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PGBD1 piggyBac transposable element derived 1 [ Homo sapiens (human) ]

Gene ID: 84547, updated on 2-Nov-2024

Summary

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Official Symbol
PGBD1provided by HGNC
Official Full Name
piggyBac transposable element derived 1provided by HGNC
Primary source
HGNC:HGNC:19398
See related
Ensembl:ENSG00000137338 AllianceGenome:HGNC:19398
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCAND4; HUCEP-4; dJ874C20.4
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. This gene product is specifically expressed in the brain, however, its exact function is not known. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in brain (RPKM 2.1), endometrium (RPKM 1.7) and 25 other tissues See more
Orthologs
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Genomic context

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See PGBD1 in Genome Data Viewer
Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28281572..28302549)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28153313..28174278)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28249349..28270326)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:28234963-28235527 Neighboring gene NFKB activating protein like Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17044 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28249721-28249897 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28251848-28252055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28278749-28279250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28279251-28279750 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28321865-28322364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24355 Neighboring gene zinc finger with KRAB and SCAN domains 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles. Raskó T, et al. Mol Biol Evol, 2022 Oct 7. PMID 36205081, Free PMC Article
  2. Monoclonal antibodies expression improvement in CHO cells by PiggyBac transposition regarding vectors ratios and design. Ahmadi S, et al. PLoS One, 2017. PMID 28662065, Free PMC Article
  3. PiggyBac transposon-mediated gene delivery efficiently generates stable transfectants derived from cultured primary human deciduous tooth dental pulp cells (HDDPCs) and HDDPC-derived iPS cells. Inada E, et al. Int J Oral Sci, 2015 Sep 14. PMID 26208039, Free PMC Article
  4. Common variants in major histocompatibility complex region and TCF4 gene are significantly associated with schizophrenia in Han Chinese. Li T, et al. Biol Psychiatry, 2010 Oct 1. PMID 20673877
  5. [Polymorphic markers G(-455)A of gene FGB and C(-1654)T of gene PROC and genetic predisposition to unfavorable outcomes patients undergoing acute coronary syndrome]. Agapkina IuV, et al. Mol Biol (Mosk), 2010 Jul-Aug. PMID 20873219

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles.
    Title: A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles.
  2. Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2.
    Title: Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2.
  3. Expression levels in the transposon-based cells were two to five -folds more than those created by conventional method except for the IRES-mediated ones, in which the observed difference increased more than 100-fold
    Title: Monoclonal antibodies expression improvement in CHO cells by PiggyBac transposition regarding vectors ratios and design.
  4. the high level of transfection achieved with PB may have significant advantages in basic scientific research for dental tissue engineering applications, such as functional studies of genes and proteins
    Title: PiggyBac transposon-mediated gene delivery efficiently generates stable transfectants derived from cultured primary human deciduous tooth dental pulp cells (HDDPCs) and HDDPC-derived iPS cells.
  5. The genes HIST1H2BJ, PRSS16, and PGBD1 were not associated with Japanese patients with schizophrenia.
    Title: No associations found between the genes situated at 6p22.1, HIST1H2BJ, PRSS16, and PGBD1 in Japanese patients diagnosed with schizophrenia.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: [Polymorphic markers G(-455)A of gene FGB and C(-1654)T of gene PROC and genetic predisposition to unfavorable outcomes patients undergoing acute coronary syndrome].
  7. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals.
  8. Meta-analysis of gene-disease association. (HuGE Navigator)
    Title: Assessment of Alzheimer's disease case-control associations using family-based methods.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
piggyBac transposable element-derived protein 1
Names
cerebral protein 4

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)

  1. NM_001184743.2 → NP_001171672.1  piggyBac transposable element-derived protein 1

    See identical proteins and their annotated locations for NP_001171672.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL021997
    Consensus CDS
    CCDS4648.1
    UniProtKB/Swiss-Prot
    Q53F43, Q6NTF5, Q8WWS4, Q96JS3
    UniProtKB/TrEMBL
    A8K5B3
    Related
    ENSP00000259883.3, ENST00000259883.3
    Conserved Domains (2) summary
    smart00431
    Location:40 → 142
    SCAN; leucine rich region
    pfam13843
    Location:418 → 775
    DDE_Tnp_1_7; Transposase IS4

  2. NM_001386059.1 → NP_001372988.1  piggyBac transposable element-derived protein 1

    Status: VALIDATED

    Source sequence(s)
    AL021997
    Consensus CDS
    CCDS4648.1
    UniProtKB/Swiss-Prot
    Q53F43, Q6NTF5, Q8WWS4, Q96JS3
    UniProtKB/TrEMBL
    A8K5B3
    Conserved Domains (2) summary
    smart00431
    Location:40 → 142
    SCAN; leucine rich region
    pfam13843
    Location:418 → 775
    DDE_Tnp_1_7; Transposase IS4

  3. NM_032507.4 → NP_115896.1  piggyBac transposable element-derived protein 1

    See identical proteins and their annotated locations for NP_115896.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL021997
    Consensus CDS
    CCDS4648.1
    UniProtKB/Swiss-Prot
    Q53F43, Q6NTF5, Q8WWS4, Q96JS3
    UniProtKB/TrEMBL
    A8K5B3
    Related
    ENSP00000506997.1, ENST00000682144.1
    Conserved Domains (2) summary
    smart00431
    Location:40 → 142
    SCAN; leucine rich region
    pfam13843
    Location:418 → 775
    DDE_Tnp_1_7; Transposase IS4

RNA

  1. NR_169855.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

  2. NR_169856.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

  3. NR_169857.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

  4. NR_169858.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

  5. NR_169859.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

  6. NR_169860.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL021997

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    28281572..28302549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    28153313..28174278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JS3.1 GenPept UniProtKB/Swiss-Prot:Q96JS3

Gene LinkOut

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