PGBD1

Summary

PGBD1 (piggyBac transposable element derived 1, HGNC:19398) is a protein-coding gene on chromosome 6p22.1, encoding PiggyBac transposable element-derived protein 1 (Q96JS3). Transposase-derived from PiggyBac DNA transposons.

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.

Source: NCBI Gene 84547 — RefSeq curated summary.

At a glance

• GWAS associations: 27
• Clinical variants (ClinVar): 118 total
• MANE Select transcript: NM_032507

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19398
Approved symbol	PGBD1
Name	piggyBac transposable element derived 1
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	HUCEP-4, dJ874C20.4, SCAND4
Ensembl gene	ENSG00000137338
Ensembl biotype	protein_coding
OMIM	621244
Entrez	84547

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000259883, ENST00000682144, ENST00000918204, ENST00000918205, ENST00000918206, ENST00000918207

RefSeq mRNA: 3 — MANE Select: NM_032507 NM_001184743, NM_001386059, NM_032507

CCDS: CCDS4648

Canonical transcript exons

ENST00000682144 — 7 exons

Exon	Start	End
ENSE00000928926	28285551	28285707
ENSE00000928927	28287080	28287168
ENSE00000928928	28296816	28296945
ENSE00000928929	28297895	28297991
ENSE00001212131	28281572	28281918
ENSE00001548550	28300724	28302549
ENSE00003917026	28283776	28284209

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 87.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.8017 / max 75.3514, expressed in 1567 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66627	6.9983	1550
66626	0.8034	505

Top tissues by expression

248 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.71	gold quality
cortical plate	UBERON:0005343	81.87	gold quality
ganglionic eminence	UBERON:0004023	81.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.41	gold quality
ventricular zone	UBERON:0003053	79.54	gold quality
cerebellar hemisphere	UBERON:0002245	78.85	gold quality
cerebellar cortex	UBERON:0002129	78.65	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.33	gold quality
cerebellum	UBERON:0002037	77.22	gold quality
stromal cell of endometrium	CL:0002255	77.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.93	gold quality
smooth muscle tissue	UBERON:0001135	76.92	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.53	gold quality
right frontal lobe	UBERON:0002810	76.08	gold quality
lower esophagus muscularis layer	UBERON:0035833	75.03	gold quality
lower esophagus	UBERON:0013473	74.98	gold quality
apex of heart	UBERON:0002098	74.87	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	74.78	gold quality
anterior cingulate cortex	UBERON:0009835	74.54	gold quality
mucosa of stomach	UBERON:0001199	74.34	gold quality
descending thoracic aorta	UBERON:0002345	74.24	gold quality
primary visual cortex	UBERON:0002436	74.24	gold quality
prefrontal cortex	UBERON:0000451	74.18	gold quality
thoracic aorta	UBERON:0001515	74.16	gold quality
ascending aorta	UBERON:0001496	74.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.80	gold quality
body of uterus	UBERON:0009853	73.67	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	73.63	gold quality
neocortex	UBERON:0001950	73.58	gold quality
left coronary artery	UBERON:0001626	73.39	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting PGBD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-7159-3P	99.51	70.17	1920
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-10B-3P	99.04	66.98	988
HSA-MIR-654-3P	98.38	67.61	905
HSA-MIR-3074-3P	97.83	67.26	922
HSA-MIR-4288	97.11	67.23	1636
HSA-MIR-6730-3P	97.03	67.54	889

Literature-anchored findings (GeneRIF, showing 5)

• Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. (PMID:22037552)
• The genes HIST1H2BJ, PRSS16, and PGBD1 were not associated with Japanese patients with schizophrenia. (PMID:22488895)
• 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 (PMID:26208039)
• 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 (PMID:28662065)
• A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles. (PMID:36205081)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pgbd1	ENSMUSG00000055313

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

PiggyBac transposable element-derived protein 1 — Q96JS3 (reviewed: Q96JS3)

Alternative names: Cerebral protein 4

All UniProt accessions (1): Q96JS3

UniProt curated annotations — full annotation on UniProt →

Function. Transposase-derived from PiggyBac DNA transposons. Although it has been fully domesticated and lacks transposase activity, PGBD1 has acquired DNA-binding capability. It preferentially binds in and around genes involved in neuronal development, leading to their transcriptional pausing. Notably, PGBD1 suppresses paraspeckle assembly in neuronal cells.

Subcellular location. Nucleus.

Miscellaneous. PGBD1 is a nonmonotreme mammal-specific horizontally transferred gene.

RefSeq proteins (3): NP_001171672, NP_001372988, NP_115896* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001190	SRCR	Domain
IPR003309	SCAN_dom	Domain
IPR029526	PGBD	Domain
IPR038269	SCAN_sf	Homologous_superfamily
IPR052638	PiggyBac_TE-derived	Family

Pfam: PF02023, PF13843

UniProt features (16 total): sequence variant 8, sequence conflict 2, region of interest 2, chain 1, domain 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96JS3-F1	66.92	0.37

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 360, 218

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GOBP_NEUROGENESIS, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP, ZHENG_BOUND_BY_FOXP3, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, JOHNSTONE_PARVB_TARGETS_2_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FEV_TARGET_GENES, SNIP1_TARGET_GENES, MIR4795_3P, MIR548N, MIR944, MIR6780A_5P, MIR29A_5P, MIR3074_3P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), neurogenesis (GO:0022008)

GO Molecular Function (5): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), identical protein binding (GO:0042802), sequence-specific DNA binding (GO:0043565), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
nervous system development	1
cell differentiation	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
protein binding	1
DNA binding	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

662 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PGBD1	NKAPL	Q5M9Q1	596
PGBD1	TNK1	Q13470	573
PGBD1	PGBD5	Q8N414	534
PGBD1	THAP9	Q9H5L6	530
PGBD1	PRSS16	Q9NQE7	526
PGBD1	POGK	Q9P215	490
PGBD1	GALP	Q9UBC7	484
PGBD1	GIN1	Q9NXP7	477
PGBD1	ZBED8	Q8IZ13	466
PGBD1	SIPA1L3	O60292	464
PGBD1	ZNF862	O60290	450
PGBD1	GAB2	Q9UQC2	447
PGBD1	DKKL1	Q9UK85	434
PGBD1	APOE	P02649	418
PGBD1	NAIF1	Q69YI7	415

IntAct

105 interactions, top by confidence:

A	B	Type	Score
PGBD1	SCAND1	psi-mi:“MI:0915”(physical association)	0.940
SCAND1	PGBD1	psi-mi:“MI:0915”(physical association)	0.940
PGBD1	SCAND1	psi-mi:“MI:0914”(association)	0.940
PGBD1	ZNF24	psi-mi:“MI:0915”(physical association)	0.900
ZNF24	PGBD1	psi-mi:“MI:0915”(physical association)	0.900
PGBD1	ZNF24	psi-mi:“MI:0914”(association)	0.900
PGBD1	ZNF446	psi-mi:“MI:0915”(physical association)	0.800
ZNF446	PGBD1	psi-mi:“MI:0915”(physical association)	0.800
PGBD1	ZSCAN22	psi-mi:“MI:0915”(physical association)	0.790
ZSCAN22	PGBD1	psi-mi:“MI:0915”(physical association)	0.790

BioGRID (70): PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), PGBD1 (Two-hybrid), ZSCAN22 (Two-hybrid), PGBD1 (Affinity Capture-MS), PGBD1 (Affinity Capture-MS), PGBD1 (Affinity Capture-MS), PGBD1 (Affinity Capture-MS), PGBD1 (Affinity Capture-MS), MEOX2 (Two-hybrid), NR4A1 (Two-hybrid)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

118 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	8
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1064 predictions. Top by Δscore:

Variant	Effect	Δscore
6:28284187:G:GT	donor_gain	1.0000
6:28296942:A:G	donor_gain	1.0000
6:28296944:GA:G	donor_gain	1.0000
6:28296946:G:GG	donor_gain	1.0000
6:28297893:A:AG	acceptor_gain	1.0000
6:28297894:G:GG	acceptor_gain	1.0000
6:28300722:A:AG	acceptor_gain	1.0000
6:28300722:A:AT	acceptor_loss	1.0000
6:28300723:G:GG	acceptor_gain	1.0000
6:28300723:G:GT	acceptor_loss	1.0000
6:28300723:GA:G	acceptor_gain	1.0000
6:28300723:GAGA:G	acceptor_gain	1.0000
6:28281711:C:G	donor_gain	0.9900
6:28283774:A:AG	acceptor_gain	0.9900
6:28283775:G:GG	acceptor_gain	0.9900
6:28284187:G:T	donor_gain	0.9900
6:28284206:ACAG:A	donor_loss	0.9900
6:28284208:AG:A	donor_loss	0.9900
6:28284209:GG:G	donor_loss	0.9900
6:28284211:T:A	donor_loss	0.9900
6:28284214:G:T	donor_gain	0.9900
6:28285698:GAA:G	donor_gain	0.9900
6:28285701:G:GG	donor_gain	0.9900
6:28285703:GAGTG:G	donor_gain	0.9900
6:28285705:GTG:G	donor_gain	0.9900
6:28287168:GGT:G	donor_loss	0.9900
6:28287169:G:GA	donor_loss	0.9900
6:28287170:TAA:T	donor_loss	0.9900
6:28296925:T:G	donor_gain	0.9900
6:28296941:GA:G	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000113926 (6:28299409 G>T), RS1000448868 (6:28286209 T>C), RS1000472666 (6:28279749 T>G), RS1000600442 (6:28293919 A>C,G), RS1000741916 (6:28294330 G>T), RS1000819624 (6:28285312 T>C), RS1001124101 (6:28286495 A>G), RS1001769562 (6:28293458 T>A), RS1002149807 (6:28281535 C>G,T), RS1002176363 (6:28301586 G>A,T), RS1002278051 (6:28295677 C>A,T), RS1002388370 (6:28288399 A>G), RS1002673161 (6:28290003 T>C), RS1002714179 (6:28290377 T>C), RS1002828133 (6:28288772 G>A)

Disease associations

OMIM: gene MIM:621244 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

27 associations (top):

Study	Trait	p-value
GCST003997_12	Myopia	1.000000e-12
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_115	Autism spectrum disorder or schizophrenia	3.000000e-16
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_212	Autism spectrum disorder or schizophrenia	5.000000e-14
GCST004521_23	Autism spectrum disorder or schizophrenia	2.000000e-11
GCST004521_43	Autism spectrum disorder or schizophrenia	2.000000e-27
GCST004521_6	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_7	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004521_77	Autism spectrum disorder or schizophrenia	1.000000e-19
GCST004748_92	Lung cancer	2.000000e-12
GCST004750_90	Squamous cell lung carcinoma	4.000000e-11
GCST007269_245	Pulse pressure	6.000000e-15
GCST008921_4	Asthma and major depressive disorder	2.000000e-11
GCST008921_6	Asthma and major depressive disorder	1.000000e-09
GCST010002_50	Refractive error	4.000000e-34
GCST010083_222	Hemoglobin levels	1.000000e-44
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST010979_11	Kawasaki disease	7.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0004509	hemoglobin measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression	2
FR900359	decreases phosphorylation	1
urushiol	decreases expression	1
trichostatin A	affects expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
Temozolomide	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Atrazine	decreases expression	1
Caffeine	increases phosphorylation	1
Doxorubicin	affects expression	1
Estradiol	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.