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Aliases for UPF1 Gene

Aliases for UPF1 Gene

  • UPF1 Regulator Of Nonsense Transcripts Homolog (Yeast) 2 3
  • RENT1 3 4 6
  • Regulator Of Nonsense Transcripts 1 2 3
  • Up-Frameshift Suppressor 1 Homolog 3 4
  • Nonsense MRNA Reducing Factor 1 3 4
  • ATP-Dependent Helicase RENT1 3 4
  • HUPF1 3 4
  • NORF1 3 4
  • Smg-2 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • Nonsense Mediated MRNA Decay Factor (C. Elegans) 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
  • H 6

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 Regulator Of Nonsense Transcripts Homolog (Yeast)) is a Protein Coding gene. Diseases associated with UPF1 include ullrich congenital muscular dystrophy. Among its related pathways are Translational Control and Gene Expression. GO annotations related to this gene include RNA binding and helicase activity. 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

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

Genomic Location for UPF1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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. Associates with the exon junction complex (EJC). Associates with the SGM1C complex; is phosphorylated by the complex kinase component SGM1. Interacts with UPF2, UPF3A and UPF3B. Interacts with EST1A and SLBP. Interacts (when hyperphosphorylated) with PNRC2. Interacts with AGO1, AGO2 and GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1.
    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 Lys220, Lys264, Lys378, Lys386, Lys439, Lys587, Lys638, Lys688, Lys926, and Lys929
  • Modification sites at PhosphoSitePlus

Other Protein References for UPF1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains 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 :
  • Q92900
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

No data available for Gene Families for UPF1 Gene

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:0004004 ATP-dependent RNA helicase activity IDA 12554878
GO:0004386 helicase activity NAS 9064659
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:

miRNA for UPF1 Gene

miRTarBase miRNAs that target UPF1

No data available for Transcription Factor Targeting 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
nucleus 5
cytosol 4
golgi apparatus 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for UPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 16488880
GO:0000932 cytoplasmic mRNA processing body IEA --
GO:0005634 nucleus IDA 18362360
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm NAS 9064659
genes like me logo Genes that share ontologies with UPF1: view

Pathways for UPF1 Gene

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

Pathways by source for UPF1 Gene

Gene Ontology (GO) - Biological Process for UPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS 8855285
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 23828042
GO:0006200 obsolete ATP catabolic process --
GO:0006260 DNA replication IMP 16488880
GO:0006281 DNA repair IDA 16488880
genes like me logo Genes that share ontologies with UPF1: view

Compounds for UPF1 Gene

(4) Novoseek inferred chemical compound relationships for UPF1 Gene

Compound -log(P) Hits PubMed IDs
nitrobenzylthioinosine 73.2 2
nucleoside 48.1 4
uridine 47.4 3
zinc 0 1
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

Integrated Proteomics: protein expression 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 expressions with UPF1: view

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
chimpanzee
(Pan troglodytes)
Mammalia UPF1 35
  • 99.2 (n)
  • 99.37 (a)
UPF1 36
  • 100 (a)
OneToOne
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
oppossum
(Monodelphis domestica)
Mammalia UPF1 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UPF1 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Upf1 35
  • 88.92 (n)
  • 98.38 (a)
chicken
(Gallus gallus)
Aves UPF1 35
  • 80.68 (n)
  • 97.23 (a)
UPF1 36
  • 96 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.10547 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.19652 35
upf1 35
  • 77.81 (n)
  • 97.27 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6509 35
zebrafish
(Danio rerio)
Actinopterygii Dr.13594 35
upf1 35
  • 82.66 (n)
  • 95.35 (a)
upf1 36
  • 95 (a)
OneToOne
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)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NAM7 35
  • 53.77 (n)
  • 56.97 (a)
NAM7 36
  • 51 (a)
OneToMany
NAM7 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B06435g 35
  • 54.56 (n)
  • 58.39 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.12563 35
thale cress
(Arabidopsis thaliana)
eudicotyledons LBA1 35
  • 58.52 (n)
  • 63.56 (a)
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
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 intestinalis)
Ascidiacea Cin.3923 35
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 MAF
rs12879 -- 18,868,014(+) GTTTC(C/T)GCGGT utr-variant-3-prime
rs15170 -- 18,868,013(+) GGTTT(C/T)CGCGG utr-variant-3-prime
rs757113 -- 18,854,146(+) GAGGG(G/T)TGTTG intron-variant
rs757114 -- 18,859,548(+) TAACA(A/G)CAGTG intron-variant
rs757115 -- 18,860,513(+) ACTTA(C/T)TTTTA intron-variant

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

Relevant External Links for UPF1 Gene

HapMap Linkage Disequilibrium report
UPF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UPF1 Gene

Disorders for UPF1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for UPF1 Gene including...

Search for UPF1 Gene in MalaCards »

(1) University of Copenhagen DISEASES for UPF1 Gene

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

No data available for UniProtKB/Swiss-Prot for UPF1 Gene

Publications for UPF1 Gene

  1. 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 4 23
  2. 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
  3. Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. (PMID: 10999600) Bhattacharya A. … Peltz S.W. (RNA 2000) 3 4 23
  4. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PMID: 12554878) Chiu S.-Y. … Maquat L.E. (RNA 2003) 3 4 23
  5. Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. (PMID: 11331269) Denning G. … Fields A.P. (J. Biol. Chem. 2001) 3 4 23

Products for UPF1 Gene

  • Addgene plasmids for UPF1

Sources for UPF1 Gene

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