is ERCC6L.

UniProtKB/Swiss-Prot for PGBD3 Gene

  • Binds in vitro to PGBD3-related transposable elements, called MER85s; these non-autonomous 140 bp elements are characterized by the presence of PGBD3 terminal inverted repeats and the absence of internal transposase ORF.

Additional gene information for PGBD3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PGBD3 Gene

Genomics for PGBD3 Gene

GeneHancer (GH) Regulatory Elements for PGBD3 Gene

Promoters and enhancers for PGBD3 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
GH10I049537 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.5 516 2.5 HDGF PKNOX1 CLOCK FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ERCC6 PGBD3 LINC00843 WASHC2A AGAP6 RNA5SP317 ENSG00000235939 PIR54050
GH10I049524 Promoter 0.6 EPDnew 550.4 +15.3 15320 0.1 ZNF274 PIR54050 PGBD3 LINC00843 ERCC6
GH10I049534 Enhancer 1.2 FANTOM5 Ensembl ENCODE 8.2 +3.9 3874 2.7 PKNOX1 JUN EBF1 BATF RELA ZNF143 ATF7 ETV6 IKZF2 RUNX3 PGBD3 ERCC6 PIR54050
GH10I049407 Enhancer 0.7 ENCODE 11.2 +131.8 131808 0.2 CTCF PKNOX1 RB1 ZNF2 RAD21 GATA3 ZNF366 ZNF143 SMC3 ZNF444 LINC00843 WASHC2A PGBD3 AGAP6 RNA5SP317 C10orf71-AS1 ENSG00000235939 GC10P049396
GH10I049549 Enhancer 0.9 Ensembl ENCODE 7.3 -12.5 -12492 4.6 HDAC1 JUN PYGO2 ZBTB40 FOSL1 GATA3 ZNF316 VEZF1 NFE2 STAT1 HMGB1P50 ERCC6 PGBD3 ENSG00000235939 GC10P049595
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PGBD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PGBD3 gene promoter:

Genomic Locations for PGBD3 Gene

Genomic Locations for PGBD3 Gene
chr10:49,455,368-49,539,538
(GRCh38/hg38)
Size:
84,171 bases
Orientation:
Minus strand
chr10:50,723,151-50,747,086
(GRCh37/hg19)

Genomic View for PGBD3 Gene

Genes around PGBD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGBD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGBD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGBD3 Gene

Proteins for PGBD3 Gene

  • Protein details for PGBD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N328-PGBD3_HUMAN
    Recommended name:
    PiggyBac transposable element-derived protein 3
    Protein Accession:
    Q8N328
    Secondary Accessions:
    • B3KQC4
    • Q5W0M0
    • Q6PIH0

    Protein attributes for PGBD3 Gene

    Size:
    593 amino acids
    Molecular mass:
    67595 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • PGBD3 gene is located within ERCC6 intron 5.

    Alternative splice isoforms for PGBD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGBD3 Gene

Post-translational modifications for PGBD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PGBD3 Gene

No data available for DME Specific Peptides for PGBD3 Gene

Domains & Families for PGBD3 Gene

Gene Families for PGBD3 Gene

Protein Domains for PGBD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGBD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PGBD3: view

No data available for UniProtKB/Swiss-Prot for PGBD3 Gene

Function for PGBD3 Gene

Molecular function for PGBD3 Gene

UniProtKB/Swiss-Prot Function:
Binds in vitro to PGBD3-related transposable elements, called MER85s; these non-autonomous 140 bp elements are characterized by the presence of PGBD3 terminal inverted repeats and the absence of internal transposase ORF.

Gene Ontology (GO) - Molecular Function for PGBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IDA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI --
GO:0005524 ATP binding IDA --
genes like me logo Genes that share ontologies with PGBD3: view

Phenotypes for PGBD3 Gene

genes like me logo Genes that share phenotypes with PGBD3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PGBD3 Gene

Localization for PGBD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGBD3 Gene

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 PGBD3 gene
Compartment Confidence
nucleus 4
cytosol 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for PGBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005730 nucleolus IDA --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with PGBD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PGBD3 Gene

Pathways & Interactions for PGBD3 Gene

SuperPathways for PGBD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PGBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000303 response to superoxide IEA --
GO:0006281 DNA repair IEA --
GO:0006283 transcription-coupled nucleotide-excision repair IMP --
GO:0006284 base-excision repair IMP --
GO:0006290 pyrimidine dimer repair IEA --
genes like me logo Genes that share ontologies with PGBD3: view

No data available for Pathways by source and SIGNOR curated interactions for PGBD3 Gene

Drugs & Compounds for PGBD3 Gene

No Compound Related Data Available

Transcripts for PGBD3 Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGBD3 Gene

No ASD Table

Relevant External Links for PGBD3 Gene

GeneLoc Exon Structure for
PGBD3
ECgene alternative splicing isoforms for
PGBD3

Expression for PGBD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PGBD3 Gene

Protein differential expression in normal tissues from HIPED for PGBD3 Gene

This gene is overexpressed in Placenta (59.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PGBD3 Gene



Protein tissue co-expression partners for PGBD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PGBD3 Gene:

PGBD3

mRNA Expression by UniProt/SwissProt for PGBD3 Gene:

Q8N328-PGBD3_HUMAN
Tissue specificity: Expressed in heart and oocytes, but not in granulosa cells (at protein level).

Evidence on tissue expression from TISSUES for PGBD3 Gene

  • Liver(4.1)
genes like me logo Genes that share expression patterns with PGBD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGBD3 Gene

Orthologs for PGBD3 Gene

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

Orthologs for PGBD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ERCC6 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ERCC6L 34
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ercc6 34
  • 79 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ERCC6 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ERCC6 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ERCC6 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves ERCC6 34
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ERCC6 34
  • 60 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii ercc6 34
  • 60 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD26 36 34
  • 37 (a)
Species where no ortholog for PGBD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PGBD3 Gene

ENSEMBL:
Gene Tree for PGBD3 (if available)
TreeFam:
Gene Tree for PGBD3 (if available)

Paralogs for PGBD3 Gene

Paralogs for PGBD3 Gene

(4) SIMAP similar genes for PGBD3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PGBD3: view

Variants for PGBD3 Gene

Sequence variations from dbSNP and Humsavar for PGBD3 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs121917902 pathogenic, Cockayne syndrome B 49,524,073(-) G/A 5_prime_UTR_variant
rs138865542 uncertain-significance, Cerebrooculofacioskeletal Syndrome, Cockayne syndrome, Macular degeneration 49,524,201(-) C/T 5_prime_UTR_variant
rs141391984 uncertain-significance, likely-benign, Macular degeneration, Cerebrooculofacioskeletal Syndrome, Cockayne syndrome 49,524,272(-) G/A/C/T 5_prime_UTR_variant
rs143260457 likely-benign, Cockayne syndrome, Cerebrooculofacioskeletal Syndrome, Macular degeneration 49,524,572(-) C/G upstream_transcript_variant
rs148295935 likely-benign, Cockayne syndrome, Cerebrooculofacioskeletal Syndrome, Macular degeneration 49,524,271(-) C/T 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PGBD3 Gene

Variant ID Type Subtype PubMed ID
nsv1042677 CNV loss 25217958
nsv1051636 CNV loss 25217958
nsv6632 CNV insertion 18451855
nsv831867 CNV gain 17160897
nsv947979 CNV duplication 23825009

Variation tolerance for PGBD3 Gene

Residual Variation Intolerance Score: 39.3% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGBD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGBD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGBD3 Gene

Disorders for PGBD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PGBD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cockayne syndrome
  • cockayne's syndrome
uv-sensitive syndrome
  • uv sensitive syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PGBD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PGBD3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PGBD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PGBD3 Gene

Publications for PGBD3 Gene

  1. The conserved Cockayne syndrome B-piggyBac fusion protein (CSB-PGBD3) affects DNA repair and induces both interferon-like and innate antiviral responses in CSB-null cells. (PMID: 22483866) Bailey AD … Weiner AM (DNA repair 2012) 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. (PMID: 18369450) Newman JC … Weiner AM (PLoS genetics 2008) 3 4 58
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 44 58
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58

Products for PGBD3 Gene

Sources for PGBD3 Gene

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