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Protein

Regulator of nonsense transcripts 1 homolog

Gene

Upf1

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 4 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. The formation of an Upf1-Upf2-Upf3 surveillance complex is believed to activate NMD (By similarity).By similarity2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei456 – 4561ATPBy similarity
Binding sitei646 – 6461ATPBy similarity
Binding sitei683 – 6831ATPBy similarity
Binding sitei813 – 8131ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri98 – 249152UPF1-typeAdd
BLAST
Nucleotide bindingi476 – 4805ATPBy similarity

GO - Molecular functioni

GO - Biological processi

  • cellular response to hypoxia Source: FlyBase
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: FlyBase
  • positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: FlyBase
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Ligandi

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

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 1 homolog (EC:3.6.4.-)
Gene namesi
Name:Upf1
ORF Names:CG1559
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome X

Organism-specific databases

FlyBaseiFBgn0030354. Upf1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11801180Regulator of nonsense transcripts 1 homologPRO_0000080720Add
BLAST

Post-translational modificationi

Phosphorylated, probably by nonC.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9VYS3.
PRIDEiQ9VYS3.

Expressioni

Gene expression databases

BgeeiFBgn0030354.
ExpressionAtlasiQ9VYS3. differential.
GenevisibleiQ9VYS3. DM.

Interactioni

Protein-protein interaction databases

BioGridi58558. 5 interactions.
IntActiQ9VYS3. 10 interactions.
STRINGi7227.FBpp0073433.

Structurei

3D structure databases

ProteinModelPortaliQ9VYS3.
SMRiQ9VYS3. Positions 93-893.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi931 – 1105175Gly-richAdd
BLAST

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri98 – 249152UPF1-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
InParanoidiQ9VYS3.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG091G01B6.
PhylomeDBiQ9VYS3.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9VYS3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVDTYAPSS ALSFLDMDDN ELLPGADTQP TQYDYRDFTM PSTSQSQTQN
60 70 80 90 100
DQLEIAQRCS AGDSHPRLAS ITNDLADLQF EEEDDEPGSS YVKELPPHAC
110 120 130 140 150
KYCGIHDPAT VVMCNNCRKW FCNGRGSTSG SHIINHLVRA KHREVTLHGE
160 170 180 190 200
GPLGETILEC YSCGVRNVFV LGFIPAKADS VVVLLCRQPC AAQNSLKDMN
210 220 230 240 250
WDQEQWKPLI ADRCFLAWLV KQPSEQGQLR ARQISAAQIN KLEELWKENI
260 270 280 290 300
EATFQDLEKP GIDSEPAHVL LRYEDGYQYE KTFGPLVRLE AEYDQKLKES
310 320 330 340 350
ATQENIEVRW DVGLNKKTIA YFTLAKTDSD MKLMHGDELR LHYVGELYNP
360 370 380 390 400
WSEIGHVIKV PDNFGDDVGL ELKSSTNAPV KCTSNFTVDF IWKCTSFDRM
410 420 430 440 450
TRALCKFAID RNSVSNFIYS RLLGHGRADS NDEVLFRGPQ PKLFSAPHLP
460 470 480 490 500
DLNRSQVYAV KHALQRPLSL IQGPPGTGKT VTSATIVYQL VKLHGGTVLV
510 520 530 540 550
CAPSNTAVDQ LTEKIHRTNL KVVRVCAKSR EAIDSPVSFL ALHNQIRNME
560 570 580 590 600
TNSELKKLQQ LKDETGELSS ADEKRYRNLK RAAENQLLEA ADVICCTCVG
610 620 630 640 650
AGDGRLSRVK FTSILIDESM QSTEPECMVP VVLGAKQLIL VGDHCQLGPV
660 670 680 690 700
VMCKKAARAG LSQSLFERLV VLGIRPFRLE VQYRMHPELS QFPSNFFYEG
710 720 730 740 750
SLQNGVCAED RRLKLDFPWP QPERPMFFLV TQGQEEIAGS GTSFLNRTEA
760 770 780 790 800
ANVEKITTRF LKAGIKPEQI GIITPYEGQR AYLVQYMQYQ GSLHSRLYQE
810 820 830 840 850
IEIASVDAFQ GREKDIIIMS CVRSNERQGI GFLNDPRRLN VALTRAKFGI
860 870 880 890 900
IIVGNPKVLA KQQLWNHLLN FYKDRKVLVE GSLNNLKESL IHFQKPKKLV
910 920 930 940 950
NSMNIGAHFM STIIADAKEV MVPGSIYDRS GGYGQGRQMV GQSMNGGQYG
960 970 980 990 1000
GSGGGPYGNS PLGYGTPSSN SMVGFGLGNG GNGAAGGNNN FGGAGPSWAA
1010 1020 1030 1040 1050
AHLHHDSIGY ISNEHGAAAL GNMPVPVGMF MNMSNIPPRF YNQHQQAIMA
1060 1070 1080 1090 1100
VKQNRAIQQQ TGNFSPGNSG PGVTGVGVGR SATPGGNKKT NKLGKSRVTG
1110 1120 1130 1140 1150
GGTGGAPLTQ GSSVCNAAPY SQHPMPLSLQ MTQPSGFALS QQPELSQDFG
1160 1170 1180
QISQMDGLLS QDVAFNASGE RSLNQFSQPY
Length:1,180
Mass (Da):129,913
Last modified:January 27, 2003 - v2
Checksum:i150EAA970D221D0E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014298 Genomic DNA. Translation: AAF48115.2.
AY061379 mRNA. Translation: AAL28927.1.
RefSeqiNP_001285145.1. NM_001298216.1.
NP_572767.1. NM_132539.3.
UniGeneiDm.3617.

Genome annotation databases

EnsemblMetazoaiFBtr0073596; FBpp0073433; FBgn0030354.
FBtr0342744; FBpp0309612; FBgn0030354.
GeneIDi32153.
KEGGidme:Dmel_CG1559.
UCSCiCG1559-RA. d. melanogaster.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014298 Genomic DNA. Translation: AAF48115.2.
AY061379 mRNA. Translation: AAL28927.1.
RefSeqiNP_001285145.1. NM_001298216.1.
NP_572767.1. NM_132539.3.
UniGeneiDm.3617.

3D structure databases

ProteinModelPortaliQ9VYS3.
SMRiQ9VYS3. Positions 93-893.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi58558. 5 interactions.
IntActiQ9VYS3. 10 interactions.
STRINGi7227.FBpp0073433.

Proteomic databases

PaxDbiQ9VYS3.
PRIDEiQ9VYS3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0073596; FBpp0073433; FBgn0030354.
FBtr0342744; FBpp0309612; FBgn0030354.
GeneIDi32153.
KEGGidme:Dmel_CG1559.
UCSCiCG1559-RA. d. melanogaster.

Organism-specific databases

CTDi5976.
FlyBaseiFBgn0030354. Upf1.

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
InParanoidiQ9VYS3.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG091G01B6.
PhylomeDBiQ9VYS3.

Enzyme and pathway databases

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

Miscellaneous databases

GenomeRNAii32153.
PROiQ9VYS3.

Gene expression databases

BgeeiFBgn0030354.
ExpressionAtlasiQ9VYS3. differential.
GenevisibleiQ9VYS3. DM.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRENT1_DROME
AccessioniPrimary (citable) accession number: Q9VYS3
Secondary accession number(s): Q95RG9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: January 27, 2003
Last modified: September 7, 2016
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Miscellaneous

In Drosophila, the definition of premature stop codons in mRNAs appears to be independent of exon boundaries and of the EJC complex.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  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.