Seroatlas · Human Serome Atlas

UPF1

Regulator of nonsense transcripts 1

Also known as: HUPF1, KIAA0221, NORF1, pNORF1, RENT1, RENT1_HUMAN, smg-2

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

Protein identityUniProt · HPA

UniProt accession: Q92900
Gene: UPF1
Ensembl: ENSG00000005007
Chromosome: 19
Canonical length: 1129 aa
Protein class: Enzymes, Plasma proteins, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Cytosol

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. 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 is located only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

Canonical amino-acid sequenceUniProt

1129 residues, UniProt reviewed canonical sequence.

>Q92900|UPF1
     1  MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTPPGG PGGPGGGGAG
    61  GPGGAGAGAA AGQLDAQVGP EGILQNGAVD DSVAKTSQLL AELNFEEDEE DTYYTKDLPI
   121  HACSYCGIHD PACVVYCNTS KKWFCNGRGN TSGSHIVNHL VRAKCKEVTL HKDGPLGETV
   181  LECYNCGCRN VFLLGFIPAK ADSVVVLLCR QPCASQSSLK DINWDSSQWQ PLIQDRCFLS
   241  WLVKIPSEQE QLRARQITAQ QINKLEELWK ENPSATLEDL EKPGVDEEPQ HVLLRYEDAY
   301  QYQNIFGPLV KLEADYDKKL KESQTQDNIT VRWDLGLNKK RIAYFTLPKT DSGNEDLVII
   361  WLRDMRLMQG DEICLRYKGD LAPLWKGIGH VIKVPDNYGD EIAIELRSSV GAPVEVTHNF
   421  QVDFVWKSTS FDRMQSALKT FAVDETSVSG YIYHKLLGHE VEDVIIKCQL PKRFTAQGLP
   481  DLNHSQVYAV KTVLQRPLSL IQGPPGTGKT VTSATIVYHL ARQGNGPVLV CAPSNIAVDQ
   541  LTEKIHQTGL KVVRLCAKSR EAIDSPVSFL ALHNQIRNMD SMPELQKLQQ LKDETGELSS
   601  ADEKRYRALK RTAERELLMN ADVICCTCVG AGDPRLAKMQ FRSILIDEST QATEPECMVP
   661  VVLGAKQLIL VGDHCQLGPV VMCKKAAKAG LSQSLFERLV VLGIRPIRLQ VQYRMHPALS
   721  AFPSNIFYEG SLQNGVTAAD RVKKGFDFQW PQPDKPMFFY VTQGQEEIAS SGTSYLNRTE
   781  AANVEKITTK LLKAGAKPDQ IGIITPYEGQ RSYLVQYMQF SGSLHTKLYQ EVEIASVDAF
   841  QGREKDFIIL SCVRANEHQG IGFLNDPRRL NVALTRARYG VIIVGNPKAL SKQPLWNHLL
   901  NYYKEQKVLV EGPLNNLRES LMQFSKPRKL VNTINPGARF MTTAMYDARE AIIPGSVYDR
   961  SSQGRPSSMY FQTHDQIGMI SAGPSHVAAM NIPIPFNLVM PPMPPPGYFG QANGPAAGRG
  1021  TPKGKTGRGG RQKNRFGLPG PSQTNLPNSQ ASQDVASQPF SQGALTQGYI SMSQPSQMSQ
  1081  PGLSQPELSQ DSYLGDEFKS QIDVALSQDS TYQGERAYQH GGVTGLSQY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against UPF1 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): 0.37
Highest tissue expression: 37 nTPM

Expression across tissuesHPA

Tissue

cerebellum: 37 nTPM
skeletal muscle: 30 nTPM
testis: 29 nTPM
skin: 28 nTPM
blood vessel: 27 nTPM
salivary gland: 26 nTPM

Single-cell type

neutrophils: 96 nCPM
respiratory secretory cells: 88 nCPM
endometrial glandular cells: 82 nCPM
endometrial luminal cells: 80 nCPM
respiratory deuterosomal cells: 79 nCPM
respiratory basal cells: 76 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

white matter: 40 nTPM
medulla oblongata: 39 nTPM
spinal cord: 36 nTPM
cerebellum: 34 nTPM
thalamus: 33 nTPM
cerebral cortex: 32 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about UPF1.

Disease | GeneticClinVar

6 pathogenic / likely-pathogenic of 198 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Frontal bossing
Hypertelorism
Global developmental delay
High anterior hairline
Intellectual disability

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): 0.16
gnomAD pLI: 1
gnomAD missense Z: 5.63
DepMap mean gene effect: -1.2
DepMap dependency class: common

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

Helicase/UvrB, N-terminal
P-loop containing nucleoside triphosphate hydrolase
DNA2/NAM7 helicase, helicase domain
DNA2/NAM7 helicase-like, C-terminal
DNA2/NAM7-like helicase
Upf1-like, C-terminal helicase domain
Type III restriction enzyme, res subunit
AAA domain
AAA domain
RNA helicase UPF1, Cys/His rich zinc-binding domain
RNA helicase UPF1, 1B domain
RNA helicase (UPF2 interacting domain)
RNA helicase UPF1, 1B domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of UPF1 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 UPF1 as an antibody target. Whether an autoantibody or antibody against UPF1 could matter depends on whether native UPF1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

UPF1 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 UPF1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...