Difference between revisions of "Part:BBa K1150007"
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| − | Sunlight is essential for plants: Not only as an energy source but also as information for their growth cycle. Therefore they need mechanisms to detect different light | + | Sunlight is essential for plants: Not only as an energy source but also as information for their growth cycle. Therefore they need mechanisms to detect different light wavelengths. E3-ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is the interaction partner of ultraviolet B (UVB) light receptor [https://parts.igem.org/Part:BBa_K1150006 UVR8] [1]. The ubiqutin ligase activity of this COP1 is eliminated, only the WD40 domain remains. This minimizes the risk of cross talk in mammalian cells [2]. |
==Biology and Usage== | ==Biology and Usage== | ||
| − | When UVB light is perceived by the UVR8 photoreceptor | + | When UVB light is perceived by the UVR8 photoreceptor it monomerizes and therefore changes in its open confuguration. Then it recruits COP1. This is a signal for plant cells to react to UVB light, for example with photomorphogenesis [3]. |
| − | Freiburg 2013 used this part to engineer a UVB light induced mechanism to activate gene expression. You need a combination of these BioBricks: [https://parts.igem.org/Part:BBa_K1150029 Cas9-UVR8], [https://parts.igem.org/Part:BBa_K1150030 COP1-VP16], [https://parts.igem.org/Part:BBa_K1150034 | + | Freiburg 2013 used this part to engineer a UVB light induced mechanism to activate gene expression. You need a combination of these BioBricks: [https://parts.igem.org/Part:BBa_K1150029 Cas9-UVR8], [https://parts.igem.org/Part:BBa_K1150030 COP1-VP16], [https://parts.igem.org/Part:BBa_K1150034 RNAimer] |
<span class='h3bb'> | <span class='h3bb'> | ||
| + | |||
==Sequence and Features== | ==Sequence and Features== | ||
</span> | </span> | ||
<partinfo>BBa_K1150007 SequenceAndFeatures</partinfo> | <partinfo>BBa_K1150007 SequenceAndFeatures</partinfo> | ||
| + | <br> | ||
| + | <html><!--- Please copy this table containing parameters for BBa_ at the end of the parametrs section ahead of the references. ---><style type="text/css">table#AutoAnnotator {border:1px solid black; width:100%; border-collapse:collapse;} th#AutoAnnotatorHeader { border:1px solid black; width:100%; background-color: rgb(221, 221, 221);} td.AutoAnnotator1col { width:100%; border:1px solid black; } span.AutoAnnotatorSequence { font-family:'Courier New', Arial; } td.AutoAnnotatorSeqNum { text-align:right; width:2%; } td.AutoAnnotatorSeqSeq { width:98% } td.AutoAnnotatorSeqFeat1 { width:3% } td.AutoAnnotatorSeqFeat2a { width:27% } td.AutoAnnotatorSeqFeat2b { width:97% } td.AutoAnnotatorSeqFeat3 { width:70% } table.AutoAnnotatorNoBorder { border:0px; width:100%; border-collapse:collapse; } table.AutoAnnotatorWithBorder { border:1px solid black; width:100%; border-collapse:collapse; } td.AutoAnnotatorOuterAmino { border:0px solid black; width:20% } td.AutoAnnotatorInnerAmino { border:1px solid black; width:50% } td.AutoAnnotatorAminoCountingOuter { border:1px solid black; width:40%; } td.AutoAnnotatorBiochemParOuter { border:1px solid black; width:60%; } td.AutoAnnotatorAminoCountingInner1 { width: 7.5% } td.AutoAnnotatorAminoCountingInner2 { width:62.5% } td.AutoAnnotatorAminoCountingInner3 { width:30% } td.AutoAnnotatorBiochemParInner1 { width: 5% } td.AutoAnnotatorBiochemParInner2 { width:55% } td.AutoAnnotatorBiochemParInner3 { width:40% } td.AutoAnnotatorCodonUsage1 { width: 3% } td.AutoAnnotatorCodonUsage2 { width:14.2% } td.AutoAnnotatorCodonUsage3 { width:13.8% } td.AutoAnnotatorAlignment1 { width: 3% } td.AutoAnnotatorAlignment2 { width: 10% } td.AutoAnnotatorAlignment3 { width: 87% } td.AutoAnnotatorLocalizationOuter {border:1px solid black; width:40%} td.AutoAnnotatorGOOuter {border:1px solid black; width:60%} td.AutoAnnotatorLocalization1 { width: 7.5% } td.AutoAnnotatorLocalization2 { width: 22.5% } td.AutoAnnotatorLocalization3 { width: 70% } td.AutoAnnotatorGO1 { width: 5% } td.AutoAnnotatorGO2 { width: 35% } td.AutoAnnotatorGO3 { width: 60% } td.AutoAnnotatorPredFeat1 { width:3% } td.AutoAnnotatorPredFeat2a { width:27% } td.AutoAnnotatorPredFeat3 { width:70% } div.AutoAnnotator_trans { position:absolute; background:rgb(11,140,143); background-color:rgba(11,140,143, 0.8); height:5px; top:100px; } div.AutoAnnotator_sec_helix { position:absolute; background:rgb(102,0,102); background-color:rgba(102,0,102, 0.8); height:5px; top:110px; } div.AutoAnnotator_sec_strand { position:absolute; background:rgb(245,170,26); background-color:rgba(245,170,26, 1); height:5px; top:110px; } div.AutoAnnotator_acc_buried { position:absolute; background:rgb(89,168,15); background-color:rgba(89,168,15, 0.8); height:5px; top:120px; } div.AutoAnnotator_acc_exposed { position:absolute; background:rgb(0, 0, 255); background-color:rgba(0, 0, 255, 0.8); height:5px; top:120px; } div.AutoAnnotator_dis { position:absolute; text-align:center; font-family:Arial,Helvetica,sans-serif; background:rgb(255, 200, 0); background-color:rgba(255, 200, 0, 1); height:16px; width:16px; top:80px; border-radius:50%; } </style><div id='AutoAnnotator_container_1381279820314'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381279820314 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K1150007<!------------------------Enter BioBrick number here------------------------>">BBa_K1150007<!------------------------Enter BioBrick number here------------------------></a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 25</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence"> <u><i>ATGGCCGGC</i>ATGTATAGC ... CTCGCTGCG<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position -8 to 1029 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1 <br>101 <br>201 <br>301 </td><td class="AutoAnnotatorSeqSeq">MAGMYSNGLADFQSVLTTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFDFSSVVNEPADMQCPIVEMSTRSKLSCLSWNKH<br>EKNHIASSDYEGIVTVWDVTTRQSLMEYEEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSNYIAVGSADHHIH<br>YYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKDNLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFG<br>SPDMDDAEEEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAATG*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2b">None of the supported features appeared in the sequence</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid composition:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Ala (A)</td><td class="AutoAnnotatorInnerAmino">23 (6.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">17 (4.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">18 (5.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">22 (6.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">9 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">6 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">22 (6.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">16 (4.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">13 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">18 (5.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">20 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">17 (4.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">9 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">14 (4.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">9 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">41 (11.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">22 (6.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">6 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">13 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">31 (9.0%)</td></tr></table></td></tr></table></td></tr><tr><td class="AutoAnnotatorAminoCountingOuter"><strong>Amino acid counting</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Total number:</td><td class="AutoAnnotatorAminoCountingInner3">346</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">34 (9.8%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">44 (12.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">46 (13.3%)</td></tr></table></td><td class="AutoAnnotatorBiochemParOuter"><strong>Biochemical parameters</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Atomic composition:</td><td class="AutoAnnotatorBiochemParInner3">C<sub>1703</sub>H<sub>2632</sub>N<sub>470</sub>O<sub>535</sub>S<sub>18</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">38827.5</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.71</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td class="AutoAnnotatorBiochemParInner3">52370 / 52933 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong> <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1381279820314()' value='Show'><span id="hydrophobicity_charge_explanation"></span><div id="hydrophobicity_charge_container" style='display:none'><div id="hydrophobicity_charge_placeholder0" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder1" style="width:100%;height:150px"></div></div></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Codon usage</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Organism:</td><td class="AutoAnnotatorCodonUsage3"><i>E. coli</i></td><td class="AutoAnnotatorCodonUsage3"><i>B. subtilis</i></td><td class="AutoAnnotatorCodonUsage3"><i>S. cerevisiae</i></td><td class="AutoAnnotatorCodonUsage3"><i>A. thaliana</i></td><td class="AutoAnnotatorCodonUsage3"><i>P. patens</i></td><td class="AutoAnnotatorCodonUsage3">Mammals</td></tr><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Codon quality (<a href="http://en.wikipedia.org/wiki/Codon_Adaptation_Index">CAI</a>):</td><td class="AutoAnnotatorCodonUsage3">good (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.67)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<br> There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.</td></tr><tr><th id='AutoAnnotatorHeader' colspan="2"><strong>Predictions</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)</th></tr><tr><td class="AutoAnnotator1col" colspan="2"> There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.</td><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table></div><br><!-- IMPORTANT: DON'T REMOVE THIS LINE, OTHERWISE NOT SUPPORTED FOR IE BEFORE 9 --><!--[if lte IE 8]><script language="javascript" type="text/javascript" src="excanvas.min.js"></script><![endif]--><script type='text/javascript' src='http://code.jquery.com/jquery-1.10.0.min.js'></script><script type='text/javascript' src='http://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js'></script><script>function show_or_hide_plot_1381279820314(){hydrophobicity_datapoints = [[2.5,0.78],[3.5,0.24],[4.5,-0.82],[5.5,-0.82],[6.5,-0.44],[7.5,0.18],[8.5,-0.36],[9.5,0.90],[10.5,0.28],[11.5,-0.64],[12.5,-0.16],[13.5,1.30],[14.5,0.60],[15.5,1.16],[16.5,1.88],[17.5,0.90],[18.5,-0.76],[19.5,-0.88],[20.5,-0.90],[21.5,-2.36],[22.5,-1.46],[23.5,-1.46],[24.5,-0.36],[25.5,0.70],[26.5,1.96],[27.5,0.50],[28.5,2.30],[29.5,0.56],[30.5,-0.98],[31.5,-1.42],[32.5,-1.42],[33.5,-1.42],[34.5,0.04],[35.5,0.04],[36.5,-0.04],[37.5,1.02],[38.5,-0.58],[39.5,-0.24],[40.5,1.24],[41.5,1.24],[42.5,0.72],[43.5,2.32],[44.5,0.72],[45.5,0.44],[46.5,-0.10],[47.5,-0.84],[48.5,-2.44],[49.5,-2.44],[50.5,-3.70],[51.5,-2.24],[52.5,-0.78],[53.5,0.28],[54.5,0.84],[55.5,1.90],[56.5,1.06],[57.5,1.34],[58.5,0.82],[59.5,0.06],[60.5,0.20],[61.5,1.18],[62.5,-0.44],[63.5,0.56],[64.5,2.02],[65.5,0.82],[66.5,0.48],[67.5,1.10],[68.5,0.10],[69.5,0.38],[70.5,1.92],[71.5,0.66],[72.5,0.12],[73.5,-0.04],[74.5,-0.52],[75.5,-2.06],[76.5,-0.98],[77.5,-0.98],[78.5,-0.16],[79.5,-0.84],[80.5,0.76],[81.5,1.22],[82.5,1.22],[83.5,1.10],[84.5,1.26],[85.5,0.22],[86.5,-1.52],[87.5,-0.98],[88.5,-2.14],[89.5,-1.22],[90.5,-1.24],[91.5,0.16],[92.5,1.08],[93.5,1.70],[94.5,0.76],[95.5,0.22],[96.5,-1.06],[97.5,-2.46],[98.5,-3.00],[99.5,-3.60],[100.5,-3.60],[101.5,-3.46],[102.5,-1.92],[103.5,-0.86],[104.5,-0.24],[105.5,0.30],[106.5,0.24],[107.5,-0.92],[108.5,-1.98],[109.5,-1.90],[110.5,-0.84],[111.5,0.70],[112.5,0.82],[113.5,2.36],[114.5,2.26],[115.5,0.66],[116.5,0.66],[117.5,0.66],[118.5,-0.32],[119.5,-1.04],[120.5,-1.04],[121.5,-2.04],[122.5,-1.14],[123.5,-0.62],[124.5,-0.42],[125.5,0.02],[126.5,-0.52],[127.5,-1.98],[128.5,-3.00],[129.5,-3.00],[130.5,-3.52],[131.5,-3.72],[132.5,-2.66],[133.5,-2.20],[134.5,-1.66],[135.5,-0.04],[136.5,0.16],[137.5,0.36],[138.5,0.38],[139.5,-0.36],[140.5,-1.34],[141.5,-1.34],[142.5,-2.22],[143.5,-2.22],[144.5,-0.94],[145.5,-0.04],[146.5,1.50],[147.5,1.66],[148.5,1.74],[149.5,1.20],[150.5,-0.26],[151.5,-1.80],[152.5,-1.14],[153.5,-1.84],[154.5,-0.84],[155.5,-0.92],[156.5,0.62],[157.5,-0.06],[158.5,1.22],[159.5,0.24],[160.5,0.12],[161.5,-1.42],[162.5,-1.94],[163.5,-2.08],[164.5,-2.10],[165.5,-0.36],[166.5,1.24],[167.5,1.24],[168.5,1.78],[169.5,1.24],[170.5,0.78],[171.5,-0.90],[172.5,0.16],[173.5,-1.44],[174.5,0.16],[175.5,0.28],[176.5,1.56],[177.5,2.04],[178.5,1.96],[179.5,0.80],[180.5,-0.40],[181.5,-1.22],[182.5,-2.14],[183.5,-1.52],[184.5,-1.42],[185.5,-1.42],[186.5,-1.36],[187.5,-0.38],[188.5,0.14],[189.5,1.14],[190.5,1.76],[191.5,1.86],[192.5,1.32],[193.5,0.26],[194.5,-1.22],[195.5,-1.78],[196.5,-0.72],[197.5,-1.72],[198.5,-1.28],[199.5,-0.90],[200.5,-0.96],[201.5,-1.10],[202.5,-1.36],[203.5,-1.80],[204.5,-0.64],[205.5,-0.10],[206.5,-1.56],[207.5,-0.98],[208.5,0.48],[209.5,-1.06],[210.5,-0.06],[211.5,1.20],[212.5,1.36],[213.5,0.52],[214.5,0.52],[215.5,-1.10],[216.5,-2.44],[217.5,-1.92],[218.5,-1.00],[219.5,-0.52],[220.5,-0.00],[221.5,1.62],[222.5,0.48],[223.5,0.20],[224.5,1.12],[225.5,1.22],[226.5,-0.32],[227.5,-0.24],[228.5,-1.50],[229.5,-1.50],[230.5,-0.98],[231.5,-0.44],[232.5,0.62],[233.5,1.16],[234.5,0.26],[235.5,-0.80],[236.5,-0.80],[237.5,-1.30],[238.5,-0.38],[239.5,-1.14],[240.5,0.32],[241.5,0.30],[242.5,-0.26],[243.5,-0.18],[244.5,-0.06],[245.5,-1.52],[246.5,-2.04],[247.5,-0.58],[248.5,-1.74],[249.5,-0.12],[250.5,-0.32],[251.5,0.24],[252.5,0.04],[253.5,-0.54],[254.5,-1.46],[255.5,-1.20],[256.5,-1.20],[257.5,-2.46],[258.5,-2.26],[259.5,-2.96],[260.5,-3.02],[261.5,-2.32],[262.5,-0.78],[263.5,-0.16],[264.5,1.38],[265.5,1.94],[266.5,2.22],[267.5,0.68],[268.5,0.60],[269.5,-0.86],[270.5,-0.98],[271.5,-1.06],[272.5,0.00],[273.5,0.66],[274.5,1.28],[275.5,1.38],[276.5,-0.08],[277.5,-0.58],[278.5,-1.78],[279.5,-2.40],[280.5,-1.40],[281.5,-0.96],[282.5,0.02],[283.5,0.46],[284.5,0.52],[285.5,-1.10],[286.5,-1.54],[287.5,-1.48],[288.5,-1.36],[289.5,-1.62],[290.5,-1.16],[291.5,0.38],[292.5,-0.66],[293.5,-0.68],[294.5,-0.42],[295.5,-1.00],[296.5,-1.28],[297.5,-1.22],[298.5,-1.22],[299.5,-0.90],[300.5,-0.70],[301.5,-0.88],[302.5,-1.50],[303.5,-2.04],[304.5,-1.36],[305.5,-1.36],[306.5,-2.44],[307.5,-2.44],[308.5,-1.38],[309.5,-1.82],[310.5,-1.28],[311.5,-0.84],[312.5,0.42],[313.5,0.96],[314.5,0.88],[315.5,1.40],[316.5,2.50],[317.5,2.44],[318.5,1.36],[319.5,0.74],[320.5,0.22],[321.5,-1.32],[322.5,-1.98],[323.5,-2.12],[324.5,-1.48],[325.5,-0.94],[326.5,0.52],[327.5,0.54],[328.5,1.22],[329.5,0.66],[330.5,0.12],[331.5,-1.34],[332.5,-1.28],[333.5,-1.78],[334.5,-0.18],[335.5,-0.80],[336.5,0.74],[337.5,1.58],[338.5,2.56],[339.5,2.42],[340.5,3.56],[341.5,3.08],[342.5,2.18],[343.5,1.26]];charge_datapoints = [[2.5,0.00],[3.5,0.00],[4.5,0.00],[5.5,0.00],[6.5,0.00],[7.5,0.00],[8.5,-0.20],[9.5,-0.20],[10.5,-0.20],[11.5,-0.20],[12.5,-0.20],[13.5,0.00],[14.5,0.00],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,0.20],[19.5,0.20],[20.5,0.20],[21.5,0.40],[22.5,0.40],[23.5,0.40],[24.5,0.40],[25.5,0.40],[26.5,0.20],[27.5,0.00],[28.5,-0.20],[29.5,0.00],[30.5,0.10],[31.5,0.10],[32.5,0.10],[33.5,0.10],[34.5,-0.10],[35.5,-0.10],[36.5,-0.10],[37.5,0.10],[38.5,0.10],[39.5,0.10],[40.5,0.00],[41.5,0.00],[42.5,0.00],[43.5,0.00],[44.5,-0.20],[45.5,-0.20],[46.5,-0.40],[47.5,-0.20],[48.5,-0.40],[49.5,-0.40],[50.5,-0.60],[51.5,-0.40],[52.5,-0.60],[53.5,-0.40],[54.5,-0.20],[55.5,-0.00],[56.5,-0.00],[57.5,-0.00],[58.5,-0.00],[59.5,0.20],[60.5,0.20],[61.5,0.20],[62.5,0.40],[63.5,0.40],[64.5,0.20],[65.5,-0.00],[66.5,-0.00],[67.5,-0.20],[68.5,-0.20],[69.5,-0.20],[70.5,-0.00],[71.5,-0.00],[72.5,-0.20],[73.5,-0.20],[74.5,-0.20],[75.5,-0.40],[76.5,-0.40],[77.5,-0.20],[78.5,-0.20],[79.5,-0.20],[80.5,-0.00],[81.5,-0.00],[82.5,-0.20],[83.5,-0.20],[84.5,-0.20],[85.5,-0.20],[86.5,-0.00],[87.5,0.20],[88.5,0.40],[89.5,0.40],[90.5,0.40],[91.5,0.20],[92.5,0.20],[93.5,-0.00],[94.5,-0.00],[95.5,-0.00],[96.5,0.20],[97.5,0.30],[98.5,0.10],[99.5,0.30],[100.5,0.30],[101.5,0.20],[102.5,0.10],[103.5,0.30],[104.5,0.10],[105.5,0.10],[106.5,-0.20],[107.5,-0.20],[108.5,-0.40],[109.5,-0.40],[110.5,-0.40],[111.5,-0.20],[112.5,-0.20],[113.5,-0.00],[114.5,-0.00],[115.5,-0.20],[116.5,-0.20],[117.5,-0.20],[118.5,-0.20],[119.5,-0.00],[120.5,0.20],[121.5,0.20],[122.5,0.20],[123.5,0.20],[124.5,-0.20],[125.5,-0.20],[126.5,-0.40],[127.5,-0.60],[128.5,-0.50],[129.5,-0.50],[130.5,-0.30],[131.5,0.10],[132.5,0.30],[133.5,0.20],[134.5,0.40],[135.5,0.20],[136.5,-0.20],[137.5,-0.20],[138.5,-0.20],[139.5,-0.00],[140.5,-0.00],[141.5,-0.00],[142.5,-0.00],[143.5,-0.00],[144.5,-0.20],[145.5,-0.20],[146.5,-0.00],[147.5,-0.00],[148.5,-0.00],[149.5,-0.00],[150.5,-0.20],[151.5,-0.40],[152.5,-0.40],[153.5,-0.20],[154.5,-0.20],[155.5,0.20],[156.5,0.40],[157.5,0.40],[158.5,0.20],[159.5,0.20],[160.5,0.20],[161.5,0.20],[162.5,-0.00],[163.5,-0.00],[164.5,-0.00],[165.5,-0.20],[166.5,-0.20],[167.5,-0.00],[168.5,-0.00],[169.5,-0.20],[170.5,-0.20],[171.5,-0.00],[172.5,-0.00],[173.5,-0.00],[174.5,0.20],[175.5,0.20],[176.5,-0.00],[177.5,-0.00],[178.5,0.20],[179.5,0.20],[180.5,0.20],[181.5,0.20],[182.5,0.20],[183.5,-0.00],[184.5,-0.00],[185.5,-0.00],[186.5,-0.00],[187.5,-0.00],[188.5,-0.00],[189.5,-0.00],[190.5,-0.00],[191.5,-0.00],[192.5,-0.00],[193.5,-0.20],[194.5,-0.10],[195.5,-0.00],[196.5,-0.00],[197.5,0.10],[198.5,0.30],[199.5,0.20],[200.5,-0.10],[201.5,-0.10],[202.5,-0.00],[203.5,-0.00],[204.5,-0.00],[205.5,0.20],[206.5,0.20],[207.5,-0.00],[208.5,-0.00],[209.5,0.10],[210.5,0.10],[211.5,0.10],[212.5,0.10],[213.5,0.10],[214.5,0.10],[215.5,0.30],[216.5,0.50],[217.5,0.50],[218.5,0.50],[219.5,0.40],[220.5,0.20],[221.5,-0.00],[222.5,0.20],[223.5,0.20],[224.5,0.20],[225.5,0.20],[226.5,0.20],[227.5,-0.00],[228.5,-0.20],[229.5,-0.20],[230.5,-0.20],[231.5,-0.20],[232.5,-0.20],[233.5,-0.00],[234.5,-0.00],[235.5,-0.20],[236.5,-0.20],[237.5,-0.20],[238.5,-0.20],[239.5,-0.00],[240.5,0.20],[241.5,0.20],[242.5,-0.00],[243.5,-0.00],[244.5,-0.00],[245.5,-0.20],[246.5,-0.20],[247.5,-0.00],[248.5,-0.00],[249.5,-0.20],[250.5,0.20],[251.5,0.20],[252.5,0.20],[253.5,0.40],[254.5,0.40],[255.5,0.30],[256.5,0.30],[257.5,0.30],[258.5,-0.10],[259.5,0.10],[260.5,-0.00],[261.5,-0.00],[262.5,-0.00],[263.5,0.20],[264.5,-0.00],[265.5,-0.00],[266.5,-0.00],[267.5,-0.00],[268.5,-0.00],[269.5,-0.20],[270.5,-0.20],[271.5,-0.20],[272.5,-0.20],[273.5,-0.20],[274.5,-0.00],[275.5,-0.00],[276.5,-0.20],[277.5,-0.20],[278.5,-0.20],[279.5,-0.40],[280.5,-0.40],[281.5,-0.20],[282.5,-0.20],[283.5,-0.20],[284.5,0.10],[285.5,0.30],[286.5,0.10],[287.5,0.10],[288.5,0.10],[289.5,0.20],[290.5,-0.00],[291.5,0.20],[292.5,0.20],[293.5,0.20],[294.5,0.10],[295.5,0.30],[296.5,0.30],[297.5,0.30],[298.5,0.30],[299.5,0.20],[300.5,-0.20],[301.5,-0.20],[302.5,-0.40],[303.5,-0.60],[304.5,-0.60],[305.5,-0.60],[306.5,-0.80],[307.5,-0.80],[308.5,-0.60],[309.5,-0.60],[310.5,-0.40],[311.5,-0.20],[312.5,-0.00],[313.5,-0.00],[314.5,-0.00],[315.5,-0.00],[316.5,-0.00],[317.5,-0.00],[318.5,-0.00],[319.5,0.20],[320.5,0.20],[321.5,-0.00],[322.5,-0.00],[323.5,-0.00],[324.5,-0.20],[325.5,-0.20],[326.5,-0.00],[327.5,-0.00],[328.5,-0.00],[329.5,-0.00],[330.5,-0.00],[331.5,-0.00],[332.5,-0.00],[333.5,-0.00],[334.5,-0.00],[335.5,0.20],[336.5,0.20],[337.5,0.20],[338.5,0.20],[339.5,0.20],[340.5,-0.00],[341.5,-0.00],[342.5,-0.00],[343.5,-0.00]];dis_datapoints = undefined;trans_datapoints = undefined;sec_helix_datapoints = undefined;sec_strand_datapoints = undefined;acc_exposed_datapoints = undefined;acc_buried_datapoints = undefined;flot_plot_options = []; flot_plot_options[0] = {grid: {borderWidth: {top: 0,right: 0,bottom: 0,left: 0}},legend: {show: false},xaxes: [{show: true,min: 0,max: 200,ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']],tickLength: -5}],yaxes: [{show: true,ticks: [[0, '0'], [4.5,'hydro-<br>phobic '], [-4.5,'hydro-<br>philic ']],min: -4.5,max: +4.5,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(100,149,237,1)'}},{show: true,ticks: [[0, ''], [1,'positive<br> charge'], [-1,'negative<br> charge']],position: 'right',min: -1,max: 1,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(255,99,71,1)'}}]};number_of_plots = 2;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{min: plot_num*200,max: (plot_num + 1)*200,ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], [plot_num*200 + 24.5, (plot_num*200 + 25).toString()], [plot_num*200 + 49.5, (plot_num*200 + 50).toString()], [plot_num*200 + 74.5, (plot_num*200 + 75).toString()], [plot_num*200 + 99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ],tickLength: -5}];};try {if( $('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br> <input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> Moving average over 5 amino acids for charge (<img src=\'https://static.igem.org/mediawiki/2013/3/3e/TUM13_charge_icon.png\' alt=\'red graph\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'> Predicted disulfid bridges (<img src=\'https://static.igem.org/mediawiki/2013/2/28/TUM13_dis_icon.png\' alt=\'yellow circle\' height=\'10\'></img>) with the number of the bridge in the center';description_html = description_html + '<br> <input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'> Predicted transmembrane helices (<img src=\'https://static.igem.org/mediawiki/2013/7/78/TUM13_trans_icon.png\' alt=\'turquois bars\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'> Predicted secondary structure: Helices (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png\' alt=\'violet bars\' height=\'10\'></img>) and beta-strands (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png\' alt=\'yellow bars\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'> Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381279820314();$('#AutoAnnotator_container_1381279820314 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381279820314);}else{$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_explanation').html('');}}catch(err){txt='There was an error with the button controlling the visibility of the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';alert(txt);}};function plot_according_to_selectors_1381279820314(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381279820314 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381279820314 #charge_checkbox').prop('checked') == true){plot_datasets[1] = {color: 'rgba(255,99,71,1)',data: charge_datapoints,label: 'Charge',lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' },yaxis: 2};}for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){$.plot('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#AutoAnnotator_container_1381279820314 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381279820314 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][1] - 1)*tick_diff - Math.floor((dis_datapoints[j][1] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');}}if($('#AutoAnnotator_container_1381279820314 #trans_checkbox').prop('checked') == true){for ( 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| − | == | + | ==References== |
<small> | <small> | ||
[1] Rizzini L., Favory J.-J., Cloix C., Faggionato D., O'Hara A., Kaiserli E., Baumeister R., Schäfer E., Nagy F., Jenkins G. I., Ulm R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science 332 | [1] Rizzini L., Favory J.-J., Cloix C., Faggionato D., O'Hara A., Kaiserli E., Baumeister R., Schäfer E., Nagy F., Jenkins G. I., Ulm R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science 332 | ||
Latest revision as of 00:50, 9 October 2013
COP1
| COP1 | |
|---|---|
| Function | interaction partner of
UVR8,reacts to UVB light |
| Use in | Mammalians |
| RFC standard | RFC 25 |
| Backbone | pSB1C3 |
| Organism | Arabidopsis thaliana |
| Source | AG Weber, Freiburg |
| Submitted by | [http://2013.igem.org/Team:Freiburg Freiburg 2013] |
Sunlight is essential for plants: Not only as an energy source but also as information for their growth cycle. Therefore they need mechanisms to detect different light wavelengths. E3-ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is the interaction partner of ultraviolet B (UVB) light receptor UVR8 [1]. The ubiqutin ligase activity of this COP1 is eliminated, only the WD40 domain remains. This minimizes the risk of cross talk in mammalian cells [2].
Biology and Usage
When UVB light is perceived by the UVR8 photoreceptor it monomerizes and therefore changes in its open confuguration. Then it recruits COP1. This is a signal for plant cells to react to UVB light, for example with photomorphogenesis [3]. Freiburg 2013 used this part to engineer a UVB light induced mechanism to activate gene expression. You need a combination of these BioBricks: Cas9-UVR8, COP1-VP16, RNAimer
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 787
Illegal BsaI.rc site found at 864
Illegal SapI.rc site found at 376
| Protein data table for BioBrick BBa_K1150007 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein) ATGGCCGGCATGTATAGC ... CTCGCTGCGACCGGT ORF from nucleotide position -8 to 1029 (excluding stop-codon) | ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
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Sequence features: (with their position in the amino acid sequence, see the list of supported features)
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Amino acid composition:
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Amino acid counting
| Biochemical parameters
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| Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges | ||||||||||||||||||||||||||||||||||||||||||||||
Codon usage
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| Alignments (obtained from PredictProtein.org) There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours. | ||||||||||||||||||||||||||||||||||||||||||||||
| Predictions (obtained from PredictProtein.org) | ||||||||||||||||||||||||||||||||||||||||||||||
| There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours. | ||||||||||||||||||||||||||||||||||||||||||||||
| The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation. If you have any questions, comments or suggestions, please leave us a comment. | ||||||||||||||||||||||||||||||||||||||||||||||
References
[1] Rizzini L., Favory J.-J., Cloix C., Faggionato D., O'Hara A., Kaiserli E., Baumeister R., Schäfer E., Nagy F., Jenkins G. I., Ulm R. (2011). Perception of UV-B by the Arabidopsis UVR8 protein. Science 332
[2] Müller K., Engesser R., Schulz S., Steinberg T., Tomakidi P., Weber C. C., Ulm R., Timmer J., Zurbriggen M. D., Weber W. (2013). Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Research Vol. 41, No. 12
[3] Favory J.-J., Stec A., Gruber H., Rizzini L., Oravecz A., Funk M., Albert A., Cloix C., Jenkins G. I., Oakeley E. J., Seidlitz H. K., Nagy F., Ulm R. (2009). Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. The EMBO Journal 28, 591-600