Seroatlas · Human Serome Atlas

PGBD1

PiggyBac transposable element-derived protein 1

Also known as: dJ874C20.4, HUCEP-4, PGBD1_HUMAN, SCAND4

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q96JS3
Gene
PGBD1
Ensembl
ENSG00000137338
Chromosome
6
Canonical length
809 aa
Protein class
Predicted intracellular proteins
Subcellular location
Nucleoplasm,Cytosol

OverviewNCBI 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. 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]

Canonical amino-acid sequenceUniProt

809 residues, UniProt reviewed canonical sequence.

>Q96JS3|PGBD1
     1  MYEALPGPAP ENEDGLVKVK EEDPTWEQVC NSQEGSSHTQ EICRLRFRHF CYQEAHGPQE
    61  ALAQLRELCH QWLRPEMHTK EQIMELLVLE QFLTILPKEL QPCVKTYPLE SGEEAVTVLE
   121  NLETGSGDTG QQASVYIQGQ DMHPMVAEYQ GVSLECQSLQ LLPGITTLKC EPPQRPQGNP
   181  QEVSGPVPHG SAHLQEKNPR DKAVVPVFNP VRSQTLVKTE EETAQAVAAE KWSHLSLTRR
   241  NLCGNSAQET VMSLSPMTEE IVTKDRLFKA KQETSEEMEQ SGEASGKPNR ECAPQIPCST
   301  PIATERTVAH LNTLKDRHPG DLWARMHISS LEYAAGDITR KGRKKDKARV SELLQGLSFS
   361  GDSDVEKDNE PEIQPAQKKL KVSCFPEKSW TKRDIKPNFP SWSALDSGLL NLKSEKLNPV
   421  ELFELFFDDE TFNLIVNETN NYASQKNVSL EVTVQEMRCV FGVLLLSGFM RHPRREMYWE
   481  VSDTDQNLVR DAIRRDRFEL IFSNLHFADN GHLDQKDKFT KLRPLIKQMN KNFLLYAPLE
   541  EYYCFDKSMC ECFDSDQFLN GKPIRIGYKI WCGTTTQGYL VWFEPYQEES TMKVDEDPDL
   601  GLGGNLVMNF ADVLLERGQY PYHLCFDSFF TSVKLLSALK KKGVRATGTI RENRTEKCPL
   661  MNVEHMKKMK RGYFDFRIEE NNEIILCRWY GDGIISLCSN AVGIEPVNEV SCCDADNEEI
   721  PQISQPSIVK VYDECKEGVA KMDQIISKYR VRIRSKKWYS ILVSYMIDVA MNNAWQLHRA
   781  CNPGASLDPL DFRRFVAHFY LEHNAHLSD

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PGBD1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.43
Highest tissue expression
5.8 nTPM

Expression across tissuesHPA

Tissue

  • retina: 5.8 nTPM
  • smooth muscle: 5.1 nTPM
  • cerebral cortex: 4.1 nTPM
  • choroid plexus: 3.6 nTPM
  • endometrium: 3.4 nTPM
  • seminal vesicle: 3 nTPM

Single-cell type

  • thymocytes: 36 nCPM
  • brain excitatory neurons: 34 nCPM
  • bergmann glia: 32 nCPM
  • retinal horizontal cells: 30 nCPM
  • oligodendrocytes: 29 nCPM
  • oligodendrocyte progenitor cells: 29 nCPM

Immune cell

  • basophil: 1.8 nTPM
  • plasmacytoid DC: 1.5 nTPM
  • NK-cell: 0.5 nTPM
  • memory CD8 T-cell: 0.4 nTPM
  • naive B-cell: 0.3 nTPM
  • gdT-cell: 0.2 nTPM

Brain region

  • hippocampal formation: 12 nTPM
  • cerebral cortex: 12 nTPM
  • white matter: 12 nTPM
  • cerebellum: 10 nTPM
  • basal ganglia: 10 nTPM
  • hypothalamus: 7.5 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.9
gnomAD pLI
0
gnomAD missense Z
0.86
DepMap mean gene effect
0.03
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PGBD1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PGBD1 as an antibody target. Whether an autoantibody or antibody against PGBD1 could matter depends on whether native PGBD1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PGBD1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PGBD1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PGBD1. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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