AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG030239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030239 MtrunA17_Chr6g0449861 82.865 356 50 4 1 354 9 355 0.0 582
MsaG030239 MtrunA17_Chr6g0457851 65.922 358 106 3 1 354 11 356 7.34e-166 467
MsaG030239 MtrunA17_Chr6g0449851 62.464 349 90 5 1 348 1 309 8.48e-149 422
MsaG030239 MtrunA17_Chr1g0212151 60.111 361 111 5 1 347 1 342 1.62e-139 400
MsaG030239 MtrunA17_Chr1g0212471 32.961 179 119 1 1 179 1 178 6.00e-32 119
MsaG030239 MtrunA17_Chr4g0059631 37.427 171 99 2 1 171 1 163 8.00e-31 117
MsaG030239 MtrunA17_Chr4g0022641 34.731 167 106 1 1 167 1 164 7.88e-28 112
MsaG030239 MtrunA17_Chr2g0303981 37.013 154 92 2 3 155 5 154 2.00e-27 106
MsaG030239 MtrunA17_Chr3g0107351 31.288 163 98 5 3 157 2 158 1.23e-15 73.6
MsaG030239 MtrunA17_Chr3g0107341 34.146 164 92 6 3 157 2 158 1.90e-15 73.2
MsaG030239 MtrunA17_Chr1g0197321 28.221 163 103 4 1 155 1 157 7.53e-15 71.2
MsaG030239 MtrunA17_Chr5g0432691 30.909 165 100 5 1 157 1 159 8.57e-15 71.2
MsaG030239 MtrunA17_Chr3g0107361 31.902 163 97 6 3 157 2 158 2.25e-14 70.1
MsaG030239 MtrunA17_Chr3g0107331 33.628 113 68 3 3 114 2 108 3.74e-14 69.7
MsaG030239 MtrunA17_Chr3g0107381 23.077 234 148 8 1 215 1 221 3.95e-14 70.9
MsaG030239 MtrunA17_Chr4g0014321 36.842 114 65 4 1 113 1 108 3.02e-13 68.6
MsaG030239 MtrunA17_Chr3g0110131 27.347 245 140 9 1 215 1 237 3.45e-13 68.6
MsaG030239 MtrunA17_Chr5g0420351 31.481 108 68 2 1 108 1 102 4.99e-13 66.2
MsaG030239 MtrunA17_Chr1g0197261 28.395 162 103 4 1 155 1 156 8.14e-13 65.5
MsaG030239 MtrunA17_Chr2g0283941 32.203 118 72 4 2 118 3 113 9.79e-13 67.4
MsaG030239 MtrunA17_Chr8g0351751 33.962 106 61 4 1 103 1 100 3.04e-12 65.9
MsaG030239 MtrunA17_Chr1g0188681 32.743 113 70 3 1 113 1 107 6.20e-12 63.2
MsaG030239 MtrunA17_Chr1g0159661 27.211 147 89 3 1 144 1 132 8.84e-12 63.2
MsaG030239 MtrunA17_Chr8g0379021 28.947 152 78 6 2 136 12 150 2.02e-11 62.0
MsaG030239 MtrunA17_Chr1g0197461 40.506 79 41 3 3 81 2 74 5.14e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030239 AT5G55690.1 33.209 268 129 12 1 257 1 229 5.89e-26 105
MsaG030239 AT5G55690.2 33.209 268 129 12 1 257 1 229 5.89e-26 105
MsaG030239 AT5G58890.1 35.211 142 87 3 6 145 6 144 3.25e-18 84.3
MsaG030239 AT3G18650.1 36.296 135 72 5 16 144 31 157 4.17e-14 73.2
MsaG030239 AT1G22590.2 29.814 161 102 4 1 156 1 155 9.63e-14 68.9
MsaG030239 AT1G65330.1 24.825 286 160 11 3 283 2 237 2.20e-13 70.1
MsaG030239 AT1G31640.1 22.807 228 144 8 3 222 2 205 7.75e-13 69.7
MsaG030239 AT3G05860.2 36.364 77 43 2 1 77 1 71 2.53e-12 65.9
MsaG030239 AT3G05860.3 37.662 77 42 3 1 77 1 71 2.53e-12 66.6
MsaG030239 AT3G05860.1 37.662 77 42 3 1 77 1 71 3.32e-12 66.2
MsaG030239 AT5G27960.1 27.742 155 105 3 5 158 3 151 1.15e-11 65.5
MsaG030239 AT2G28700.1 25.269 186 129 5 1 185 1 177 1.33e-11 65.5
MsaG030239 AT1G65300.1 31.818 110 68 4 5 113 4 107 3.38e-11 63.5
MsaG030239 AT5G26650.1 30.508 118 75 3 5 121 3 114 3.72e-11 64.3

Find 62 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGTCTTTCGGCCATGTTTC+AGG 0.186338 6:+5335444 None:intergenic
AAGCTCTCAACCTTCTTCTA+TGG 0.280995 6:-5334926 MsaT030239.1:CDS
TTGAAGAATATTTGAATCAT+AGG 0.295703 6:+5334615 None:intergenic
ATCTTCCTAGATTTCTCCTT+TGG 0.315866 6:+5335588 None:intergenic
TATGCTAGAAGGAGATCTTC+TGG 0.319876 6:-5335166 MsaT030239.1:CDS
CTTCTACCATGTAGAGTCTA+AGG 0.320406 6:-5334887 MsaT030239.1:CDS
GATGAATCTTTCAATTCTCT+TGG 0.356712 6:-5335258 MsaT030239.1:CDS
AAAATATTCTTGAACATCAT+AGG 0.366937 6:+5335359 None:intergenic
CTCTATGCTCCCAACTTTGA+AGG 0.376410 6:-5335483 MsaT030239.1:CDS
GAGGTTATTTGCTAGGATCT+TGG 0.377459 6:-5335223 MsaT030239.1:CDS
TACCCTTGGCCTTCAAAGTT+GGG 0.397006 6:+5335474 None:intergenic
GTATTGCAAAAGAGAAAGAT+TGG 0.420157 6:-5335564 MsaT030239.1:CDS
CTAAAGATGAATATGCTAGA+AGG 0.421397 6:-5335177 MsaT030239.1:CDS
ATTCATTAAGTAGATGTTCA+TGG 0.428966 6:+5334638 None:intergenic
TCATTCCAAAGGAGAAATCT+AGG 0.429671 6:-5335593 MsaT030239.1:CDS
TGCACGAGATTGAGGCTACT+TGG 0.432844 6:+5335075 None:intergenic
GCCACCAATGATCTCAAAAT+CGG 0.446186 6:-5334793 MsaT030239.1:CDS
ACTTGGATTTGAGTCTAAGT+AGG 0.446409 6:+5335092 None:intergenic
GAAATTCTCTTTGCGCACTT+TGG 0.447716 6:+5335302 None:intergenic
ATACCCTTGGCCTTCAAAGT+TGG 0.453181 6:+5335473 None:intergenic
AGCATCAACATCACAAAGAA+TGG 0.454348 6:+5335515 None:intergenic
TAAGTAGATGTTCATGGGAT+AGG 0.458812 6:+5334644 None:intergenic
TCAAGATGAAGTATCAAACT+TGG 0.459665 6:-5335281 MsaT030239.1:CDS
ACTATAACACAACAATTGAT+AGG 0.461207 6:-5335392 MsaT030239.1:CDS
CTCTTGGACATGAACAATTG+AGG 0.461839 6:-5335242 MsaT030239.1:CDS
AACAATTGAGGTTATTTGCT+AGG 0.466918 6:-5335230 MsaT030239.1:CDS
TTTCAGGTTCAGCATACCCT+TGG 0.467005 6:+5335460 None:intergenic
TAGATTGCATGCATCAAGCT+TGG 0.474063 6:+5335197 None:intergenic
AAGCTCTCAACCCTCTCATA+TGG 0.474118 6:-5334962 MsaT030239.1:CDS
TTAAAATCAATCTGCTTGCA+AGG 0.480005 6:+5334841 None:intergenic
ATGCTAGAAGGAGATCTTCT+GGG 0.483728 6:-5335165 MsaT030239.1:CDS
TAAGTGGCCAAAACCCTAAA+GGG 0.486281 6:+5334995 None:intergenic
TTATCACTAATATTCATCAA+TGG 0.491553 6:+5335021 None:intergenic
GGAAGAGCAGGCATAGCAAT+GGG 0.507599 6:+5334685 None:intergenic
TTCATTAAGTAGATGTTCAT+GGG 0.507722 6:+5334639 None:intergenic
ATGGTAGAAGCTCTGTGCTC+GGG 0.509126 6:+5334900 None:intergenic
GCTCCCAACTTTGAAGGCCA+AGG 0.509495 6:-5335477 MsaT030239.1:CDS
ATAAGTGGCCAAAACCCTAA+AGG 0.517760 6:+5334994 None:intergenic
GAGCTTTGATCCGATATAAG+TGG 0.519447 6:+5334979 None:intergenic
CTTGGATTTGAGTCTAAGTA+GGG 0.520886 6:+5335093 None:intergenic
TGGCATTAGCATCAACATGA+TGG 0.525287 6:+5334812 None:intergenic
CATGGTAGAAGCTCTGTGCT+CGG 0.530303 6:+5334899 None:intergenic
TGTTCGTAGCAAATGGGTCG+TGG 0.542436 6:-5335633 None:intergenic
CAAGATGAAGTATCAAACTT+GGG 0.553379 6:-5335280 MsaT030239.1:CDS
TGCAGTTGAAACCATATGAG+AGG 0.566645 6:+5334951 None:intergenic
TGTTCAACTACATGTATGAA+AGG 0.567684 6:-5334585 MsaT030239.1:CDS
GGCATTAGCATCAACATGAT+GGG 0.570214 6:+5334813 None:intergenic
TACCATGTAGAGTCTAAGGC+AGG 0.584231 6:-5334883 MsaT030239.1:CDS
ATCTGTGGAATTCATTCCAA+AGG 0.586943 6:-5335604 MsaT030239.1:CDS
CTCCCAACTTTGAAGGCCAA+GGG 0.588006 6:-5335476 MsaT030239.1:CDS
TCACTAATATTCATCAATGG+AGG 0.597003 6:+5335024 None:intergenic
TAAAATCAATCTGCTTGCAA+GGG 0.599195 6:+5334842 None:intergenic
GCTCGGGAAACCATAGAAGA+AGG 0.599676 6:+5334916 None:intergenic
AGGAAGAGCAGGCATAGCAA+TGG 0.601693 6:+5334684 None:intergenic
AGGTGCAACGAATTCTTCAA+AGG 0.607816 6:-5335416 MsaT030239.1:CDS
TACCTGCCTTAGACTCTACA+TGG 0.609420 6:+5334881 None:intergenic
TTAGCACCACACTATTACAA+CGG 0.610413 6:-5334733 MsaT030239.1:CDS
GGGTCGTGGAAGAGTATCTG+TGG 0.635324 6:-5335619 MsaT030239.1:CDS
GGTATGCTGAACCTGAAACA+TGG 0.642114 6:-5335455 MsaT030239.1:CDS
GTATTTCCGTTGTAATAGTG+TGG 0.643654 6:+5334727 None:intergenic
ATGGCCGAAAGACACAAAAG+AGG 0.657999 6:-5335436 MsaT030239.1:CDS
GCAGTTGAAACCATATGAGA+GGG 0.704855 6:+5334952 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 5334579 5335643 5334579 ID=MsaG030239
Chr6 mRNA 5334579 5335643 5334579 ID=MsaT030239.1;Parent=MsaG030239
Chr6 exon 5334579 5335643 5334579 ID=MsaT030239.1.exon1;Parent=MsaT030239.1
Chr6 CDS 5334579 5335643 5334579 ID=cds.MsaT030239.1;Parent=MsaT030239.1
Gene Sequence

>MsaT030239.1

ATGGGTCGTGGAAGAGTATCTGTGGAATTCATTCCAAAGGAGAAATCTAGGAAGATAGTATTGCAAAAGAGAAAGATTGGTTTGATGAAAAAAGTTGAGGAACTTTCCATTCTTTGTGATGTTGATGCTTGTGTGATTCTCTATGCTCCCAACTTTGAAGGCCAAGGGTATGCTGAACCTGAAACATGGCCGAAAGACACAAAAGAGGTGCAACGAATTCTTCAAAGGTACTATAACACAACAATTGATAGGCGTCTTAAGACCTATGATGTTCAAGAATATTTTAACGAAAGGATGAAAAAAGTTGAATTTGAGATTTCCAAAGTGCGCAAAGAGAATTTCAAGATGAAGTATCAAACTTGGGATGAATCTTTCAATTCTCTTGGACATGAACAATTGAGGTTATTTGCTAGGATCTTGGATTCCAAGCTTGATGCATGCAATCTAAAGATGAATATGCTAGAAGGAGATCTTCTGGGAAAATCAATAGCTCTTGAGACAAACAAGATTGATAATCTTAATAGTTCTCCCTACTTAGACTCAAATCCAAGTAGCCTCAATCTCGTGCAAAACAACATGTCTCAAGCACACATTTATCCTCCATTGATGAATATTAGTGATAAAAACCCTTTAGGGTTTTGGCCACTTATATCGGATCAAAGCTCTCAACCCTCTCATATGGTTTCAACTGCACAAAGCTCTCAACCTTCTTCTATGGTTTCCCGAGCACAGAGCTTCTACCATGTAGAGTCTAAGGCAGGTATATATGCACAATCTTACCCTTGCAAGCAGATTGATTTTAATTGGACCCATCATGTTGATGCTAATGCCACCAATGATCTCAAAATCGGTATGAAGAAGAATGATGAAGTTGAAAATGATAAAAACTTAGCACCACACTATTACAACGGAAATACATTGACATTGCAATCATATCCCATTGCTATGCCTGCTCTTCCTTTTCAAAATCTTTCAAACCTATCCCATGAACATCTACTTAATGAATCCTATGATTCAAATATTCTTCAAGCTCAAATGTTCAACTACATGTATGAAAGGAAGTAG
Protein sequence

>MsaT030239.1

MGRGRVSVEFIPKEKSRKIVLQKRKIGLMKKVEELSILCDVDACVILYAPNFEGQGYAEPETWPKDTKEVQRILQRYYNTTIDRRLKTYDVQEYFNERMKKVEFEISKVRKENFKMKYQTWDESFNSLGHEQLRLFARILDSKLDACNLKMNMLEGDLLGKSIALETNKIDNLNSSPYLDSNPSSLNLVQNNMSQAHIYPPLMNISDKNPLGFWPLISDQSSQPSHMVSTAQSSQPSSMVSRAQSFYHVESKAGIYAQSYPCKQIDFNWTHHVDANATNDLKIGMKKNDEVENDKNLAPHYYNGNTLTLQSYPIAMPALPFQNLSNLSHEHLLNESYDSNILQAQMFNYMYERK*