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Protein Overview: NMD2

General Information:
Name(s) found: NMD2 / YHR077C [SGD]
Description(s) found:
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  • gi|806704|gb|AAA66521.1| Upf2p [NCBI NR]
  • gi|6579193|ref|NP_011944.2| Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance; Nmd2p [Saccharomyces cerevisiae] [NCBI NR]
  • pir||S48244 NMD2 protein - yeast (Saccharomyces cerevisiae) [NCBI NR]
  • gi|555939|gb|AAA67724.1| Nmd2p [NCBI NR]
  • gi|1171737|sp|P38798.2|NMD2_YEAST RecName: Full=Nonsense-mediated mRNA decay protein 2; AltName: Full=Up-frameshift suppressor 2 [NCBI NR]
  • Nonsense-mediated mRNA decay protein 2 OS=Saccharomyces cerevisiae GN=NMD2 PE=1 SV=2 [Swiss-Prot]
  • NMD2 Nonsense-mediated mRNA decay protein 2 [mips]
  • Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance [SGD]
  • NMD2, Chr VIII from 252375-252380,252494-255757, reverse complement [yeast_orfs2]
  • Chr VIII from 252375-252380,252494-255757, reverse complement [yeastorf3.fasta]
  • Chr VIII from 255757-255752,255638-252375, reverse complement [yeastorf5.fasta]
  • (P38798) Nonsense-mediated mRNA decay protein 2 (Up-frameshift suppressor 2) [4932.FASTACCERV.txt]
  • NMD2 SGDID:S0001119, Chr VIII from 255757-255752,255638-252375, reverse complement, Verified ORF [yeastflysequest.fasta]
  • Component of the nonsense-mediated mRNA decay (NMD) pathway; Highly acidic C-terminus [Saccharomyces cerevisiae]gi|1171737|sp|P38798|NMD2_YEAST Nonsense-mediated mRNA decay protein 2 (Up-frameshift suppressor 2)gi|630283|pir||S48244 NMD2 protein - yeast [nrdb_11152004_Chlamydomonas]
  • NMD2 SGDID:S000001119, Chr VIII from 255758-255753,255639-252376, reverse complement, Verified ORF, "Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta]
  • NMD2 SGDID:S000001119, Chr VIII from 255758-255753,255639-252376, reverse complement, Verified ORF, "Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance" [yeast-contam.fasta]
  • Upf2p [nr-271106-contam.fasta]
  • Nmd2p [nr-271106-contam.fasta]
  • Nonsense-mediated mRNA decay protein 2 (Up-frameshift suppressor 2) [nr-271106-contam.fasta]
  • Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance; Nmd2p [Saccharomyces cerevisiae] [nr-271106-contam.fasta]
  • [chemostatdb.fasta]
  • Nonsense-mediated mRNA decay protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NMD2 PE=1 SV=2 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta]
  • NMD2 SGDID:S000001119, Chr VIII from 255637-252374,255756-255751, Genome Release 64-1-1, reverse complement, Verified ORF, "Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance" [yeast-030211-contam.fasta]
  • NMD2 SGDID:S000001119, Chr VIII from 255637-252374,255756-255751, Genome Release 64-2-1, reverse complement, Verified ORF, "Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance" [20141208_orf_trans.fasta]
  • YHR077C SGDID:S000001119, Chr VIII from 255637-252374,255756-255751, Genome Release 64-1-1, reverse complement, Verified ORF, "Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
    • Organism: Saccharomyces cerevisiae
    Length: 1089 amino acids

    Gene Ontology:
    Cellular Component: polysome [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: protein binding [TASLink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDGRKKELH DLNTRAWNGE EVFPLKSKKL DSSIKRNTGF IKKLKKGFVK GSESSLLKDL  60
   61 SEASLEKYLS EIIVTVTECL LNVLNKNDDV IAAVEIISGL HQRFNGRFTS PLLGAFLQAF 120
  121 ENPSVDIESE RDELQRITRV KGNLRVFTEL YLVGVFRTLD DIESKDAIPN FLQKKTGRKD 180
  181 PLLFSILREI LNYKFKLGFT TTIATAFIKK FAPLFRDDDN SWDDLIYDSK LKGALQSLFK 240
  241 NFIDATFARA TELHKKVNKL QREHQKCQIR TGKLRDEYVE EYDKLLPIFI RFKTSAITLG 300
  301 EFFKLEIPEL EGASNDDLKE TASPMITNQI LPPNQRLWEN EDTRKFYEIL PDISKTVEES 360
  361 QSSKTEKDSN VNSKNINLFF TDLEMADCKD IIDDLSNRYW SSYLDNKATR NRILKFFMET 420
  421 QDWSKLPVYS RFIATNSKYM PEIVSEFINY LDNGFRSQLH SNKINVKNII FFSEMIKFQL 480
  481 IPSFMIFHKI RTLIMYMQVP NNVEILTVLL EHSGKFLLNK PEYKELMEKM VQLIKDKKND 540
  541 RQLNMNMKSA LENIITLLYP PSVKSLNVTV KTITPEQQFY RILIRSELSS LDFKHIVKLV 600
  601 RKAHWDDVAI QKVLFSLFSK PHKISYQNIP LLTKVLGGLY SYRRDFVIRC IDQVLENIER 660
  661 GLEINDYGQN MHRISNVRYL TEIFNFEMIK SDVLLDTIYH IIRFGHINNQ PNPFYLNYSD 720
  721 PPDNYFRIQL VTTILLNINR TPAAFTKKCK LLLRFFEYYT FIKEQPLPKE TEFRVSSTFK 780
  781 KYENIFGNTK FERSENLVES ASRLESLLKS LNAIKSKDDR VKGSSASIHN GKESAVPIES 840
  841 ITEDDEDEDD ENDDGVDLLG EDEDAEISTP NTESAPGKHQ AKQDESEDED DEDDDEDDDD 900
  901 DDDDDDDDGE EGDEDDDEDD DDEDDDDEEE EDSDSDLEYG GDLDADRDIE MKRMYEEYER 960
  961 KLKDEEERKA EEELERQFQK MMQESIDARK SEKVVASKIP VISKPVSVQK PLLLKKSEEP1020
 1021 SSSKETYEEL SKPKKIAFTF LTKSGKKTQS RILQLPTDVK FVSDVLEEEE KLKTERNKIK1080
 1081 KIVLKRSFD

    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 NMD2

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run RPA135 No Comments Schneider, DA, et al. (2006)
    View Run MLP2 #12 Mitotic Prep1-TiO2 Flowthrough Keck JM, et al. (2011)
    View Run MLP2 #30 Asynchronous Prep6-TiO2 Phosphopeptide enrichment Keck JM, et al. (2011)
    View Run MLP2 #11 Mitotic Prep1-TiO2 enriched, new search criteria Keck JM, et al. (2011)

    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 NMD2 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..272] Pfam 28.070581 MIF4G domain No confident structure predictions are available.
    2 View Details [273..336] deduced N/A Confident ab initio structure predictions are available.
    3 View Details [337..589] ORFEUS 13.8 CBP80, 80KDa nuclear cap-binding protein
    4 View Details [590..944] PSI-BLAST 48.522879 Heavy meromyosin subfragment
    5 View Details [945..1089] PSI-BLAST 17.221849 Tropomyosin

    Functions predicted (by domain):

    # Gene Ontology predictions
    1 No functions predicted.
    2 No functions predicted.
    3
    Term Confidence Notes
  • RNA binding
    		•  4.05046860305563 bayes_pls_golite062009
  • mRNA binding
    		•  2.35042158577052 bayes_pls_golite062009
  • binding
    		•  1.72811847650743 bayes_pls_golite062009
  • protein binding
    		•  1.3800948965226 bayes_pls_golite062009
  • nucleic acid binding
    		•  0.916304573557693 bayes_pls_golite062009
  • structural molecule activity
    		•  0.867897004862886 bayes_pls_golite062009
  • RNA cap binding
    		•  0.357520253345298 bayes_pls_golite062009
  • hydrolase activity
    		•  0.33256091835104 bayes_pls_golite062009
  • transcription regulator activity
    		•  0.0462205765670426 bayes_pls_golite062009
    4
    Term Confidence Notes
  • RNA binding
    		•  4.20683443264388 bayes_pls_golite062009
  • mRNA binding
    		•  2.49094746544717 bayes_pls_golite062009
  • binding
    		•  1.83406697369076 bayes_pls_golite062009
  • protein binding
    		•  1.50566694420704 bayes_pls_golite062009
  • nucleic acid binding
    		•  0.967597910409065 bayes_pls_golite062009
  • structural molecule activity
    		•  0.868289396026548 bayes_pls_golite062009
  • RNA cap binding
    		•  0.66277586901495 bayes_pls_golite062009
  • hydrolase activity
    		•  0.29428275639657 bayes_pls_golite062009
  • transcription regulator activity
    		•  0.022274123463527 bayes_pls_golite062009
    5 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