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Aliases for PGBD4 Gene

Aliases for PGBD4 Gene

  • PiggyBac Transposable Element Derived 4 2 3 5
  • PiggyBac Transposable Element-Derived Protein 4 3

External Ids for PGBD4 Gene

Previous GeneCards Identifiers for PGBD4 Gene

  • GC15P027111
  • GC15P031973
  • GC15P032110
  • GC15P032181
  • GC15P034394
  • GC15P011257

Summaries for PGBD4 Gene

Entrez Gene Summary for PGBD4 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, Jul 2008]

GeneCards Summary for PGBD4 Gene

PGBD4 (PiggyBac Transposable Element Derived 4) is a Protein Coding gene. An important paralog of this gene is PGBD2.

Additional gene information for PGBD4 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PGBD4 Gene

Genomics for PGBD4 Gene

GeneHancer (GH) Regulatory Elements for PGBD4 Gene

Promoters and enhancers for PGBD4 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
GH15J034100 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 657.1 -0.4 -350 2.6 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 IRF4 YY1 PGBD4 EMC7 AVEN KATNBL1 HNRNPLP2 EMC4 RPL32P2
GH15J034513 Enhancer 1.2 Ensembl ENCODE 10.3 +412.6 412628 2.2 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 ZNF766 E2F8 AQR ENSG00000259287 HNRNPLP2 GOLGA8A NUTM1 ENSG00000259408 LINC02252 ENSG00000259468 FSCN1P1 ENSG00000259336
GH15J034121 Enhancer 0.9 Ensembl ENCODE 12.4 +21.6 21627 4.4 PKNOX1 BACH1 EBF1 BATF IRF4 ATF7 IKZF2 RUNX3 ZBTB20 ZBED1 EMC7 PGBD4 KATNBL1 NOP10 SLC12A6 GOLGA8B PIR44117
GH15J034116 Enhancer 0.5 ENCODE 5.7 +16.2 16174 3.8 CTCF GATA3 IKZF1 SMC3 RAD21 KATNBL1 AVEN PGBD4 PIR44117
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGBD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PGBD4 gene promoter:
  • Max1
  • c-Myc
  • deltaCREB
  • CREB
  • AP-2gamma
  • GATA-2
  • E47
  • Tal-1beta

Genomic Locations for PGBD4 Gene

Genomic Locations for PGBD4 Gene
chr15:34,102,073-34,108,684
(GRCh38/hg38)
Size:
6,612 bases
Orientation:
Plus strand
chr15:34,394,274-34,396,591
(GRCh37/hg19)
Size:
2,318 bases
Orientation:
Plus strand

Genomic View for PGBD4 Gene

Genes around PGBD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGBD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGBD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGBD4 Gene

Proteins for PGBD4 Gene

  • Protein details for PGBD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DM1-PGBD4_HUMAN
    Recommended name:
    PiggyBac transposable element-derived protein 4
    Protein Accession:
    Q96DM1
    Secondary Accessions:
    • A1L487
    • A8K0C6
    • Q8N9E8

    Protein attributes for PGBD4 Gene

    Size:
    585 amino acids
    Molecular mass:
    67004 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC04428.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for PGBD4 Gene

Post-translational modifications for PGBD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PGBD4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PGBD4 Gene

Domains & Families for PGBD4 Gene

Gene Families for PGBD4 Gene

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

Protein Domains for PGBD4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGBD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PGBD4: view

No data available for UniProtKB/Swiss-Prot for PGBD4 Gene

Function for PGBD4 Gene

genes like me logo Genes that share phenotypes with PGBD4: view

Animal Model Products

miRNA for PGBD4 Gene

miRTarBase miRNAs that target PGBD4

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PGBD4 Gene

Localization for PGBD4 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 PGBD4 gene
Compartment Confidence
nucleus 3
cytosol 2

Subcellular locations from the

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

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PGBD4 Gene

Pathways & Interactions for PGBD4 Gene

SuperPathways for PGBD4 Gene

No Data Available

Interacting Proteins for PGBD4 Gene

Gene Ontology (GO) - Biological Process for PGBD4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PGBD4 Gene

Drugs & Compounds for PGBD4 Gene

No Compound Related Data Available

Transcripts for PGBD4 Gene

mRNA/cDNA for PGBD4 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PGBD4 Gene

PiggyBac transposable element derived 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGBD4 Gene

No ASD Table

Relevant External Links for PGBD4 Gene

GeneLoc Exon Structure for
PGBD4
ECgene alternative splicing isoforms for
PGBD4

Expression for PGBD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PGBD4 Gene

Protein differential expression in normal tissues from HIPED for PGBD4 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PGBD4 Gene



Protein tissue co-expression partners for PGBD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of PGBD4 Gene:

PGBD4

SOURCE GeneReport for Unigene cluster for PGBD4 Gene:

Hs.156317
genes like me logo Genes that share expression patterns with PGBD4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGBD4 Gene

Orthologs for PGBD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PGBD4 Gene

Organism Taxonomy Gene Similarity Type Details
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101732865 33
  • 48.45 (n)
zebrafish
(Danio rerio)
Actinopterygii PGBD4 (6 of 8) 34
  • 27 (a)
OneToMany
PGBD4 (3 of 8) 34
  • 25 (a)
OneToMany
PGBD4 (2 of 8) 34
  • 23 (a)
OneToMany
PGBD4 (7 of 8) 34
  • 23 (a)
OneToMany
PGBD4 (5 of 8) 34
  • 22 (a)
OneToMany
PGBD4 (8 of 8) 34
  • 21 (a)
OneToMany
PGBD4 (1 of 8) 34
  • 17 (a)
OneToMany
PGBD4 (4 of 8) 34
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 21 (a)
ManyToMany
Species where no ortholog for PGBD4 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 PGBD4 Gene

ENSEMBL:
Gene Tree for PGBD4 (if available)
TreeFam:
Gene Tree for PGBD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGBD4: view image

Paralogs for PGBD4 Gene

Variants for PGBD4 Gene

Sequence variations from dbSNP and Humsavar for PGBD4 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1001325299 -- 34,100,517(+) C/T upstream_transcript_variant
rs1002095010 -- 34,104,875(+) C/T downstream_transcript_variant
rs1002726343 -- 34,101,414(+) C/T upstream_transcript_variant
rs1002751173 -- 34,101,103(+) T/G upstream_transcript_variant
rs1004062033 -- 34,104,525(+) C/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PGBD4 Gene

Variant ID Type Subtype PubMed ID
dgv4456n54 CNV gain 21841781
esv33337 CNV gain+loss 17666407
esv3569431 CNV gain 25503493
nsv1052620 CNV gain 25217958
nsv456789 CNV gain 19166990
nsv471235 CNV gain 18288195
nsv568920 CNV gain 21841781

Variation tolerance for PGBD4 Gene

Residual Variation Intolerance Score: 28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.27; 40.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGBD4 Gene

Human Gene Mutation Database (HGMD)
PGBD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGBD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGBD4 Gene

Disorders for PGBD4 Gene

Additional Disease Information for PGBD4

No disorders were found for PGBD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PGBD4 Gene

Publications for PGBD4 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 4 58
  3. Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. (PMID: 12955498) Sarkar A … Collins FH (Molecular genetics and genomics : MGG 2003) 3 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for PGBD4 Gene

Sources for PGBD4 Gene

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