IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ cui-2007-3 An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Cui H., Levesque MP., Vernoux T., Jung JW., Paquette AJ., Gallagher KL., Wang JY., Blilou I., Scheres B., Benfey PN. Root tissue from transgenic arabidopsis plants expressing epitope tagged SHR protein were used in this study. The proteins were identified from references given in the text as no identifiers for the SHR or Scarecrow proteins were provided by the authors. philip.benfey@duke.edu Science (0036-8075) 2007 Only protein-protein interactions imex curation cui-2007-1 An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. arath-root Arabidopsis thaliana root tissue root In vascular plants, the root is that organ of a plant body that typically lies below the surface of the soil (compare with stem). However, this is not always the case, since a root can also be aerial (that is, growing above the ground) or aerating (that is, growing up above the ground or especially above water). On the other hand, a stem normally occurring below ground is not exceptional either (see rhizome). So, it is better to define root as a part of a plant body that bears no leaves, and therefore also lacks nodes. There are also important internal structural differences between stems and roots. The two major functions of roots are 1) absorption of water and inorganic nutrients and 2) anchoring the plant body to the ground. Roots also function in cytokinin synthesis, which supplies some of shoot needs. They often function in storage of food. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Cui H., Levesque MP., Vernoux T., Jung JW., Paquette AJ., Gallagher KL., Wang JY., Blilou I., Scheres B., Benfey PN. Root tissue from transgenic arabidopsis plants expressing epitope tagged SHR protein were used in this study. The proteins were identified from references given in the text as no identifiers for the SHR or Scarecrow proteins were provided by the authors. philip.benfey@duke.edu Science (0036-8075) 2007 Only protein-protein interactions imex curation cui-2007-2 An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. arath-root Arabidopsis thaliana root tissue root In vascular plants, the root is that organ of a plant body that typically lies below the surface of the soil (compare with stem). However, this is not always the case, since a root can also be aerial (that is, growing above the ground) or aerating (that is, growing up above the ground or especially above water). On the other hand, a stem normally occurring below ground is not exceptional either (see rhizome). So, it is better to define root as a part of a plant body that bears no leaves, and therefore also lacks nodes. There are also important internal structural differences between stems and roots. The two major functions of roots are 1) absorption of water and inorganic nutrients and 2) anchoring the plant body to the ground. Roots also function in cytokinin synthesis, which supplies some of shoot needs. They often function in storage of food. anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Cui H., Levesque MP., Vernoux T., Jung JW., Paquette AJ., Gallagher KL., Wang JY., Blilou I., Scheres B., Benfey PN. Root tissue from transgenic arabidopsis plants expressing epitope tagged SHR protein were used in this study. The proteins were identified from references given in the text as no identifiers for the SHR or Scarecrow proteins were provided by the authors. philip.benfey@duke.edu Science (0036-8075) 2007 Only protein-protein interactions imex curation scr_arath Protein SCARECROW SCR At3g54220 GRAS family protein 20 SGR1 Protein SHOOT GRAVITROPISM 1 F24B22.180 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MAESGDFNGGQPPPHSPLRTTSSGSSSSNNRGPPPPPPPPLVMVRKRLASEMSSNPDYNNSSRPPRRVSHLLDSNYNTVTPQQPPSLTAAATVSSQPNPPLSVCGFSGLPVFPSDRGGRNVMMSVQPMDQDSSSSSASPTVWVDAIIRDLIHSSTSVSIPQLIQNVRDIIFPCNPNLGALLEYRLRSLMLLDPSSSSDPSPQTFEPLYQISNNPSPPQQQQQHQQQQQQHKPPPPPIQQQERENSSTDAPPQPETVTATVPAVQTNTAEALRERKEEIKRQKQDEEGLHLLTLLLQCAEAVSADNLEEANKLLLEISQLSTPYGTSAQRVAAYFSEAMSARLLNSCLGIYAALPSRWMPQTHSLKMVSAFQVFNGISPLVKFSHFTANQAIQEAFEKEDSVHIIDLDIMQGLQWPGLFHILASRPGGPPHVRLTGLGTSMEALQATGKRLSDFADKLGLPFEFCPLAEKVGNLDTERLNVRKREAVAVHWLQHSLYDVTGSDAHTLWLLQRLAPKVVTVVEQDLSHAGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQLLSKEIRNVLAVGGPSRSGEVKFESWREKMQQCGFKGISLAGNAATQATLLLGMFPSDGYTLVDDNGTLKLGWKDLSLLTASAWTPRS shr_arath Protein SHORT-ROOT SHR SGR7 Protein SHOOT GRAVITROPISM 7 At4g37650 F19F18.140 GRAS family protein 26 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDTLFRLVSLQQQQQSDSIITNQSSLSRTSTTTTGSPQTAYHYNFPQNDVVEECFNFFMDEEDLSSSSSHHNHHNHNNPNTYYSPFTTPTQYHPATSSTPSSTAAAAALASPYSSSGHHNDPSAFSIPQTPPSFDFSANAKWADSVLLEAARAFSDKDTARAQQILWTLNELSSPYGDTEQKLASYFLQALFNRMTGSGERCYRTMVTAAATEKTCSFESTRKTVLKFQEVSPWATFGHVAANGAILEAVDGEAKIHIVDISSTFCTQWPTLLEALATRSDDTPHLRLTTVVVANKFVNDQTASHRMMKEIGNRMEKFARLMGVPFKFNIIHHVGDLSEFDLNELDVKPDEVLAINCVGAMHGIASRGSPRDAVISSFRRLRPRIVTVVEEEADLVGEEEGGFDDEFLRGFGECLRWFRVCFESWEESFPRTSNERLMLERAAGRAIVDLVACEPSDSTERRETARKWSRRMRNSGFGAVGYSDEVADDVRALLRRYKEGVWSMVQCPDAAGIFLCWRDQPVVWASAWRPT shr1_orysj Protein SHORT-ROOT 1 SHR1 GRAS family protein 38 OJ1047_C01.1 OJ1113_E01.116 OsJ_24926 LOC_Os07g39820 Os07g0586900 protein protein orysj Oryza sativa subsp. japonica (Rice) Rice MDTLFRLVSLQAASEQQQQQQQSASYNSRSTTSSGSRSSSHQTNASYSYYHHSSNSGGGGGGGGGYYYGGQQPPPSQYYYLEPYQEECGNAPHHQLYMDEDFSSSSSSRHFHHGARVQQQQPPASSTPTGTAPTPPLSTSSTAAGAGHGLFEAADLSFPPDLNLDFSSPASSSGGGTASSGAVGGGGGGRWASQLLLECARSVAARDSQRVQQLMWMLNELASPYGDVEQKLASYFLQGLFARLTASGPRTLRTLAAASDRNTSFDSTRRTALRFQELSPWSSFGHVAANGAILESFLEVAAAASSETQRFHILDLSNTFCTQWPTLLEALATRSADETPHLSITTVVSAAPSAPTAAVQRVMREIGQRMEKFARLMGVPFRFRAVHHSGDLAELDLDALDLREGGATTALAVNCVNSLRGVVPGRARRRDAFAASLRRLDPRVVTVVEEEADLVASDPDASSATEEGGDTEAAFLKVFGEGLRFFSAYMDSLEESFPKTSNERLALERGAGRAIVDLVSCPASESMERRETAASWARRMRSAGFSPVAFSEDVADDVRSLLRRYREGWSMREAGTDDSAAGAGVFLAWKEQPLVWASAWRP scr2_orysj Protein SCARECROW 2 SCR2 OsSCR2 OsJ_033689 Os12g0122000 LOC_Os12g02870 protein protein orysj Oryza sativa subsp. japonica (Rice) Rice MGSSSLLLFPSSSSSATHSSYSPSSSSHAITSLLPPLPSDHHLLLYLDHQEQHHLAAAMVRKRPASDMDLPPPRRHVTGDLSDVTAAAAGAPTLSASAQLPALPTQLPAFHHTDMDLAAPAPPAPQQVAAGEGGPPSTAWVDGIIRDIIASSGAAVSVAQLIHNVREIIRPCNPDLASILELRLRSLLNSDPAPPPPPPSHPALLPPDATAPPPPPTSVAALPPPPPAQPDKRRREPQCQEQEPNQPQSPKPPTAEETAAAAAAAAAAAAAAAKERKEEQRRKQRDEEGLHLLTLLLQCAESVNADNLDEAHRALLEIAELATPFGTSTQRVAAYFAEAMSARLVSSCLGLYAPLPSPSPAGARVHGRVAAAFQVFNGISPFVKFSHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPGGPPRVRLTGLGASMEALEATGKRLSDFADTLGLPFEFCPVADKAGNLDPEKLGVTRREAVAVHWLRHSLYDVTGSDSNTLWLIQRLAPKVVTMVEQDLSHSGSFLARFVEAIHYYSALFDSLDASYSEDSPERHVVEQQLLSREIRNVLAVGGPARTGDVKFGSWREKLAQSGFRVSSLAGSAAAQAALLLGMFPSDGYTLIEENGALKLGWKDLCLLTASAWRPIQASGR scr-shr-2 Yeast two hybrid reveals interaction between Arabidopsis Short-Root protein and Arabidopsis Scarecrow protein 607319 N/A 607322 unspecified role unspecified role bait bait N/A 607323 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 2D The length of the SHR protein was taken from the UniProt entry fro this protein. scr-shr-3 Yeast two hybrid reveals interaction between Arabidopsis Short-Root protein and Arabidopsis Scarecrow protein 607319 N/A 607322 unspecified role unspecified role bait bait region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false N/A 607323 unspecified role unspecified role prey prey physical association physical association false false false S5 scr-shr-4 Yeast two hybrid reveals interaction between Arabidopsis Short-Rort protein and Arabidopsis Scarecrow1 protein 607319 N/A 607323 unspecified role unspecified role prey prey N/A 607322 unspecified role unspecified role bait bait physical association physical association false false false 4B scr-shr-5 Yeast two hybrid reveals interaction between Rice Short-Root protein and Arabidopsis Scarecrow protein 607319 N/A 607324 unspecified role unspecified role prey prey N/A 607322 unspecified role unspecified role bait bait physical association physical association false false false 4B scr-shr-6 Yeast two hybrid reveals interaction between Rice Short-Root protein and Rice Scarecrow 1 protein 607319 N/A 607325 unspecified role unspecified role bait bait N/A 607324 unspecified role unspecified role prey prey physical association physical association false false false 4B scr-shr-7 Yeast two hybrid reveals interaction between Arabidopsis Short-Root protein and Rice Scarecrow 1 protein 607319 N/A 607325 unspecified role unspecified role bait bait N/A 607323 unspecified role unspecified role prey prey physical association physical association false false false 4B scr-shr Coimmunoprecipitation analysis reveals interaction between Short-Root protein and Scarecrow protein 607320 N/A 607322 unspecified role unspecified role prey prey N/A 607323 unspecified role unspecified role bait bait region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false 2B scr-shr-1 Coimmunoprecipitation analysis reveals interaction between Short-Root protein and Scarecrow protein 607321 N/A 607323 unspecified role unspecified role prey prey region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 607322 unspecified role unspecified role bait bait physical association physical association false false false 2A