PGBD5 piggyBac transposable element derived 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PGBD5provided by HGNC
Official Full Name: piggyBac transposable element derived 5provided by HGNC
Primary source: HGNC:HGNC:19405
See related: Ensembl:ENSG00000177614 MIM:616791; AllianceGenome:HGNC:19405
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: 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]
Expression: Biased expression in brain (RPKM 13.1), adrenal (RPKM 4.4) and 9 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q42.13

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (230314490..230426332, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (229693950..229806671, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (230450236..230562078, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Knockdown of PGBD5 inhibits the malignant progression of glioma through upregulation of the PPAR pathway.
Title: Knockdown of PGBD5 inhibits the malignant progression of glioma through upregulation of the PPAR pathway.
Childhood cancer mutagenesis caused by transposase-derived PGBD5.
Title: Childhood cancer mutagenesis caused by transposase-derived PGBD5.
Cognate restriction of transposition by piggyBac-like proteins.
Title: Cognate restriction of transposition by piggyBac-like proteins.
The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition.
Title: The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition.
Previously undefined genomic rearrangements in rhabdoid tumors involved PGBD5-specific signal (PSS) sequences at their breakpoints and recurrently inactivated tumor-suppressor genes. PGBD5 physically associated with genomic PSS sequences mediating PGBD5-induced DNA rearrangements in rhabdoid tumor cells. In immortalized cells, PGBD5 sufficed for transformation via specific catalytic residues in the transposase domain.
Title: PGBD5 promotes site-specific oncogenic mutations in human tumors.
DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites.
Title: Genomic DNA transposition induced by human PGBD5.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G20244 (e-PCR)
- UniSTS:40782

A005B21 (e-PCR)
- UniSTS:40783

RH26826 (e-PCR)
- UniSTS:52380

RH64527 (e-PCR)
- UniSTS:43421

RH119186 (e-PCR)
- UniSTS:138695

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables transposase activity	IBA Inferred from Biological aspect of Ancestor more info
enables transposase activity	IDA Inferred from Direct Assay more info	PubMed
enables transposase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in non-replicative DNA transposition	IBA Inferred from Biological aspect of Ancestor more info
involved_in non-replicative DNA transposition	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: piggyBac transposable element-derived protein 5

Names: piggyBac domain related protein 5; piggyBac transposase 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001258311.2 → NP_001245240.1 piggyBac transposable element-derived protein 5

See identical proteins and their annotated locations for NP_001245240.1

Status: REVIEWED

Source sequence(s)

AL133516, AL691479, BC013901, BC036865, CX757968

Consensus CDS

CCDS81430.1

UniProtKB/Swiss-Prot

A0A0A0MS21, A0PJF3, B4DM72, B7Z9K3, B9EK58, Q5SR37, Q6PJN2, Q8N414, U3REJ1

Related

ENSP00000375733.2, ENST00000391860.7

Conserved Domains (1) summary

pfam13843
Location:121 → 487

DDE_Tnp_1_7; Transposase IS4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

230314490..230426332 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

229693950..229806671 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_024554.3: Suppressed sequence

Description

NM_024554.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.