Seroatlas · Human Serome Atlas

PGBD2

PiggyBac transposable element-derived protein 2

Also known as: PGBD2_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q6P3X8
Gene: PGBD2
Ensembl: ENSG00000185220
Chromosome: 1
Canonical length: 592 aa
Protein class: Plasma proteins, Predicted intracellular proteins
Subcellular location: Vesicles

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. The exact function of this gene is not known. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

592 residues, UniProt reviewed canonical sequence.

>Q6P3X8|PGBD2
     1  MASTSRDVIA GRGIHSKVKS AKLLEVLNAM EEEESNNNRE EIFIAPPDNA AGEFTDEDSG
    61  DEDSQRGAHL PGSVLHASVL CEDSGTGEDN DDLELQPAKK RQKAVVKPQR IWTKRDIRPD
   121  FGSWTASDPH IEDLKSQELS PVGLFELFFD EGTINFIVNE TNRYAWQKNV NLSLTAQELK
   181  CVLGILILSG YISYPRRRMF WETSPDSHHH LVADAIRRDR FELIFSYLHF ADNNELDASD
   241  RFAKVRPLII RMNCNFQKHA PLEEFYSFGE SMCEYFGHRG SKQLHRGKPV RLGYKIWCGT
   301  TSRGYLVWFE PSQGTLFTKP DRSLDLGGSM VIKFVDALQE RGFLPYHIFF DKVFTSVKLM
   361  SILRKKGVKA TGTVREYRTE RCPLKDPKEL KKMKRGSFDY KVDESEEIIV CRWHDSSVVN
   421  ICSNAVGIEP VRLTSRHSGA AKTRTQVHQP SLVKLYQEKV GGVGRMDQNI AKYKVKIRGM
   481  KWYSSFIGYV IDAALNNAWQ LHRICCQDAQ VDLLAFRRYI ACVYLESNAD TTSQGRRSRR
   541  LETESRFDMI GHWIIHQDKR TRCALCHSQT NTRCEKCQKG VHAKCFREYH IR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PGBD2 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: Unknown
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.28
Highest tissue expression: 7.5 nTPM

Expression across tissuesHPA

Tissue

skin: 7.5 nTPM
spleen: 7.2 nTPM
lymph node: 6.9 nTPM
tonsil: 6.7 nTPM
thyroid gland: 6 nTPM
liver: 5.7 nTPM

Single-cell type

syncytiotrophoblasts: 39 nCPM
breast lactating cells: 23 nCPM
respiratory ionocytes: 15 nCPM
late primary spermatocytes: 15 nCPM
early primary spermatocytes: 14 nCPM
cytotrophoblasts: 14 nCPM

Immune cell

basophil: 11 nTPM
eosinophil: 9.4 nTPM
naive B-cell: 8.5 nTPM
memory B-cell: 8.3 nTPM
naive CD8 T-cell: 6.8 nTPM
non-classical monocyte: 6.8 nTPM

Brain region

white matter: 22 nTPM
cerebellum: 20 nTPM
hypothalamus: 19 nTPM
thalamus: 18 nTPM
medulla oblongata: 18 nTPM
basal ganglia: 17 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): 1.59
gnomAD pLI: 0
gnomAD missense Z: -0.23
DepMap mean gene effect: -0.08
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 9% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Molecular functions

sequence-specific DNA binding

Protein domainsUniProt · Pfam · InterPro

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PGBD2 as an antibody target. Whether an autoantibody or antibody against PGBD2 could matter depends on whether native PGBD2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PGBD2 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 PGBD2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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