Seroatlas · Human Serome Atlas

UPF3A

Regulator of nonsense transcripts 3A

Also known as: HUPF3A, REN3A_HUMAN, RENT3A, UPF3

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

Protein identityUniProt · HPA

UniProt accession: Q9H1J1
Gene: UPF3A
Ensembl: ENSG00000169062
Chromosome: 13
Canonical length: 476 aa
Protein class: Predicted intracellular proteins
Subcellular location: Nucleoplasm,Vesicles,Plasma membrane

OverviewNCBI Gene

This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

Canonical amino-acid sequenceUniProt

476 residues, UniProt reviewed canonical sequence.

>Q9H1J1|UPF3A
     1  MRSEKEGAGG LRAAVAARGP SGREKLSALE VQFHRDSQQQ EAETPPTSSS GCGGGAGKPR
    61  EEKRTALSKV VIRRLPPGLT KEQLEEQLRP LPAHDYFEFF AADLSLYPHL YSRAYINFRN
   121  PDDILLFRDR FDGYIFLDSK GLEYPAVVEF APFQKIAKKK LRKKDAKTGS IEDDPEYKKF
   181  LETYCVEEEK TSANPETLLG EMEAKTRELI ARRTTPLLEY IKNRKLEKQR IREEKREERR
   241  RRELEKKRLR EEEKRRRREE ERCKKKETDK QKKIAEKEVR IKLLKKPEKG EEPTTEKPKE
   301  RGEEIDTGGG KQESCAPGAV VKARPMEGSL EEPQETSHSG SDKEHRDVER SQEQESEAQR
   361  YHVDDGRRHR AHHEPERLSR RSEDEQRWGK GPGQDRGKKG SQDSGAPGEA MERLGRAQRC
   421  DDSPAPRKER LANKDRPALQ LYDPGARFRA RECGGNRRIC KAEGSGTGPE KREEAE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against UPF3A 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): 0.6
Highest tissue expression: 43 nTPM

Expression across tissuesHPA

Tissue

testis: 43 nTPM
spinal cord: 38 nTPM
cerebellum: 32 nTPM
thyroid gland: 28 nTPM
midbrain: 27 nTPM
hippocampal formation: 23 nTPM

Single-cell type

late primary spermatocytes: 708 nCPM
myonuclei: 304 nCPM
early primary spermatocytes: 292 nCPM
oligodendrocyte progenitor cells: 289 nCPM
platelets: 217 nCPM
differentiating spermatogonia: 205 nCPM

Immune cell

plasmacytoid DC: 17 nTPM
memory B-cell: 13 nTPM
NK-cell: 12 nTPM
T-reg: 11 nTPM
naive B-cell: 9.7 nTPM
memory CD8 T-cell: 7.2 nTPM

Brain region

cerebellum: 41 nTPM
pons: 37 nTPM
cerebral cortex: 37 nTPM
hypothalamus: 36 nTPM
white matter: 36 nTPM
medulla oblongata: 35 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): 0.94
gnomAD pLI: 0
gnomAD missense Z: -0.6
DepMap mean gene effect: -0.12
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% 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 UPF3A 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 UPF3A as an antibody target. Whether an autoantibody or antibody against UPF3A could matter depends on whether native UPF3A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

UPF3A 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 UPF3A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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