Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Regulator of nonsense transcripts 1

Gene

Upf1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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. 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 (By similarity). Essential for embryonic viability.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei481ATPBy similarity1
Binding sitei671ATPBy similarity1
Binding sitei708ATPBy similarity1
Binding sitei839ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri116 – 267UPF1-typeAdd BLAST152
Nucleotide bindingi501 – 505ATPBy similarity5

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Nonsense-mediated mRNA decay

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-MMU-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 1 (EC:3.6.4.-)
Alternative name(s):
ATP-dependent helicase RENT1
Nonsense mRNA reducing factor 1
Short name:
NORF1
Up-frameshift suppressor 1 homolog
Short name:
mUpf1
Gene namesi
Name:Upf1
Synonyms:Rent1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:107995. Upf1.

Subcellular locationi

  • Cytoplasm
  • CytoplasmP-body By similarity
  • Nucleus By similarity

  • Note: Hyperphosphorylated form is targeted to the P-body, while unphosphorylated protein is distributed throughout the cytoplasm.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Embryos are viable in pre-implantation period, show complete loss of NMD but are resorbed shortly after implantation.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000807171 – 1124Regulator of nonsense transcripts 1Add BLAST1124

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei10PhosphoserineBy similarity1
Modified residuei31PhosphoserineBy similarity1
Modified residuei560PhosphoserineBy similarity1
Modified residuei951PhosphoserineBy similarity1
Modified residuei1014Omega-N-methylarginineBy similarity1
Modified residuei1084PhosphoserineBy similarity1
Modified residuei1102PhosphoserineCombined sources1
Modified residuei1105PhosphoserineCombined sources1
Modified residuei1122PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated by SMG1; required for formation of mRNA surveillance complexes.By similarity

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9EPU0.
PeptideAtlasiQ9EPU0.
PRIDEiQ9EPU0.

PTM databases

iPTMnetiQ9EPU0.
PhosphoSitePlusiQ9EPU0.

Expressioni

Gene expression databases

BgeeiENSMUSG00000058301.
GenevisibleiQ9EPU0. MM.

Interactioni

Subunit structurei

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. Interacts with UPF3A and UPF3B. Interacts with EST1A. Interacts with SLBP. Interacts (when hyperphosphorylated) with PNRC2. Interacts with AGO1 and AGO2. Interacts with GSPT2. Interacts with isoform 1 and isoform 5 of ADAR/ADAR1. Interacts with SMG7. 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.By similarity

Protein-protein interaction databases

BioGridi202860. 3 interactors.
DIPiDIP-60114N.
IntActiQ9EPU0. 5 interactors.
MINTiMINT-4132192.
STRINGi10090.ENSMUSP00000075089.

Structurei

3D structure databases

ProteinModelPortaliQ9EPU0.
SMRiQ9EPU0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 410Sufficient for interaction with RENT2By similarityAdd BLAST410

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1084 – 1085[ST]-Q motif 12
Motifi1102 – 1103[ST]-Q motif 22

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi47 – 75Ala/Gly/Pro-richAdd BLAST29
Compositional biasi1037 – 1124Gln/Ser-richAdd BLAST88

Domaini

The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.By similarity

Sequence similaritiesi

Belongs to the DNA2/NAM7 helicase family.Curated
Contains 1 C2H2-type zinc finger.Curated
Contains 1 UPF1-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri116 – 267UPF1-typeAdd BLAST152

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
GeneTreeiENSGT00800000124068.
HOGENOMiHOG000205990.
HOVERGENiHBG061556.
InParanoidiQ9EPU0.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG091G01B6.
PhylomeDBiQ9EPU0.
TreeFamiTF300554.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR006935. Helicase/UvrB_N.
IPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF04851. ResIII. 1 hit.
PF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9EPU0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTPPGG
60 70 80 90 100
PGGAGGPGGA GAGGAAGQLD AQVGPEGILQ NGAVDDSVAK TSQLLAELNF
110 120 130 140 150
EEDEEDTYYT KDLPVHACSY CGIHDPACVV YCNTSKKWFC NGRGNTSGSH
160 170 180 190 200
IVNHLVRAKC KEVTLHKDGP LGETVLECYN CGCRNVFLLG FIPAKADSVV
210 220 230 240 250
VLLCRQPCAS QSSLKDINWD SSQWQPLIQD RCFLSWLVKI PSEQEQLRAR
260 270 280 290 300
QITAQQINKL EELWKENPSA TLEDLEKPGV DEEPQHVLLR YEDAYQYQNI
310 320 330 340 350
FGPLVKLEAD YDKKLKESQT QDNITVRWDL GLNKKRIAFF TLPKTDSGNE
360 370 380 390 400
DLVIIWLRDM RLMQGDEICL RYKGDLAPLW KGIGHVIKVP DNYGDEIAIE
410 420 430 440 450
LRSSVGAPVE VTHNFQVDFV WKSTSFDRMQ SALKTFAVDE TSVSGYIYHK
460 470 480 490 500
LLGHEVEDVV IKCQLPKRFT AQGLPDLNHS QVYAVKTVLQ RPLSLIQGPP
510 520 530 540 550
GTGKTVTSAT IVYHLARQGN GPVLVCAPSN IAVDQLTEKI HQTGLKVVRL
560 570 580 590 600
CAKSREAIDS PVSFLALHNQ IRNMDSMPEL QKLQQLKDET GELSSADEKR
610 620 630 640 650
YRALKRTAER ELLMNADVIC CTCVGAGDPR LAKMQFRSIL IDESTQATEP
660 670 680 690 700
ECMVPVVLGA KQLILVGDHC QLGPVVMCKK AAKAGLSQSL FERLVVLGIR
710 720 730 740 750
PIRLQVQYRM HPALSAFPSN IFYEGSLQNG VTAADRVKKG FDFQWPQPDK
760 770 780 790 800
PMFFYVTQGQ EEIASSGTSY LNRTEAANVE KITTKLLKAG AKPDQIGIIT
810 820 830 840 850
PYEGQRSYLV QYMQFSGSLH TKLYQEVEIA SVDAFQGREK DFIILSCVRA
860 870 880 890 900
NEHQGIGFLN DPRRLNVALT RARYGVIIVG NPKALSKQPL WNHLLSYYKE
910 920 930 940 950
QKALVEGPLN NLRESLMQFS KPRKLVNTVN PGARFMTTAM YDAREAIIPG
960 970 980 990 1000
SVYDRSSQGR PSNMYFQTHD QISMISAGPS HVAAMNIPIP FNLVMPPMPP
1010 1020 1030 1040 1050
PGYFGQANGP AAGRGTPKTK TGRGGRQKNR FGLPGPSQTT LPNSQASQDV
1060 1070 1080 1090 1100
ASQPFSQGAL TQGYVSMSQP SQMSQPGLSQ PELSQDSYLG DEFKSQIDVA
1110 1120
LSQDSTYQGE RAYQHGGVTG LSQY
Length:1,124
Mass (Da):123,967
Last modified:May 29, 2007 - v2
Checksum:i5F1B0ED50F63C52E
GO
Isoform 2 (identifier: Q9EPU0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     348-358: Missing.

Show »
Length:1,113
Mass (Da):122,657
Checksum:iBFE8D50AD49DAA54
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti56G → S in AAT46119 (Ref. 3) Curated1
Sequence conflicti58G → A in BAE28409 (PubMed:16141072).Curated1
Sequence conflicti60A → P in AAT46119 (Ref. 3) Curated1
Sequence conflicti71A → S in AAT46119 (Ref. 3) Curated1
Sequence conflicti428R → K in AAT46119 (Ref. 3) Curated1
Sequence conflicti439D → E in AAT46119 (Ref. 3) Curated1
Sequence conflicti460V → F in AAT46119 (Ref. 3) Curated1
Sequence conflicti495L → F in AAT46119 (Ref. 3) Curated1
Sequence conflicti633K → E in BAE28409 (PubMed:16141072).Curated1
Sequence conflicti820H → Y in BAE28409 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_025764348 – 358Missing in isoform 2. 4 PublicationsAdd BLAST11

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF322655 mRNA. Translation: AAG42830.1.
AY597039, AY597038 Genomic DNA. Translation: AAT46119.1.
AK148196 mRNA. Translation: BAE28409.1.
BC030916 mRNA. Translation: AAH30916.1.
BC052149 mRNA. Translation: AAH52149.1.
BC056442 mRNA. Translation: AAH56442.1.
AF182947 mRNA. Translation: AAK08652.1.
CCDSiCCDS52572.1. [Q9EPU0-1]
RefSeqiNP_001116301.1. NM_001122829.2. [Q9EPU0-1]
NP_109605.2. NM_030680.3. [Q9EPU0-2]
XP_006509667.1. XM_006509604.3. [Q9EPU0-1]
XP_006509668.1. XM_006509605.3. [Q9EPU0-1]
UniGeneiMm.258280.
Mm.390048.

Genome annotation databases

EnsembliENSMUST00000075666; ENSMUSP00000075089; ENSMUSG00000058301. [Q9EPU0-1]
GeneIDi19704.
KEGGimmu:19704.
UCSCiuc009mab.2. mouse. [Q9EPU0-1]
uc012gfa.1. mouse. [Q9EPU0-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF322655 mRNA. Translation: AAG42830.1.
AY597039, AY597038 Genomic DNA. Translation: AAT46119.1.
AK148196 mRNA. Translation: BAE28409.1.
BC030916 mRNA. Translation: AAH30916.1.
BC052149 mRNA. Translation: AAH52149.1.
BC056442 mRNA. Translation: AAH56442.1.
AF182947 mRNA. Translation: AAK08652.1.
CCDSiCCDS52572.1. [Q9EPU0-1]
RefSeqiNP_001116301.1. NM_001122829.2. [Q9EPU0-1]
NP_109605.2. NM_030680.3. [Q9EPU0-2]
XP_006509667.1. XM_006509604.3. [Q9EPU0-1]
XP_006509668.1. XM_006509605.3. [Q9EPU0-1]
UniGeneiMm.258280.
Mm.390048.

3D structure databases

ProteinModelPortaliQ9EPU0.
SMRiQ9EPU0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202860. 3 interactors.
DIPiDIP-60114N.
IntActiQ9EPU0. 5 interactors.
MINTiMINT-4132192.
STRINGi10090.ENSMUSP00000075089.

PTM databases

iPTMnetiQ9EPU0.
PhosphoSitePlusiQ9EPU0.

Proteomic databases

PaxDbiQ9EPU0.
PeptideAtlasiQ9EPU0.
PRIDEiQ9EPU0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000075666; ENSMUSP00000075089; ENSMUSG00000058301. [Q9EPU0-1]
GeneIDi19704.
KEGGimmu:19704.
UCSCiuc009mab.2. mouse. [Q9EPU0-1]
uc012gfa.1. mouse. [Q9EPU0-2]

Organism-specific databases

CTDi5976.
MGIiMGI:107995. Upf1.

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
GeneTreeiENSGT00800000124068.
HOGENOMiHOG000205990.
HOVERGENiHBG061556.
InParanoidiQ9EPU0.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG091G01B6.
PhylomeDBiQ9EPU0.
TreeFamiTF300554.

Enzyme and pathway databases

ReactomeiR-MMU-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-MMU-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

ChiTaRSiUpf1. mouse.
PROiQ9EPU0.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000058301.
GenevisibleiQ9EPU0. MM.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR006935. Helicase/UvrB_N.
IPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF04851. ResIII. 1 hit.
PF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRENT1_MOUSE
AccessioniPrimary (citable) accession number: Q9EPU0
Secondary accession number(s): Q3UG00
, Q6GYP5, Q6PHQ5, Q8K0N4, Q99PR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: May 29, 2007
Last modified: November 30, 2016
This is version 143 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.