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Protein Overview: UPF3

General Information:
Name(s) found: UPF3 / YGR072W [SGD]
Description(s) found:
Found 26 descriptions.
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  • Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 387 amino acids

    Gene Ontology:
    Cellular Component: polysome [IDALink to PubMed article]
    nucleus [IDALink to PubMed article]
    cytoplasm [TASLink to PubMed article]
    Biological Process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [TASLink to PubMed article]
    telomere maintenance [IMPLink to PubMed articleLink to PubMed article]
    [NOT]translational frameshifting [IMPLink to PubMed article]
    mRNA catabolic process [TASLink to PubMed article]
    Molecular Function: molecular_function [ND]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNVAGELKN SEGKKKGRGN RYHNKNRGKS KNETVDPKKN ENKVNNATNA THNNSKGRRN  60
   61 NKKRNREYYN YKRKARLGKS TENEGFKLVI RLLPPNLTAD EFFAILRDNN NDDGDKQDIQ 120
  121 GKLKYSDWCF FEGHYSSKVF KNSTYSRCNF LFDNLSDLEK CANFIKTCKF IDNKDNITIP 180
  181 DMKLSPYVKK FTQTSKKDAA LVGTIEEDEI FKTFMNSMKQ LNENDEYSFQ DFSVLKSLEK 240
  241 EFSKSIELEN KIAERTERVL TELVGTGDKV KNKNKKKKNK NAKKKFKEEE ASAKIPKKKR 300
  301 NRGKKKRENR EKSTISKTKN SNVVIIEEAG KEVLKQRKKK MLLQEKLKIS NSSQPQSSSA 360
  361 QTQPSFQPKE NLFVPRVKIL HRDDTKK

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details (MIPS) Mewes HW, et al. (2004) NAM7 NMD2 UPF3
    View Details Krogan NJ, et al. (2006) CHS3 LYS14 MSL1 NMD2 SUR7 UPF3
    View Details Qiu et al. (2008) NAM7 UPF3

    Mass Spectrometry Data

    No mass spectrometry results found for this protein.

    Yeast Two-Hybrid Data

    The following interactions contain this protein:

    NOT SHOWING SINGLE HITS. [ Show Single Hits ]

    [View our yeast two-hybrid interpretation guidelines.]

      BAIT PREY HITS PUBLICATION
    View Screen UPF3 NMD2 2 Unpublished Fields Lab Data

    Microscopy / Localization Data

    New Feature: Upload Your Own Microscopy Data

      PROTEIN(S) PUBLICATION
    View Data UPF3 Huh WK, et al. (2003)

    Protein Structure Data


    [What does the above image mean?]
    [View Top Sequence Alignments] [Show Ginzu Version Information]

    Domains predicted:

    #   Region(s) Method Confidence Match Description
    1 View Details [1..60] deduced N/A No confident structure predictions are available.
    2 View Details [61..280] Pfam 121.070581 Smg-4/UPF3 family No confident structure predictions are available.
    3 View Details [281..387] deduced N/A No confident structure predictions are available.
    4 View Details [303..387] deduced N/A No confident structure predictions are available.

    Functions predicted (by domain):

    # Gene Ontology predictions
    1 No functions predicted.
    2
    Term Confidence Notes
  • RNA binding
    		•  6.32219487559982 bayes_pls_golite062009
  • mRNA binding
    		•  4.87640532914983 bayes_pls_golite062009
    		• 3.85463717617256 bayes_pls_golite062009
  • nucleic acid binding
    		•  3.74344299117899 bayes_pls_golite062009
  • binding
    		•  2.88749864706998 bayes_pls_golite062009
  • single-stranded RNA binding
    		•  2.55628738360472 bayes_pls_golite062009
  • poly-pyrimidine tract binding
    		•  2.0656412663177 bayes_pls_golite062009
  • ubiquitin-protein ligase activity
    		•  1.79747940153321 bayes_pls_golite062009
  • structural molecule activity
    		•  1.57342338925793 bayes_pls_golite062009
  • small conjugating protein ligase activity
    		•  1.54918359800898 bayes_pls_golite062009
  • poly(U) RNA binding
    		•  1.23190154914055 bayes_pls_golite062009
  • protein binding
    		•  1.19509385638328 bayes_pls_golite062009
  • transcription regulator activity
    		•  1.10029555513317 bayes_pls_golite062009
  • acid-amino acid ligase activity
    		•  1.0920515408093 bayes_pls_golite062009
  • DNA binding
    		•  0.984725930713243 bayes_pls_golite062009
  • snRNA binding
    		•  0.840923669704678 bayes_pls_golite062009
  • snoRNA binding
    		•  0.516511855622792 bayes_pls_golite062009
  • hydrolase activity
    		•  0.418157930682314 bayes_pls_golite062009
  • transcription factor activity
    		•  0.255891228964936 bayes_pls_golite062009
  • mRNA 3'-UTR binding
    		•  0.229644510503376 bayes_pls_golite062009
  • ligase activity, forming carbon-nitrogen bonds
    		•  0.205114038263623 bayes_pls_golite062009
  • ligase activity
    		•  0.115699011007988 bayes_pls_golite062009
    3 No functions predicted.
    4 No functions predicted.


    Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076


    Philius Transmembrane Prediction:

    Protein predicted to be: GLOBULAR (No transmembrane regions or signal peptide)
    Confidence of classification: 0.99

    Source: Reynolds et al. (2008)

    YRC Informatics Platform - Version 3.0
    Created and Maintained by: Michael Riffle