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Q92900

- RENT1_HUMAN

UniProt

Q92900 - RENT1_HUMAN

Protein

Regulator of nonsense transcripts 1

Gene

UPF1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 149 (01 Oct 2014)
      Sequence version 2 (18 Oct 2001)
      Previous versions | rss
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    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 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.5 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei486 – 4861ATP
    Binding sitei676 – 6761ATP
    Binding sitei713 – 7131ATP
    Binding sitei844 – 8441ATP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri121 – 272152UPF1-typeAdd
    BLAST
    Nucleotide bindingi506 – 5105ATP

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ATP-dependent RNA helicase activity Source: UniProtKB
    3. chromatin binding Source: HGNC
    4. DNA binding Source: InterPro
    5. helicase activity Source: UniProtKB
    6. poly(A) RNA binding Source: UniProtKB
    7. protein binding Source: IntAct
    8. RNA binding Source: UniProtKB
    9. zinc ion binding Source: InterPro

    GO - Biological processi

    1. ATP catabolic process Source: GOC
    2. DNA repair Source: HGNC
    3. DNA replication Source: HGNC
    4. dosage compensation by inactivation of X chromosome Source: Ensembl
    5. gene expression Source: Reactome
    6. histone mRNA catabolic process Source: UniProtKB
    7. mRNA export from nucleus Source: HGNC
    8. mRNA metabolic process Source: Reactome
    9. nuclear-transcribed mRNA catabolic process Source: UniProt
    10. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
    11. regulation of translational termination Source: UniProtKB
    12. RNA metabolic process Source: Reactome

    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

    ReactomeiREACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_75822. 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:
    hUpf1
    Gene namesi
    Name:UPF1
    Synonyms:KIAA0221, RENT1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 19

    Organism-specific databases

    HGNCiHGNC:9962. UPF1.

    Subcellular locationi

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

    GO - Cellular componenti

    1. chromatin Source: HGNC
    2. cytoplasm Source: UniProtKB
    3. cytoplasmic mRNA processing body Source: UniProtKB-SubCell
    4. cytosol Source: Reactome
    5. exon-exon junction complex Source: UniProtKB
    6. nucleus Source: UniProtKB
    7. supraspliceosomal complex Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi126 – 1261C → S: Abolishes ability to interact with UPF2/RENT2 and copurifies with greater amounts of SMG1, SMG8 and SMG9. 2 Publications
    Mutagenesisi506 – 5083GTG → RTE: Prevents dephosphorylation and targets the protein to the P-body.
    Mutagenesisi509 – 5091K → A: Inhibits histone mRNA degradation, ATPase activity and ATP binding. 3 Publications
    Mutagenesisi610 – 6112KR → AA: Impairs RNA binding.
    Mutagenesisi615 – 6151R → A: Impairs RNA binding. 1 Publication
    Mutagenesisi647 – 6482DE → AA: Loss of ATPase activity and helicase activity.
    Mutagenesisi676 – 6761Q → A: Impairs ATPase activity, no effect on ATP binding. 1 Publication
    Mutagenesisi714 – 7141R → A: Impairs ATPase activity and ATP binding. 1 Publication
    Mutagenesisi843 – 8431R → A: Inhibits histone mRNA degradation. 2 Publications
    Mutagenesisi843 – 8431R → C: Abolishes NMD. 2 Publications
    Mutagenesisi876 – 8761R → A: Impairs ATPase activity and ATP binding. 1 Publication
    Mutagenesisi1084 – 10841S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1089, A-1107 and A-1127. 1 Publication
    Mutagenesisi1089 – 10891S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1107 and A-1127. 2 Publications
    Mutagenesisi1089 – 10891S → A: Still phosphorylated but with less efficiency. 2 Publications
    Mutagenesisi1107 – 11071S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1089 and A-1127. 2 Publications
    Mutagenesisi1107 – 11071S → A: Impairs phosphorylation. 2 Publications
    Mutagenesisi1108 – 11081Q → N: Impairs phosphorylation. 1 Publication
    Mutagenesisi1127 – 11271S → A: Impairs association with UPF2, SMG1 and SMG7 and impairs phosphorylation; when associated with A-1084, A-1089 and A-1107. 1 Publication

    Organism-specific databases

    PharmGKBiPA34328.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11291129Regulator of nonsense transcripts 1PRO_0000080716Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1089 – 10891Phosphoserine2 Publications
    Modified residuei1107 – 11071Phosphoserine7 Publications
    Modified residuei1110 – 11101Phosphoserine2 Publications
    Modified residuei1127 – 11271Phosphoserine1 Publication

    Post-translational modificationi

    Phosphorylated by SMG1; required for formation of mRNA surveillance complexes.10 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ92900.
    PaxDbiQ92900.
    PRIDEiQ92900.

    PTM databases

    PhosphoSiteiQ92900.

    Expressioni

    Tissue specificityi

    Ubiquitous.

    Gene expression databases

    ArrayExpressiQ92900.
    BgeeiQ92900.
    CleanExiHS_UPF1.
    GenevestigatoriQ92900.

    Organism-specific databases

    HPAiHPA019587.
    HPA020857.

    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, 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/ADAR1.14 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ACDQ96AP03EBI-373471,EBI-717666
    DCP1AQ9NPI613EBI-373471,EBI-374238
    DCP2Q8IU603EBI-373471,EBI-521577
    EIF3AQ141525EBI-373492,EBI-366617
    GSPT1P151702EBI-373471,EBI-948993
    GSPT2Q8IYD13EBI-373471,EBI-3869637
    L1RE1Q9UN816EBI-373471,EBI-722458
    PNRC2Q9NPJ49EBI-373471,EBI-726549
    SKI7Q084912EBI-373471,EBI-1389From a different organism.
    SMG5Q9UPR32EBI-373492,EBI-3400861
    SMG6Q86US82EBI-373492,EBI-3232100
    STAU1O957935EBI-373471,EBI-358174
    TERTO147463EBI-373471,EBI-1772203
    UPF2Q9HAU525EBI-373471,EBI-372073
    UPF3AQ9H1J14EBI-373471,EBI-521530
    UPF3BQ9BZI78EBI-373471,EBI-372780

    Protein-protein interaction databases

    BioGridi111908. 92 interactions.
    DIPiDIP-29875N.
    IntActiQ92900. 79 interactions.
    MINTiMINT-5005507.
    STRINGi9606.ENSP00000262803.

    Structurei

    Secondary structure

    1
    1129
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni124 – 1263
    Helixi131 – 1333
    Beta strandi134 – 1374
    Turni138 – 1414
    Beta strandi142 – 1465
    Beta strandi151 – 1533
    Helixi155 – 1639
    Beta strandi168 – 1703
    Beta strandi174 – 1763
    Turni184 – 1863
    Turni191 – 1933
    Beta strandi195 – 1973
    Beta strandi200 – 2023
    Beta strandi204 – 2096
    Turni210 – 2134
    Turni216 – 2183
    Turni220 – 2223
    Helixi226 – 2283
    Beta strandi230 – 2334
    Beta strandi235 – 2384
    Turni240 – 2423
    Helixi248 – 2536
    Helixi259 – 26911
    Helixi299 – 32123
    Beta strandi326 – 3294
    Beta strandi332 – 3354
    Turni337 – 3393
    Beta strandi341 – 3455
    Helixi364 – 3663
    Beta strandi372 – 3776
    Beta strandi379 – 3824
    Beta strandi385 – 3939
    Beta strandi396 – 3983
    Beta strandi402 – 4076
    Beta strandi410 – 4123
    Beta strandi418 – 4258
    Helixi429 – 44315
    Helixi450 – 4567
    Helixi484 – 49310
    Beta strandi497 – 5026
    Helixi509 – 52214
    Beta strandi523 – 5253
    Beta strandi528 – 5347
    Helixi535 – 54713
    Beta strandi552 – 5543
    Helixi558 – 5603
    Helixi568 – 5703
    Helixi572 – 5776
    Helixi582 – 59110
    Turni593 – 5953
    Helixi600 – 62021
    Beta strandi622 – 6276
    Helixi630 – 6323
    Helixi634 – 6363
    Beta strandi642 – 6465
    Helixi649 – 6513
    Helixi654 – 6618
    Turni662 – 6643
    Beta strandi665 – 6728
    Helixi684 – 6885
    Turni689 – 6924
    Helixi695 – 7028
    Helixi717 – 72711
    Beta strandi733 – 7364
    Helixi739 – 7413
    Beta strandi751 – 7544
    Beta strandi757 – 7615
    Beta strandi766 – 7683
    Beta strandi770 – 7734
    Beta strandi775 – 7773
    Helixi778 – 79417
    Helixi798 – 8003
    Beta strandi801 – 8066
    Helixi808 – 81912
    Helixi826 – 8305
    Beta strandi832 – 8365
    Turni837 – 8426
    Beta strandi845 – 8517
    Beta strandi857 – 8593
    Helixi862 – 8654
    Helixi867 – 8748
    Beta strandi875 – 88511
    Helixi887 – 8904
    Helixi894 – 90512
    Beta strandi909 – 9124
    Helixi914 – 9163

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GJKX-ray2.60A295-925[»]
    2GK6X-ray2.40A/B295-925[»]
    2GK7X-ray2.80A295-925[»]
    2IYKX-ray2.95A/B115-272[»]
    2WJVX-ray2.85A/B115-925[»]
    2WJYX-ray2.50A115-925[»]
    2XZOX-ray2.40A295-925[»]
    2XZPX-ray2.72A295-925[»]
    ProteinModelPortaliQ92900.
    SMRiQ92900. Positions 116-925.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ92900.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 415415Sufficient for interaction with RENT2Add
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1089 – 10902[ST]-Q motif 1
    Motifi1107 – 11082[ST]-Q motif 2

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi47 – 8034Ala/Gly/Pro-richAdd
    BLAST
    Compositional biasi1042 – 112988Gln/Ser-richAdd
    BLAST

    Domaini

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

    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 fingeri121 – 272152UPF1-typeAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG1112.
    HOGENOMiHOG000205990.
    HOVERGENiHBG061556.
    InParanoidiQ92900.
    KOiK14326.
    OMAiFLALHEQ.
    OrthoDBiEOG76QFGF.
    PhylomeDBiQ92900.
    TreeFamiTF300554.

    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.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q92900-1) [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

    MSVEAYGPSS QTLTFLDTEE AELLGADTQG SEFEFTDFTL PSQTQTPPGG     50
    PGGPGGGGAG GPGGAGAGAA AGQLDAQVGP EGILQNGAVD DSVAKTSQLL 100
    AELNFEEDEE DTYYTKDLPI HACSYCGIHD PACVVYCNTS KKWFCNGRGN 150
    TSGSHIVNHL VRAKCKEVTL HKDGPLGETV LECYNCGCRN VFLLGFIPAK 200
    ADSVVVLLCR QPCASQSSLK DINWDSSQWQ PLIQDRCFLS WLVKIPSEQE 250
    QLRARQITAQ QINKLEELWK ENPSATLEDL EKPGVDEEPQ HVLLRYEDAY 300
    QYQNIFGPLV KLEADYDKKL KESQTQDNIT VRWDLGLNKK RIAYFTLPKT 350
    DSGNEDLVII WLRDMRLMQG DEICLRYKGD LAPLWKGIGH VIKVPDNYGD 400
    EIAIELRSSV GAPVEVTHNF QVDFVWKSTS FDRMQSALKT FAVDETSVSG 450
    YIYHKLLGHE VEDVIIKCQL PKRFTAQGLP DLNHSQVYAV KTVLQRPLSL 500
    IQGPPGTGKT VTSATIVYHL ARQGNGPVLV CAPSNIAVDQ LTEKIHQTGL 550
    KVVRLCAKSR EAIDSPVSFL ALHNQIRNMD SMPELQKLQQ LKDETGELSS 600
    ADEKRYRALK RTAERELLMN ADVICCTCVG AGDPRLAKMQ FRSILIDEST 650
    QATEPECMVP VVLGAKQLIL VGDHCQLGPV VMCKKAAKAG LSQSLFERLV 700
    VLGIRPIRLQ VQYRMHPALS AFPSNIFYEG SLQNGVTAAD RVKKGFDFQW 750
    PQPDKPMFFY VTQGQEEIAS SGTSYLNRTE AANVEKITTK LLKAGAKPDQ 800
    IGIITPYEGQ RSYLVQYMQF SGSLHTKLYQ EVEIASVDAF QGREKDFIIL 850
    SCVRANEHQG IGFLNDPRRL NVALTRARYG VIIVGNPKAL SKQPLWNHLL 900
    NYYKEQKVLV EGPLNNLRES LMQFSKPRKL VNTINPGARF MTTAMYDARE 950
    AIIPGSVYDR SSQGRPSSMY FQTHDQIGMI SAGPSHVAAM NIPIPFNLVM 1000
    PPMPPPGYFG QANGPAAGRG TPKGKTGRGG RQKNRFGLPG PSQTNLPNSQ 1050
    ASQDVASQPF SQGALTQGYI SMSQPSQMSQ PGLSQPELSQ DSYLGDEFKS 1100
    QIDVALSQDS TYQGERAYQH GGVTGLSQY 1129
    Length:1,129
    Mass (Da):124,345
    Last modified:October 18, 2001 - v2
    Checksum:i6CCA6FE42B15BA28
    GO
    Isoform 2 (identifier: Q92900-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         353-363: Missing.

    Show »
    Length:1,118
    Mass (Da):123,036
    Checksum:iA485D3ED52C39D06
    GO

    Sequence cautioni

    The sequence BAA19664.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti61 – 611G → S in AAC51140. (PubMed:9064659)Curated
    Sequence conflicti466 – 4661I → T in AAC51140. (PubMed:9064659)Curated
    Sequence conflicti478 – 4781G → A in AAC50771. (PubMed:8855285)Curated
    Sequence conflicti524 – 5241G → D in AAC50771. (PubMed:8855285)Curated
    Sequence conflicti557 – 5571A → P in AAC50771. (PubMed:8855285)Curated
    Sequence conflicti901 – 9022NY → IF in AAC50771. (PubMed:8855285)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti69 – 691A → S.1 Publication
    Corresponds to variant rs17339451 [ dbSNP | Ensembl ].
    VAR_056207

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei353 – 36311Missing in isoform 2. 4 PublicationsVSP_003393Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U65533 mRNA. Translation: AAC50771.1.
    U59323 mRNA. Translation: AAC51140.1.
    D86988 mRNA. Translation: BAA19664.2. Different initiation.
    AF074016 mRNA. Translation: AAC26788.1.
    AC003972 Genomic DNA. Translation: AAB94785.1.
    BC039817 mRNA. Translation: AAH39817.1.
    CCDSiCCDS12386.1. [Q92900-2]
    RefSeqiNP_002902.2. NM_002911.3. [Q92900-2]
    XP_005260072.1. XM_005260015.1. [Q92900-1]
    UniGeneiHs.515266.

    Genome annotation databases

    EnsembliENST00000262803; ENSP00000262803; ENSG00000005007. [Q92900-2]
    ENST00000599848; ENSP00000470142; ENSG00000005007. [Q92900-1]
    GeneIDi5976.
    KEGGihsa:5976.
    UCSCiuc002nkf.3. human. [Q92900-2]
    uc002nkg.3. human. [Q92900-1]

    Polymorphism databases

    DMDMi17380291.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U65533 mRNA. Translation: AAC50771.1 .
    U59323 mRNA. Translation: AAC51140.1 .
    D86988 mRNA. Translation: BAA19664.2 . Different initiation.
    AF074016 mRNA. Translation: AAC26788.1 .
    AC003972 Genomic DNA. Translation: AAB94785.1 .
    BC039817 mRNA. Translation: AAH39817.1 .
    CCDSi CCDS12386.1. [Q92900-2 ]
    RefSeqi NP_002902.2. NM_002911.3. [Q92900-2 ]
    XP_005260072.1. XM_005260015.1. [Q92900-1 ]
    UniGenei Hs.515266.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2GJK X-ray 2.60 A 295-925 [» ]
    2GK6 X-ray 2.40 A/B 295-925 [» ]
    2GK7 X-ray 2.80 A 295-925 [» ]
    2IYK X-ray 2.95 A/B 115-272 [» ]
    2WJV X-ray 2.85 A/B 115-925 [» ]
    2WJY X-ray 2.50 A 115-925 [» ]
    2XZO X-ray 2.40 A 295-925 [» ]
    2XZP X-ray 2.72 A 295-925 [» ]
    ProteinModelPortali Q92900.
    SMRi Q92900. Positions 116-925.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111908. 92 interactions.
    DIPi DIP-29875N.
    IntActi Q92900. 79 interactions.
    MINTi MINT-5005507.
    STRINGi 9606.ENSP00000262803.

    PTM databases

    PhosphoSitei Q92900.

    Polymorphism databases

    DMDMi 17380291.

    Proteomic databases

    MaxQBi Q92900.
    PaxDbi Q92900.
    PRIDEi Q92900.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000262803 ; ENSP00000262803 ; ENSG00000005007 . [Q92900-2 ]
    ENST00000599848 ; ENSP00000470142 ; ENSG00000005007 . [Q92900-1 ]
    GeneIDi 5976.
    KEGGi hsa:5976.
    UCSCi uc002nkf.3. human. [Q92900-2 ]
    uc002nkg.3. human. [Q92900-1 ]

    Organism-specific databases

    CTDi 5976.
    GeneCardsi GC19P018942.
    HGNCi HGNC:9962. UPF1.
    HPAi HPA019587.
    HPA020857.
    MIMi 601430. gene.
    neXtProti NX_Q92900.
    PharmGKBi PA34328.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1112.
    HOGENOMi HOG000205990.
    HOVERGENi HBG061556.
    InParanoidi Q92900.
    KOi K14326.
    OMAi FLALHEQ.
    OrthoDBi EOG76QFGF.
    PhylomeDBi Q92900.
    TreeFami TF300554.

    Enzyme and pathway databases

    Reactomei REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

    Miscellaneous databases

    ChiTaRSi UPF1. human.
    EvolutionaryTracei Q92900.
    GeneWikii UPF1.
    GenomeRNAii 5976.
    NextBioi 23259.
    PROi Q92900.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q92900.
    Bgeei Q92900.
    CleanExi HS_UPF1.
    Genevestigatori Q92900.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR027417. P-loop_NTPase.
    IPR018999. RNA-helicase_UPF1_UPF2-interct.
    [Graphical view ]
    Pfami PF09416. UPF1_Zn_bind. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Mammalian orthologues of a yeast regulator of nonsense transcript stability."
      Perlick H.A., Medghalchi S.M., Spencer F.A., Kendzior R.J. Jr., Dietz H.C.
      Proc. Natl. Acad. Sci. U.S.A. 93:10928-10932(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
      Tissue: Heart.
    2. "Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein."
      Applequist S.E., Selg M., Raman C., Jaeck H.-M.
      Nucleic Acids Res. 25:814-821(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), CHARACTERIZATION.
    3. "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain."
      Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N.
      DNA Res. 3:321-329(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT SER-69.
      Tissue: Bone marrow.
    4. "SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast."
      Page M.F., Carr B., Anders K.R., Grimson A., Anderson P.
      Mol. Cell. Biol. 19:5943-5951(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
    5. "The DNA sequence and biology of human chromosome 19."
      Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
      , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
      Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Uterus.
    7. "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon."
      Lykke-Andersen J., Shu M.-D., Steitz J.A.
      Cell 103:1121-1131(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, INTERACTION WITH WITH UPF2; UPF3A AND UPF3B, SUBCELLULAR LOCATION, MUTAGENESIS OF ARG-843.
    8. "Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes."
      Mendell J.T., Medghalchi S.M., Lake R.G., Noensie E.N., Dietz H.C.
      Mol. Cell. Biol. 20:8944-8957(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH UPF2.
    9. "Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay."
      Bhattacharya A., Czaplinski K., Trifillis P., He F., Jacobson A., Peltz S.W.
      RNA 6:1226-1235(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME ACTIVITY, RNA-BINDING, MUTAGENESIS OF 647-ASP-GLU-648.
    10. "Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay."
      Yamashita A., Ohnishi T., Kashima I., Taya Y., Ohno S.
      Genes Dev. 15:2215-2228(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION AT SER-1089 AND SER-1107, MUTAGENESIS OF SER-1089; SER-1107 AND GLN-1108.
    11. "Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein."
      Denning G., Jamieson L., Maquat L.E., Thompson E.A., Fields A.P.
      J. Biol. Chem. 276:22709-22714(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION.
    12. "Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)."
      Serin G., Gersappe A., Black J.D., Aronoff R., Maquat L.E.
      Mol. Cell. Biol. 21:209-223(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH UPF2, SUBCELLULAR LOCATION.
    13. "Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1."
      Lykke-Andersen J., Shu M.-D., Steitz J.A.
      Science 293:1836-1839(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX, ASSOCIATION WITH THE EJC COMPLEX.
    14. "Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7."
      Ohnishi T., Yamashita A., Kashima I., Schell T., Anders K.R., Grimson A., Hachiya T., Hentze M.W., Anderson P., Ohno S.
      Mol. Cell 12:1187-1200(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION.
    15. "Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1."
      Chiu S.-Y., Serin G., Ohara O., Maquat L.E.
      RNA 9:77-87(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH EST1A.
    16. "SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway."
      Fukuhara N., Ebert J., Unterholzner L., Lindner D., Izaurralde E., Conti E.
      Mol. Cell 17:537-547(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SMG7.
    17. "Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1."
      Kaygun H., Marzluff W.F.
      Nat. Struct. Mol. Biol. 12:794-800(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH SLBP, MUTAGENESIS OF LYS-509 AND ARG-843.
    18. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
      Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
      Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    19. "Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay."
      Kashima I., Yamashita A., Izumi N., Kataoka N., Morishita R., Hoshino S., Ohno M., Dreyfuss G., Ohno S.
      Genes Dev. 20:355-367(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE SURF COMPLEX, PHOSPHORYLATION AT SER-1089 AND SER-1107, MUTAGENESIS OF CYS-126; LYS-509; SER-1084; SER-1089; SER-1107 AND SER-1127.
    20. "Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells."
      Hoeck J., Weinmann L., Ender C., Ruedel S., Kremmer E., Raabe M., Urlaub H., Meister G.
      EMBO Rep. 8:1052-1060(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH AGO1 AND AGO2.
    21. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Embryonic kidney.
    22. "Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'."
      Mullen T.E., Marzluff W.F.
      Genes Dev. 22:50-65(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN HISTONE MRNA DEGRADATION ACTIVITY.
    23. "A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay."
      Singh G., Rebbapragada I., Lykke-Andersen J.
      PLoS Biol. 6:E111-E111(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH GSPT2.
    24. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    25. "The editing enzyme ADAR1 and the mRNA surveillance protein hUpf1 interact in the cell nucleus."
      Agranat L., Raitskin O., Sperling J., Sperling R.
      Proc. Natl. Acad. Sci. U.S.A. 105:5028-5033(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ADAR, SUBCELLULAR LOCATION.
    26. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    27. "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."
      Yamashita A., Izumi N., Kashima I., Ohnishi T., Saari B., Katsuhata Y., Muramatsu R., Morita T., Iwamatsu A., Hachiya T., Kurata R., Hirano H., Anderson P., Ohno S.
      Genes Dev. 23:1091-1105(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ASSOCIATION WITH THE SMG1C COMPLEX, MUTAGENESIS OF CYS-126.
    28. "Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex."
      Cho H., Kim K.M., Kim Y.K.
      Mol. Cell 33:75-86(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION, INTERACTION WITH PNRC2, MUTAGENESIS OF 506-GLY--GLY-508.
    29. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    30. "Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay."
      Franks T.M., Singh G., Lykke-Andersen J.
      Cell 143:938-950(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNP DISASSEMBLY.
    31. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107; SER-1110 AND SER-1127, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    32. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    33. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1107 AND SER-1110, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    34. "Structural and functional insights into the human Upf1 helicase core."
      Cheng Z., Muhlrad D., Lim M.K., Parker R., Song H.
      EMBO J. 26:253-264(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 295-914, MUTAGENESIS OF LYS-509; 610-LYS--ARG-612; ARG-615; 647-ASP-GLU-648; GLN-676; ARG-714 AND ARG-876.
    35. "Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2."
      Clerici M., Mourao A., Gutsche I., Gehring N.H., Hentze M.W., Kulozik A., Kadlec J., Sattler M., Cusack S.
      EMBO J. 28:2293-2306(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 115-914 IN COMPLEX WITH UPF2.
    36. "Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2."
      Chakrabarti S., Jayachandran U., Bonneau F., Fiorini F., Basquin C., Domcke S., Le Hir H., Conti E.
      Mol. Cell 41:693-703(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 295-925 IN COMPLEX WITH ATP ANALOG AND RNA, FUNCTION.

    Entry informationi

    Entry nameiRENT1_HUMAN
    AccessioniPrimary (citable) accession number: Q92900
    Secondary accession number(s): O00239
    , O43343, Q86Z25, Q92842
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 18, 2001
    Last sequence update: October 18, 2001
    Last modified: October 1, 2014
    This is version 149 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 19
      Human chromosome 19: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3