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Protein

Regulator of nonsense transcripts 1 homolog

Gene

UPF1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (premature termination codon PTC) by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Eliminates the production of nonsense-containing RNAs (ncRNAs). Required for plant development and adaptation to environmental stresses, including plant defense and response to wounding.5 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei493 – 4931ATPBy similarity
Binding sitei685 – 6851ATPBy similarity
Binding sitei722 – 7221ATPBy similarity
Binding sitei853 – 8531ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri138 – 291154UPF1-typeAdd
BLAST
Nucleotide bindingi513 – 5175ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • defense response to bacterium Source: UniProtKB
  • jasmonic acid mediated signaling pathway Source: UniProtKB
  • long-day photoperiodism Source: UniProtKB
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  • response to wounding Source: UniProtKB
  • salicylic acid mediated signaling pathway Source: UniProtKB
  • sugar mediated signaling pathway Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Nonsense-mediated mRNA decay, Plant defense

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciARA:AT5G47010-MONOMER.
ReactomeiR-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-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.-)
Alternative name(s):
ATP-dependent helicase UPF1
Gene namesi
Name:UPF1
Synonyms:LBA1
Ordered Locus Names:At5g47010
ORF Names:MQD22.15
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G47010.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic mRNA processing body Source: TAIR
  • cytosol Source: TAIR
  • plasma membrane Source: TAIR
  • plasmodesma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Seedling lethal. Increased expression of not only protein-coding transcripts but also many mRNA-like nonprotein-coding RNAs (mlncRNAs), including natural antisense transcript RNAs (nat-RNAs). Dwarf with curly leaves and late flowering. Photoperiod-dependent altered development and stress responses; in long days (16 hours light), altered organ morphologies (e.g. narrow and epinastic leaves with wide petiole, small rosette size, long seeds, some abnormal flowers and stunted stem growth), disturbed homeostasis of wounding-induced jasmonic acid and pathogen-elicited salicylic acid. Increased resistance to Pseudomonas syringae pv. tomato strain DC3000.4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi852 – 8521R → C: Abolishes NMD. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12541254Regulator of nonsense transcripts 1 homologPRO_0000080721Add
BLAST

Post-translational modificationi

Highly phosphorylated in S/TQ-enriched N-terminal and C-terminal regions; required for formation of mRNA surveillance complexes.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9FJR0.
PRIDEiQ9FJR0.

PTM databases

iPTMnetiQ9FJR0.

Expressioni

Inductioni

Down-regulated upon Pseudomonas syringae pv. tomato strain DC3000 infection.

Gene expression databases

GenevisibleiQ9FJR0. AT.

Interactioni

Protein-protein interaction databases

BioGridi19995. 1 interaction.
STRINGi3702.AT5G47010.1.

Structurei

3D structure databases

ProteinModelPortaliQ9FJR0.
SMRiQ9FJR0. Positions 134-931.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini497 – 629133Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 106106S/TQ motifs-rich, involved in the target transcript degradation steps of nonsense-mediated decay (NMD)Add
BLAST
Regioni1013 – 1254242S/TQ motifs-rich, involved in the target transcript degradation steps of nonsense-mediated decay (NMD)Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi102 – 1054Poly-Ser

Domaini

The helicase ATP-binding domain is implicated in early steps of nonsense-mediated decay (NMD).1 Publication

Sequence similaritiesi

Belongs to the DNA2/NAM7 helicase family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 UPF1-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri138 – 291154UPF1-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
HOGENOMiHOG000205990.
InParanoidiQ9FJR0.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG093600GR.
PhylomeDBiQ9FJR0.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR014001. Helicase_ATP-bd.
IPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9FJR0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSQQSDLFD TASQPDTVAD EYTFLEFNTQ GDSEFDYQDF GSPTAWPTPS
60 70 80 90 100
DSISIADVAD RGEGGAAADH HSEASSPSSL SAGAGNGAKV GRGGVGGSGG
110 120 130 140 150
VSSSSQVDAL AAGVGNLNFE ETGDDDGFDY GKNDFTEHAC KYCGISNPAC
160 170 180 190 200
VVRCNVASCR KWFCNSRGNT SGSHIVNHLV RAKHKEVCLH RDSPLGETIL
210 220 230 240 250
ECYNCGCRNV FLLGFISAKT DSVVVLLCRD PCLNVNALKD MNWDLSQWCP
260 270 280 290 300
LIDDRCFLPW LVKVPSEQEQ LRARQISAQQ INKIEELWKT NPDATLEDLE
310 320 330 340 350
KPGVDDEPQP VQPKYEDAYQ YQNVFAPLIK LEADYDKMMK ESQSKENLTV
360 370 380 390 400
RWDIGLNKKR VAYFVFPKEE NELRLVPGDE LRLRYSGDAV HPSWQSVGHV
410 420 430 440 450
IKLTAQEEVA LELRANQGVP IDVNHGFSVD FVWKSTSFDR MQGAMKNFAV
460 470 480 490 500
DETSVSGYIY HQLLGHEVEA QMVRNTLPRR FGVPGLPELN ASQVNAVKSV
510 520 530 540 550
LQKPISLIQG PPGTGKTVTS AAIVYHMAKQ GQGQVLVCAP SNVAVDQLAE
560 570 580 590 600
KISATGLKVV RLCAKSREAV SSPVEYLTLH YQVRHLDTSE KSELHKLQQL
610 620 630 640 650
KDEQGELSSS DEKKYKNLKR ATEREITQSA DVICCTCVGA ADLRLSNFRF
660 670 680 690 700
RQVLIDESTQ ATEPECLIPL VLGVKQVVLV GDHCQLGPVI MCKKAARAGL
710 720 730 740 750
AQSLFERLVT LGIKPIRLQV QYRMHPALSE FPSNSFYEGT LQNGVTIIER
760 770 780 790 800
QTTGIDFPWP VPNRPMFFYV QLGQEEISAS GTSYLNRTEA ANVEKLVTAF
810 820 830 840 850
LKSGVVPSQI GVITPYEGQR AYIVNYMARN GSLRQQLYKE IEVASVDSFQ
860 870 880 890 900
GREKDYIILS CVRSNEHQGI GFLNDPRRLN VALTRARYGI VILGNPKVLS
910 920 930 940 950
KQPLWNGLLT HYKEHECLVE GPLNNLKQSM VQFQKPRKIY NDRRLFYGGG
960 970 980 990 1000
AGMIGNDNFG SGNPNADRRG SRGRAGGSYL PSGPPNGARP GLHPAGYPIP
1010 1020 1030 1040 1050
RVPLSPFPGG PPSQPYAIPT RGPVGAVPHA PQPGNHGFGA GRGTSVGGHL
1060 1070 1080 1090 1100
PHQQATQHNV GTIGPSLNFP LDSPNSQPSP GGPLSQPGYG SQAFRDGFSM
1110 1120 1130 1140 1150
GGISQDFLAD DIKSQGSHDP YNMADFATQA SPGGFAVDYA TQGAHGAFPG
1160 1170 1180 1190 1200
NFMNQNSQGG YSRFSGINDF MSQEYMAHGG QGLFTQAGFI DSSQDDGQQN
1210 1220 1230 1240 1250
PYGVNNPNLQ SQGLPNSLYS QPFAHYNTQP LNLSGPQQSQ PNQSSQNPKH

PYNG
Length:1,254
Mass (Da):136,868
Last modified:February 21, 2006 - v2
Checksum:iAE68846E70B27DC9
GO

Sequence cautioni

The sequence BAB10240 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013394 Genomic DNA. Translation: BAB10240.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED95457.1.
AF484122 mRNA. Translation: AAL92018.1.
RefSeqiNP_199512.2. NM_124072.2.
UniGeneiAt.8584.

Genome annotation databases

EnsemblPlantsiAT5G47010.1; AT5G47010.1; AT5G47010.
GeneIDi834747.
GrameneiAT5G47010.1; AT5G47010.1; AT5G47010.
KEGGiath:AT5G47010.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013394 Genomic DNA. Translation: BAB10240.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED95457.1.
AF484122 mRNA. Translation: AAL92018.1.
RefSeqiNP_199512.2. NM_124072.2.
UniGeneiAt.8584.

3D structure databases

ProteinModelPortaliQ9FJR0.
SMRiQ9FJR0. Positions 134-931.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19995. 1 interaction.
STRINGi3702.AT5G47010.1.

PTM databases

iPTMnetiQ9FJR0.

Proteomic databases

PaxDbiQ9FJR0.
PRIDEiQ9FJR0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G47010.1; AT5G47010.1; AT5G47010.
GeneIDi834747.
GrameneiAT5G47010.1; AT5G47010.1; AT5G47010.
KEGGiath:AT5G47010.

Organism-specific databases

TAIRiAT5G47010.

Phylogenomic databases

eggNOGiKOG1802. Eukaryota.
COG1112. LUCA.
HOGENOMiHOG000205990.
InParanoidiQ9FJR0.
KOiK14326.
OMAiHDSIGYI.
OrthoDBiEOG093600GR.
PhylomeDBiQ9FJR0.

Enzyme and pathway databases

BioCyciARA:AT5G47010-MONOMER.
ReactomeiR-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

PROiQ9FJR0.

Gene expression databases

GenevisibleiQ9FJR0. AT.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR014001. Helicase_ATP-bd.
IPR027417. P-loop_NTPase.
IPR018999. RNA-helicase_UPF1_UPF2-interct.
[Graphical view]
PfamiPF09416. UPF1_Zn_bind. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRENT1_ARATH
AccessioniPrimary (citable) accession number: Q9FJR0
Secondary accession number(s): Q8S3K7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: February 21, 2006
Last modified: September 7, 2016
This is version 109 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  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.