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Aliases for UPF1 Gene

Aliases for UPF1 Gene

  • UPF1, RNA Helicase And ATPase 2 3
  • UPF1 Regulator Of Nonsense Transcripts Homolog (Yeast) 2 5
  • Up-Frameshift Suppressor 1 Homolog 3 4
  • Nonsense MRNA Reducing Factor 1 3 4
  • ATP-Dependent Helicase RENT1 3 4
  • HUPF1 3 4
  • RENT1 3 4
  • NORF1 3 4
  • Smg-2 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • UPF1 Regulator Of Nonsense Transcripts Homolog 3
  • Regulator Of Nonsense Transcripts 1 2
  • Up-Frameshift Mutation 1 Homolog 3
  • Yeast Upf1p Homolog 3
  • UP Frameshift 1 2
  • Delta Helicase 3
  • Smg-2 Homolog 2
  • EC 3.6.4.- 4
  • KIAA0221 4
  • EC 3.6.1 63
  • PNORF1 3
  • Smg-2 3

External Ids for UPF1 Gene

Previous HGNC Symbols for UPF1 Gene

  • RENT1

Previous GeneCards Identifiers for UPF1 Gene

  • GC19P018942
  • GC19P018507

Summaries for UPF1 Gene

Entrez Gene Summary for UPF1 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]

GeneCards Summary for UPF1 Gene

UPF1 (UPF1, RNA Helicase And ATPase) is a Protein Coding gene. Among its related pathways are Gene Expression and RNA transport. GO annotations related to this gene include poly(A) RNA binding and chromatin binding. An important paralog of this gene is ZGRF1.

UniProtKB/Swiss-Prot for UPF1 Gene

  • RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.

Gene Wiki entry for UPF1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UPF1 Gene

Genomics for UPF1 Gene

Regulatory Elements for UPF1 Gene

Enhancers for UPF1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around UPF1 on UCSC Golden Path with GeneCards custom track

Promoters for UPF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around UPF1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the UPF1 gene promoter:

Genomic Location for UPF1 Gene

Chromosome:
19
Start:
18,831,935 bp from pter
End:
18,868,236 bp from pter
Size:
36,302 bases
Orientation:
Plus strand

Genomic View for UPF1 Gene

Genes around UPF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UPF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UPF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UPF1 Gene

Proteins for UPF1 Gene

  • Protein details for UPF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92900-RENT1_HUMAN
    Recommended name:
    Regulator of nonsense transcripts 1
    Protein Accession:
    Q92900
    Secondary Accessions:
    • O00239
    • O43343
    • Q86Z25
    • Q92842

    Protein attributes for UPF1 Gene

    Size:
    1129 amino acids
    Molecular mass:
    124345 Da
    Quaternary structure:
    • Found in a post-splicing messenger ribonucleoprotein (mRNP) complex (PubMed:21419344). Associates with the exon junction complex (EJC) (PubMed:11546874, PubMed:16452507). Associates with the SGM1C complex; is phosphorylated by the complex kinase component SGM1 (PubMed:19417104). Interacts with UPF2 (PubMed:11163187, PubMed:11073994, PubMed:11113196, PubMed:19556969). Interacts with UPF3A and UPF3B (PubMed:11163187). Interacts with EST1A (PubMed:12554878). Interacts with SLBP (PubMed:16086026). Interacts (when hyperphosphorylated) with PNRC2 (PubMed:19150429). Interacts with AGO1 and AGO2 (PubMed:17932509). Interacts with GSPT2 (PubMed:18447585). Interacts with isoform 1 and isoform 5 of ADAR/ADAR1 (PubMed:18362360). Interacts with SMG7 (PubMed:15721257). Interacts with ZC3H12A; this interaction occurs in a mRNA translationally active- and termination-dependent manner and is essential for ZC3H12A-mediated degradation of target mRNAs (PubMed:26000482).
    SequenceCaution:
    • Sequence=BAA19664.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for UPF1 Gene

    Alternative splice isoforms for UPF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UPF1 Gene

Proteomics data for UPF1 Gene at MOPED

Post-translational modifications for UPF1 Gene

  • Phosphorylated by SMG1; required for formation of mRNA surveillance complexes.
  • Ubiquitination at Lys 220, Lys 264, Lys 378, Lys 386, Lys 439, Lys 587, Lys 638, Lys 688, Lys 926, and Lys 929
  • Modification sites at PhosphoSitePlus

Other Protein References for UPF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for UPF1 (RENT1)

Domains & Families for UPF1 Gene

Gene Families for UPF1 Gene

Protein Domains for UPF1 Gene

Suggested Antigen Peptide Sequences for UPF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92900

UniProtKB/Swiss-Prot:

RENT1_HUMAN :
  • The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.
  • Belongs to the DNA2/NAM7 helicase family.
  • Contains 1 UPF1-type zinc finger.
Domain:
  • The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.
Family:
  • Belongs to the DNA2/NAM7 helicase family.
Similarity:
  • Contains 1 UPF1-type zinc finger.
genes like me logo Genes that share domains with UPF1: view

Function for UPF1 Gene

Molecular function for UPF1 Gene

UniProtKB/Swiss-Prot Function:
RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.

Enzyme Numbers (IUBMB) for UPF1 Gene

Gene Ontology (GO) - Molecular Function for UPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IDA 16488880
GO:0003723 RNA binding NAS 10999600
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with UPF1: view
genes like me logo Genes that share phenotypes with UPF1: view

Animal Models for UPF1 Gene

MGI Knock Outs for UPF1:

Animal Model Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for UPF1 Gene

Localization for UPF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for UPF1 Gene

Cytoplasm. Cytoplasm, P-body. Nucleus. Note=Hyperphosphorylated form is targeted to the P-body, while unphosphorylated protein is distributed throughout the cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for UPF1 Gene COMPARTMENTS Subcellular localization image for UPF1 gene
Compartment Confidence
cytosol 5
nucleus 5
golgi apparatus 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for UPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,NAS 9064659
genes like me logo Genes that share ontologies with UPF1: view

Pathways & Interactions for UPF1 Gene

genes like me logo Genes that share pathways with UPF1: view

SIGNOR curated interactions for UPF1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for UPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000723 telomere maintenance IMP 17916692
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 23828042
GO:0006281 DNA repair IDA 16488880
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0061158 3-UTR-mediated mRNA destabilization IMP 26255671
genes like me logo Genes that share ontologies with UPF1: view

Drugs & Compounds for UPF1 Gene

(2) Drugs for UPF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for UPF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with UPF1: view

Transcripts for UPF1 Gene

Unigene Clusters for UPF1 Gene

UPF1 regulator of nonsense transcripts homolog (yeast):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for UPF1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d · 12e ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^
SP1: - - - - - - -
SP2: - - - - - -
SP3:
SP4:
SP5:
SP6: - - - -
SP7: - - -
SP8: - -
SP9: -
SP10:
SP11: -
SP12:
SP13: - - - -

ExUns: 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
SP1: - - -
SP2: - - -
SP3: - -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13:

Relevant External Links for UPF1 Gene

GeneLoc Exon Structure for
UPF1
ECgene alternative splicing isoforms for
UPF1

Expression for UPF1 Gene

mRNA expression in normal human tissues for UPF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for UPF1 Gene

This gene is overexpressed in Lymph node (9.2) and Peripheral blood mononuclear cells (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for UPF1 Gene



SOURCE GeneReport for Unigene cluster for UPF1 Gene Hs.515266

mRNA Expression by UniProt/SwissProt for UPF1 Gene

Q92900-RENT1_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with UPF1: view

Protein tissue co-expression partners for UPF1 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues for UPF1 Gene

Orthologs for UPF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for UPF1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia UPF1 35
  • 91.9 (n)
  • 99.46 (a)
UPF1 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF1 35
  • 90.7 (n)
  • 99.73 (a)
UPF1 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Upf1 35
  • 88.65 (n)
  • 98.38 (a)
Upf1 16
Upf1 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia UPF1 35
  • 99.2 (n)
  • 99.37 (a)
UPF1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Upf1 35
  • 88.92 (n)
  • 98.38 (a)
oppossum
(Monodelphis domestica)
Mammalia UPF1 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UPF1 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves UPF1 35
  • 80.68 (n)
  • 97.23 (a)
UPF1 36
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.19652 35
upf1 35
  • 77.81 (n)
  • 97.27 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.10547 35
zebrafish
(Danio rerio)
Actinopterygii Dr.13594 35
upf1 35
  • 82.66 (n)
  • 95.35 (a)
upf1 36
  • 95 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6509 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001133 35
  • 63.93 (n)
  • 68.84 (a)
fruit fly
(Drosophila melanogaster)
Insecta Upf1 35
  • 68.5 (n)
  • 71.54 (a)
Upf1 36
  • 63 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smg-2 35
  • 54.63 (n)
  • 52.19 (a)
smg-2 36
  • 51 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR022C 35
  • 58.67 (n)
  • 56.83 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B06435g 35
  • 54.56 (n)
  • 58.39 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NAM7 35
  • 53.77 (n)
  • 56.97 (a)
NAM7 36
  • 51 (a)
OneToMany
NAM7 38
thale cress
(Arabidopsis thaliana)
eudicotyledons LBA1 35
  • 58.52 (n)
  • 63.56 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.12563 35
barley
(Hordeum vulgare)
Liliopsida Hv.5158 35
rice
(Oryza sativa)
Liliopsida Os.18837 35
Os07g0495900 35
  • 60.13 (n)
  • 67.78 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.4661 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3923 35
bread mold
(Neurospora crassa)
Ascomycetes NCU04242 35
  • 61.18 (n)
  • 61.15 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes upf1 35
  • 54.57 (n)
  • 59.98 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10770 36
  • 75 (a)
OneToOne
Species with no ortholog for UPF1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for UPF1 Gene

ENSEMBL:
Gene Tree for UPF1 (if available)
TreeFam:
Gene Tree for UPF1 (if available)

Paralogs for UPF1 Gene

Paralogs for UPF1 Gene

genes like me logo Genes that share paralogs with UPF1: view

Variants for UPF1 Gene

Sequence variations from dbSNP and Humsavar for UPF1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs17339451 - 18,832,414(+) CGGGC(G/T)CTGCG reference, missense
rs7257086 -- 18,862,888(+) GAAGT(C/T)GGGGG intron-variant
rs12976276 -- 18,832,389(+) gcggg(A/T)ggccc reference, synonymous-codon
rs12976930 -- 18,832,390(+) cggga(A/G)gcccg reference, missense
rs8103462 -- 18,857,526(+) GGTGT(C/T)ACTGC reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for UPF1 Gene

Variant ID Type Subtype PubMed ID
dgv3786n71 CNV Loss 21882294
nsv833777 CNV Loss 17160897
dgv3787n71 CNV Loss 21882294
nsv911299 CNV Loss 21882294
nsv470132 CNV Loss 18288195
nsv828473 CNV Gain 20364138
nsv828474 CNV Gain 20364138
nsv828477 CNV Gain 20364138

Variation tolerance for UPF1 Gene

Residual Variation Intolerance Score: 1.14% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.22; 24.52% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for UPF1 Gene

Disorders for UPF1 Gene

Relevant External Links for UPF1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UPF1

No disorders were found for UPF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for UPF1 Gene

Publications for UPF1 Gene

  1. Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. (PMID: 9064659) Applequist S.E. … Jaeck H.-M. (Nucleic Acids Res. 1997) 2 3 4 23 67
  2. Mammalian orthologues of a yeast regulator of nonsense transcript stability. (PMID: 8855285) Perlick H.A. … Dietz H.C. (Proc. Natl. Acad. Sci. U.S.A. 1996) 2 3 23
  3. Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. (PMID: 19150429) Cho H. … Kim Y.K. (Mol. Cell 2009) 3 23
  4. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. (PMID: 19417104) Yamashita A. … Ohno S. (Genes Dev. 2009) 3 23
  5. NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. (PMID: 18066079) Chamieh H. … Le Hir H. (Nat. Struct. Mol. Biol. 2008) 3 23

Products for UPF1 Gene

Sources for UPF1 Gene

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