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CRISPR CasX Coronavirus possible target sequences

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Mar 25th, 2020
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  1. Made from http://chopchop.cbu.uib.no
  2. ​
  3.  
  4. https://chopchop.cbu.uib.no/results/1583089233820.9504/
  5. https://pastebin.com/tgFMTrzJ
  6. ​
  7.  
  8. "Knock-out"
  9.  
  10. ​
  11.  
  12. Rank Target sequence Genomic location Strand GC content (%) Self-complementarity Efficiency MM0 MM1 MM2 MM3
  13.  
  14. 1 TTCCATTTGTAGTTTCAACTGGATACCA seq:1013 + 33 0 0 1 0 0 0
  15.  
  16. 2 TTCAACTGGATACCACTTCAGAGAGCTA seq:1026 + 46 0 0 1 0 0 0
  17.  
  18. 3 TTCAGAGAGCTAGGTGTTGTACATAATC seq:1042 + 42 0 0 1 0 0 0
  19.  
  20. 4 TTCCTTAAAACTAAGTCTAGAGCTATGT seq:1083 - 29 0 0 1 0 0 0
  21.  
  22. 5 TTCTGGTAATCTATTACTAGATAAACGC seq:1149 + 33 0 0 1 0 0 0
  23.  
  24. 6 TTCAGTAGCTGCACTTACTAACAATGTT seq:1188 + 38 0 0 1 0 0 0
  25.  
  26. 7 TTCAAACTGTCAAACCCGGTAATTTTAA seq:1220 + 33 0 0 1 0 0 0
  27.  
  28. 8 TTCTATGACTTTGCTGTGTCTAAGGGTT seq:1255 + 42 0 0 1 0 0 0
  29.  
  30. 9 TTCCTTAAAGAAACCCTTAGACACAGCA seq:1266 - 38 0 0 1 0 0 0
  31.  
  32. 10 TTCCTTCCTTAAAGAAACCCTTAGACAC seq:1270 - 38 0 0 1 0 0 0
  33.  
  34. 11 TTCAACAGAACTTCCTTCCTTAAAGAAA seq:1281 - 33 0 0 1 0 0 0
  35.  
  36. 12 TTCTTTAAGGAAGGAAGTTCTGTTGAAT seq:1282 + 33 0 0 1 0 0 0
  37.  
  38. 13 TTCTGTTGAATTAAAACACTTCTTCTTT seq:1299 + 25 0 0 1 0 0 0
  39.  
  40. 14 TTCTTCTTTGCTCAGGATGGTAATGCTG seq:1318 + 46 0 0 1 0 0 0
  41.  
  42. 15 TTCTTTGCTCAGGATGGTAATGCTGCTA seq:1321 + 46 0 0 1 0 0 0
  43.  
  44. 16 TTCCTAAAAACTAATTGTTGTCGCTTCC seq:142 + 33 0 0 1 0 0 0
  45.  
  46. 17 TTCTTGGAAGCGACAACAATTAGTTTTT seq:147 - 33 0 0 1 0 0 0
  47.  
  48. 18 TTCCATTTAATAAATGGGGTAAGGCTAG seq:1511 + 33 0 0 1 0 0 0
  49.  
  50. 19 TTCGTCCTTTTCTTGGAAGCGACAACAA seq:156 - 42 0 0 1 0 0 0
  51.  
  52. 20 TTCAATGAGTTATGAGGATCAAGATGCA seq:1551 + 38 0 0 1 0 0 0
  53.  
  54. 21 TTCGCATATACAAAACGTAATGTCATCC seq:1582 + 33 0 0 1 0 0 0
  55.  
  56. 22 TTCATTTGAGTTATAGTAGGGATGACAT seq:1601 - 33 0 0 1 0 0 0
  57.  
  58. 23 TTCTTTGCACTAATGGCATACTTAAGAT seq:1628 - 33 0 0 1 0 0 0
  59.  
  60. 24 TTCCAAGAAAAGGACGAAGATGACAATT seq:166 + 33 0 0 1 0 0 0
  61.  
  62. 25 TTCAATAATTTTTGATGAAACTGTCTAT seq:1703 - 21 0 0 1 0 0 0
  63.  
  64. 26 TTCATCAAAAATTATTGAAATCAATAGC seq:1712 + 21 0 0 1 0 0 0
  65.  
  66. 27 TTCTACATCACTATAAACAGTTTTTAAC seq:1803 - 25 0 0 1 0 0 0
  67.  
  68. 28 TTCTATAGATTAGCTAATGAGTGTGCTC seq:1954 + 38 0 0 1 0 0 0
  69.  
  70. 29 TTCTTACTTTGTAGTTAAGAGACACACT seq:201 + 33 0 0 1 0 0 0
  71.  
  72. 30 TTCCACCTGGTTTAACATATAGTGAACC seq:2011 - 38 0 0 1 0 0 0
  73.  
  74. 31 TTCACTATATGTTAAACCAGGTGGAACC seq:2013 + 42 0 0 1 0 0 0
  75.  
  76. 32 TTCTATAGAGACACTCATAAAGTCTGTG seq:2173 - 38 0 0 1 0 0 0
  77.  
  78. 33 TTCATGTTGGTAGTTAGAGAAAGTGTGT seq:222 - 38 0 0 1 0 0 0
  79.  
  80. 34 TTCTTCATGTTGGTAGTTAGAGAAAGTG seq:225 - 38 0 0 1 0 0 0
  81.  
  82. 35 TTCTCAATGATGATACTCTCTGACGATG seq:2257 + 42 0 0 1 0 0 0
  83.  
  84. 36 TTCTCTAACTACCAACATGAAGAAACAA seq:229 + 33 0 0 1 0 0 0
  85.  
  86. 37 TTCAATAGCACTTATGCATCTCAAGGTC seq:2296 + 42 0 0 1 0 0 0
  87.  
  88. 38 TTCTTTATTATCAAAACAATGTTTTTAT seq:2354 + 12 0 0 1 0 0 0
  89.  
  90. 39 TTCAGACATAAAAACATTGTTTTGATAA seq:2361 - 21 0 0 1 0 0 0
  91.  
  92. 40 TTCTTGATGGATCTGGGTAAGGAAGGTA seq:2482 - 46 0 0 1 0 0 0
  93.  
  94. 41 TTCCTTACCCAGATCCATCAAGAATCCT seq:2486 + 42 0 0 1 0 0 0
  95.  
  96. 42 TTCAATCATAAGTGTACCATCTGTTTTT seq:2544 - 29 0 0 1 0 0 0
  97.  
  98. 43 TTCGTGTCTTTAGCTATAGATGCTTACC seq:2575 + 38 0 0 1 0 0 0
  99.  
  100. 44 TTCTTATGTATTGTAAGTACAAATGAAA seq:2641 - 21 0 0 1 0 0 0
  101.  
  102. 45 TTCATTTGTACTTACAATACATAAGAAA seq:2642 + 21 0 0 1 0 0 0
  103.  
  104. 46 TTCTGTTATGCTTACTAATGATAACACT seq:2709 + 29 0 0 1 0 0 0
  105.  
  106. 47 TTCCCAATACCTTGAAGTGTTATCATTA seq:2724 - 29 0 0 1 0 0 0
  107.  
  108. 48 TTCTAAACTTAAAGAAGTCATGTTTAGC seq:289 - 29 0 0 1 0 0 0
  109.  
  110. 49 TTCTTTAAGTTTAGAATAGACGGTGACA seq:301 + 33 0 0 1 0 0 0
  111.  
  112. 50 TTCAATAAAAAGGACTGGTATGATTTTG seq:469 + 29 0 0 1 0 0 0
  113.  
  114. 51 TTCTACAAAATCATACCAGTCCTTTTTA seq:474 - 29 0 0 1 0 0 0
  115.  
  116. 52 TTCGCATGGCATCACAGAATTGTACTGT seq:565 - 42 0 0 1 0 0 0
  117.  
  118. 53 TTCTGTGATGCCATGCGAAATGCTGGTA seq:574 + 50 0 0 1 0 0 0
  119.  
  120. 54 TTCGGTGATTTCATACAAACCACGCCAG seq:655 + 46 0 0 1 0 0 0
  121.  
  122. 55 TTCCTGTTGTAGATTCTTATTATTCATT seq:692 + 21 0 0 1 0 0 0
  123.  
  124. 56 TTCTTATTATTCATTGTTAATGCCTATA seq:705 + 21 0 0 1 0 0 0
  125.  
  126. 57 TTCATTGTTAATGCCTATATTAACCTTG seq:714 + 29 0 0 1 0 0 0
  127.  
  128. 58 TTCCGTGAAGTCATATTTTAACAAATCC seq:804 - 29 0 0 1 0 0 0
  129.  
  130. 59 TTCTGCATTGTGCAAACTTTAATGTTTT seq:920 + 29 0 0 1 0 0 0
  131.  
  132. 60 TTCTCTACAGTGTTCCCACCTACAAGTT seq:949 + 46 0 0 1 0 0 0
  133.  
  134. 61 TTCCCACCTACAAGTTTTGGACCACTAG seq:961 + 46 0 0 1 0 0 0
  135.  
  136. 62 TTCTCACTAGTGGTCCAAAACTTGTAGG seq:967 - 46 0 0 1 0 0 0
  137.  
  138. 63 TTCCAATTACTACAGTAGCTCCTCTAGT seq:1744 - 38 1 0 1 0 0 0
  139.  
  140. 64 TTCTATGGTGGTTGGCACAACATGTTAA seq:1780 + 42 1 0 1 0 0 0
  141.  
  142. 65 TTCTAAGCATGTTAGGCATGGCTCTATC seq:1867 - 46 1 0 1 0 0 0
  143.  
  144. 66 TTCTTGCTCGCAAACATACAACGTGTTG seq:1910 + 46 1 0 1 0 0 0
  145.  
  146. 67 TTCACTCAATACTTGAGCACACTCATTA seq:1968 - 38 1 0 1 0 0 0
  147.  
  148. 68 TTCACAAAGTCTGTGTCAACATCTCTAT seq:2201 - 38 1 0 1 0 0 0
  149.  
  150. 69 TTCTTTATGCTAGCCACTAGACCTTGAG seq:2315 - 46 1 0 1 0 0 0
  151.  
  152. 70 TTCATGAGGTCCTTTAGTAAGGTCAGTC seq:2406 - 46 1 0 1 0 0 0
  153.  
  154. 71 TTCAAGGTATTGGGAACCTGAGTTTTAT seq:2736 + 38 1 0 1 0 0 0
  155.  
  156. 72 TTCATCAAAATGCCTTAAAGCATAGACG seq:381 - 38 1 0 1 0 0 0
  157.  
  158. 73 TTCTTTTAATGTGTCACAATTACCTTCA seq:405 - 29 1 0 1 0 0 0
  159.  
  160. 74 TTCACCTAAGTTGGCGTATACGCGTAAT seq:513 - 46 1 0 1 0 0 0
  161.  
  162. 75 TTCATACAAACCACGCCAGGTAGTGGAG seq:664 + 54 1 0 1 0 0 0
  163.  
  164. 76 TTCAACTACAAATAGTAGTTGTCTGATA seq:1395 - 29 2 0 1 0 0 0
  165.  
  166. 77 TTCACGGAAGAGAGGTTAAAACTCTTTG seq:823 + 42 2 0 1 0 0 0
  167.  
  168. ​
  169.  
  170. ​
  171.  
  172. Polyamerase RNA
  173. ​
  174.  
  175. gtcagctgatgcacaatcgtttttaaacgggtttgcggtgtaagtgcagcccgtcttacaccgtgcggcacaggcactagtactgatgtcgtatacagggcttttgacatctacaatgataaagtagctggttttgctaaattcctaaaaactaattgttgtcgcttccaagaaaaggacgaagatgacaatttaattgattcttactttgtagttaagagacacactttctctaactaccaacatgaagaaacaatttataatttacttaaggattgtccagctgttgctaaacatgacttctttaagtttagaatagacggtgacatggtaccacatatatcacgtcaacgtcttactaaatacacaatggcagacctcgtctatgctttaaggcattttgatgaaggtaattgtgacacattaaaagaaatacttgtcacatacaattgttgtgatgatgattatttcaataaaaaggactggtatgattttgtagaaaacccagatatattacgcgtatacgccaacttaggtgaacgtgtacgccaagctttgttaaaaacagtacaattctgtgatgccatgcgaaatgctggtattgttggtgtactgacattagataatcaagatctcaatggtaactggtatgatttcggtgatttcatacaaaccacgccaggtagtggagttcctgttgtagattcttattattcattgttaatgcctatattaaccttgaccagggctttaactgcagagtcacatgttgacactgacttaacaaagccttacattaagtgggatttgttaaaatatgacttcacggaagagaggttaaaactctttgaccgttattttaaatattgggatcagacataccacccaaattgtgttaactgtttggatgacagatgcattctgcattgtgcaaactttaatgttttattctctacagtgttcccacctacaagttttggaccactagtgagaaaaatatttgttgatggtgttccatttgtagtttcaactggataccacttcagagagctaggtgttgtacataatcaggatgtaaacttacatagctctagacttagttttaaggaattacttgtgtatgctgctgaccctgctatgcacgctgcttctggtaatctattactagataaacgcactacgtgcttttcagtagctgcacttactaacaatgttgcttttcaaactgtcaaacccggtaattttaacaaagacttctatgactttgctgtgtctaagggtttctttaaggaaggaagttctgttgaattaaaacacttcttctttgctcaggatggtaatgctgctatcagcgattatgactactatcgttataatctaccaacaatgtgtgatatcagacaactactatttgtagttgaagttgttgataagtactttgattgttacgatggtggctgtattaatgctaaccaagtcatcgtcaacaacctagacaaatcagctggttttccatttaataaatggggtaaggctagactttattatgattcaatgagttatgaggatcaagatgcacttttcgcatatacaaaacgtaatgtcatccctactataactcaaatgaatcttaagtatgccattagtgcaaagaatagagctcgcaccgtagctggtgtctctatctgtagtactatgaccaatagacagtttcatcaaaaattattgaaatcaatagccgccactagaggagctactgtagtaattggaacaagcaaattctatggtggttggcacaacatgttaaaaactgtttatagtgatgtagaaaaccctcaccttatgggttgggattatcctaaatgtgatagagccatgcctaacatgcttagaattatggcctcacttgttcttgctcgcaaacatacaacgtgttgtagcttgtcacaccgtttctatagattagctaatgagtgtgctcaagtattgagtgaaatggtcatgtgtggcggttcactatatgttaaaccaggtggaacctcatcaggagatgccacaactgcttatgctaatagtgtttttaacatttgtcaagctgtcacggccaatgttaatgcacttttatctactgatggtaacaaaattgccgataagtatgtccgcaatttacaacacagactttatgagtgtctctatagaaatagagatgttgacacagactttgtgaatgagttttacgcatatttgcgtaaacatttctcaatgatgatactctctgacgatgctgttgtgtgtttcaatagcacttatgcatctcaaggtctagtggctagcataaagaactttaagtcagttctttattatcaaaacaatgtttttatgtctgaagcaaaatgttggactgagactgaccttactaaaggacctcatgaattttgctctcaacatacaatgctagttaaacagggtgatgattatgtgtaccttccttacccagatccatcaagaatcctaggggccggctgttttgtagatgatatcgtaaaaacagatggtacacttatgattgaacggttcgtgtctttagctatagatgcttacccacttactaaacatcctaatcaggagtatgctgatgtctttcatttgtacttacaatacataagaaagctacatgatgagttaacaggacacatgttagacatgtattctgttatgcttactaatgataacacttcaaggtattgggaacctgagttttatgaggctatgtacacaccgcatacagtcttacagg
  176.  
  177. ​
  178.  
  179. EXPASY translation tool: https://web.expasy.org/translate/
  180. Full Coronavirus genome: https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3?report=fasta
  181. RNA polyamerase https://www.ncbi.nlm.nih.gov/protein/YP_009725307.1?report=genpept
  182. ​
  183.  
  184. Coronavirus 3'5' exoribonuclease
  185. gctgaaaatgtaacaggactctttaaagattgtagtaaggtaatcactgggttacatcctacacaggcacctacacacctcagtgttgacactaaattcaaaactgaaggtttatgtgttgacatacctggcatacctaaggacatgacctatagaagactcatctctatgatgggttttaaaatgaattatcaagttaatggttaccctaacatgtttatcacccgcgaagaagctataagacatgtacgtgcatggattggcttcgatgtcgaggggtgtcatgctactagagaagctgttggtaccaatttacctttacagctaggtttttctacaggtgttaacctagttgctgtacctacaggttatgttgatacacctaataatacagatttttccagagttagtgctaaaccaccgcctggagatcaatttaaacacctcataccacttatgtacaaaggacttccttggaatgtagtgcgtataaagattgtacaaatgttaagtgacacacttaaaaatctctctgacagagtcgtatttgtcttatgggcacatggctttgagttgacatctatgaagtattttgtgaaaataggacctgagcgcacctgttgtctatgtgatagacgtgccacatgcttttccactgcttcagacacttatgcctgttggcatcattctattggatttgattacgtctataatccgtttatgattgatgttcaacaatggggttttacaggtaacctacaaagcaaccatgatctgtattgtcaagtccatggtaatgcacatgtagctagttgtgatgcaatcatgactaggtgtctagctgtccacgagtgctttgttaagcgtgttgactggactattgaatatcctataattggtgatgaactgaagattaatgcggcttgtagaaaggttcaacacatggttgttaaagctgcattattagcagacaaattcccagttcttcacgacattggtaaccctaaagctattaagtgtgtacctcaagctgatgtagaatggaagttctatgatgcacagccttgtagtgacaaagcttataaaatagaagaattattctattcttatgccacacattctgacaaattcacagatggtgtatgcctattttggaattgcaatgtcgatagatatcctgctaattccattgtttgtagatttgacactagagtgctatctaaccttaacttgcctggttgtgatggtggcagtttgtatgtaaataaacatgcattccacacaccagcttttgataaaagtgcttttgttaatttaaaacaattaccatttttctattactctgacagtccatgtgagtctcatggaaaacaagtagtgtcagatatagattatgtaccactaaagtctgctacgtgtataacacgttgcaatttaggtggtgctgtctgtagacatcatgctaatgagtacagattgtatctcgatgcttataacatgatgatctcagctggctttagcttgtgggtttacaaacaatttgatacttataacctctggaacacttttacaagacttcaga
  186.  
  187. Programmable Inhibition and Detection of RNA Viruses Using Cas13 https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30698-7
  188. ​
  189.  
  190. crRNA design helper
  191. http://bioinfolab.miamioh.edu/CRISPR-RT/interface/C2c2.php
  192.  
  193. AsCpf1 guided nuclease on-target genomic hits of gRNA for coronavirus polyamerase
  194. http://grna.ctegd.uga.edu/jobs/jobs/zADMqfxw0Cu4uCEpCLsMp6Xc1Vh9E7-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.blastout.parsed.on.html
  195.  
  196. http://grna.ctegd.uga.edu/jobs/jobs/zADMqfxw0Cu4uCEpCLsMp6Xc1Vh9E7-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.score.html
  197.  
  198. http://grna.ctegd.uga.edu/jobs/jobs/nfhRgKsv75BEv4qG6zCmlpV3pEt9db-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.score.html
  199.  
  200. FnCpf1 guided nuclease on-target genomic hits of gRNA for coronavirus polyamerase
  201. http://grna.ctegd.uga.edu/jobs/jobs/vhOjQp4lHcxqEhze8s2OjDkaG7BVm3-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.score.html
  202.  
  203. http://grna.ctegd.uga.edu/jobs/jobs/vhOjQp4lHcxqEhze8s2OjDkaG7BVm3-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.blastout.parsed.on.html
  204.  
  205. http://grna.ctegd.uga.edu/jobs/jobs/vhOjQp4lHcxqEhze8s2OjDkaG7BVm3-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.blastout.parsed.off.html
  206.  
  207. LbCpf1 guided nuclease on-target genomic hits of gRNA for coronavirus polyamerase
  208. http://grna.ctegd.uga.edu/jobs/jobs/nfhRgKsv75BEv4qG6zCmlpV3pEt9db-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.score.html
  209.  
  210. http://grna.ctegd.uga.edu/jobs/jobs/nfhRgKsv75BEv4qG6zCmlpV3pEt9db-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.blastout.parsed.on.html
  211.  
  212. http://grna.ctegd.uga.edu/jobs/jobs/nfhRgKsv75BEv4qG6zCmlpV3pEt9db-SARS2019/SARS2019.gRNA.fasta.SARS2.txt.blastout.parsed.on.html
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