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' ... See more...

Aliases for PGBD3 Gene

Aliases for PGBD3 Gene

  • PiggyBac Transposable Element Derived 3 2 3
  • PiggyBac Transposable Element-Derived Protein 3 3 4
  • FLJ90201 2

External Ids for PGBD3 Gene

Previous GeneCards Identifiers for PGBD3 Gene

  • GC10U900015
  • GC10M050560
  • GC10M050012
  • GC10M050015
  • GC10M050337
  • GC10M050393
  • GC10M050723
  • GC10M044987
  • GC10M049516
  • GC10M049455

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 B and De Sanctis-Cacchione Syndrome.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for PGBD3 Gene

Genomics for PGBD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH10J049521 Enhancer 0.3 Ensembl 605.9 +1.6 1580 2.2 ZNF133 PGBD3 lnc-DRGX-3 piR-33051 ENSG00000226576 ERCC6 DRGX
GH10J049549 Enhancer 0.9 Ensembl ENCODE 18.6 -27.6 -27620 5 JUND DDX20 ZNF740 HDAC1 SOX6 NR3C1 ZNF316 JUN NR2C2 MEF2D HMGB1P50 lnc-CHAT-1 PGBD3 ERCC6 ENSG00000235939 piR-50437-050 CHAT
GH10J049407 Enhancer 0.9 Ensembl ENCODE 11.2 +116.1 116098 2 CTCF RFX1 FOXA1 REST RAD21 TRIM22 ZNF444 SMC3 YY1 PKNOX1 TIMM23B-AGAP6 WASHC2A PGBD3 AGAP6 RNA5SP317 C10orf71-AS1 DRGX ENSG00000235939
GH10J049534 Enhancer 0.9 FANTOM5 ENCODE 7.9 -11.3 -11301 2.5 SP1 ZNF692 POLR2A PRDM1 ZNF143 RELA IKZF2 RCOR1 PKNOX1 ARID3A PGBD3 ERCC6 lnc-CHAT-3 lnc-DRGX-4
GH10J049526 Enhancer 0.8 Ensembl ENCODE 5.9 -2.5 -2533 1.2 DPF2 TCF12 EP300 HMBOX1 GATAD2A NCOR1 NFIC STAT5A FOXM1 TAL1 DRGX ERCC6 PGBD3 lnc-DRGX-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGBD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGBD3

Top Transcription factor binding sites by QIAGEN in the PGBD3 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • GATA-1
  • Pax-2a
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for PGBD3 Gene

Genomic Locations for PGBD3 Gene
chr10:49,515,105-49,524,281
(GRCh38/hg38)
Size:
9,177 bases
Orientation:
Minus strand
chr10:50,723,151-50,747,086
(GRCh37/hg19)
Size:
23,936 bases
Orientation:
Minus strand

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

REFSEQ proteins:

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:
  • PiggyBac transposable element-derived protein 3 (PGBD3_HUMAN)
genes like me logo Genes that share domains with PGBD3: view

No data available for Graphical View of Domain Structure and 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:0043565 sequence-specific DNA binding IDA, IBA 22483866
genes like me logo Genes that share ontologies with PGBD3: view
genes like me logo Genes that share phenotypes with PGBD3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGBD3

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
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PGBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0016604 nuclear body 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

PathCards logo

SuperPathways for PGBD3 Gene

No Data Available

Interacting Proteins for PGBD3 Gene

Selected Interacting proteins: Q8N328-PGBD3_HUMAN for PGBD3 Gene via IID

Gene Ontology (GO) - Biological Process for PGBD3 Gene

None

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

mRNA/cDNA for PGBD3 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGBD3

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

No ASD Table

Relevant External Links for PGBD3 Gene

GeneLoc Exon Structure for
PGBD3

Expression for PGBD3 Gene

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



Protein tissue co-expression partners for PGBD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

No data available for Orthologs and Evolution for PGBD3 Gene

Paralogs for PGBD3 Gene

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

  • PGBD3_HUMAN
genes like me logo Genes that share paralogs with PGBD3: view

No data available for Paralogs for PGBD3 Gene

Variants for PGBD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGBD3 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
658237 Pathogenic: not provided 49,524,133(-) C/A NONSENSE,FIVE_PRIME_UTR_VARIANT
753304 Likely Benign: not provided 49,524,158(-) A/G SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
763167 Likely Benign: not provided 49,524,200(-) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
764660 Likely Benign: not provided 49,524,176(-) T/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
765824 Likely Benign: not provided 49,516,677(-) A/G SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PGBD3 Gene

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

(7) MalaCards diseases for PGBD3 Gene - From: GeneCards

- 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
  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 41
  3. An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. (PMID: 18369450) Newman JC … Weiner AM (PLoS genetics 2008) 3 4
  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 41
  5. CSB-PGBD3 Mutations Cause Premature Ovarian Failure. (PMID: 26218421) Qin Y … Chen ZJ (PLoS genetics 2015) 4

Products for PGBD3 Gene

Sources for PGBD3 Gene