AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0527590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0527590 MtrunA17_Chr2g0290441 88.889 135 1 1 4 124 234 368 1.63e-75 236
Msa0527590 MtrunA17_Chr4g0076151 47.403 154 57 2 4 133 266 419 9.28e-41 143
Msa0527590 MtrunA17_Chr2g0290431 51.128 133 51 1 4 122 109 241 3.28e-36 129
Msa0527590 MtrunA17_Chr2g0290451 50.376 133 52 1 4 122 232 364 6.54e-36 129
Msa0527590 MtrunA17_Chr4g0054821 36.567 134 71 1 5 124 276 409 8.34e-25 98.2
Msa0527590 MtrunA17_Chr7g0257371 32.353 136 76 2 6 125 307 442 7.63e-17 75.5
Msa0527590 MtrunA17_Chr3g0099661 32.824 131 74 1 6 122 434 564 7.52e-16 72.8
Msa0527590 MtrunA17_Chr3g0099661 29.286 140 84 3 5 129 222 361 1.12e-12 63.5
Msa0527590 MtrunA17_Chr3g0099661 38.095 84 52 0 43 126 345 428 6.52e-12 61.6
Msa0527590 MtrunA17_Chr3g0099661 25.564 133 84 1 8 125 260 392 1.15e-11 60.8
Msa0527590 MtrunA17_Chr7g0220501 29.231 130 78 1 8 123 408 537 9.83e-14 66.6
Msa0527590 MtrunA17_Chr7g0220501 32.584 89 60 0 43 131 352 440 1.59e-11 60.5
Msa0527590 MtrunA17_Chr7g0220481 27.692 130 80 1 8 123 373 502 5.69e-13 64.7
Msa0527590 MtrunA17_Chr5g0446971 34.940 83 54 0 43 125 44 126 2.26e-12 60.5
Msa0527590 MtrunA17_Chr5g0446971 42.647 68 39 0 43 110 79 146 1.62e-11 58.2
Msa0527590 MtrunA17_Chr5g0396041 28.099 121 73 1 25 131 442 562 7.70e-12 61.2
Msa0527590 MtrunA17_Chr5g0412071 33.333 108 66 2 26 130 419 523 1.19e-11 60.8
Msa0527590 MtrunA17_Chr8g0391651 28.333 120 65 1 4 123 362 460 2.07e-11 60.1
Msa0527590 MtrunA17_Chr3g0133151 28.058 139 83 3 1 122 245 383 3.31e-11 59.3
Msa0527590 MtrunA17_Chr1g0166071 31.325 83 57 0 44 126 141 223 8.50e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0527590 AT4G16390.1 48.026 152 55 2 4 131 260 411 4.67e-42 147
Msa0527590 AT5G46580.1 38.060 134 69 1 5 124 272 405 3.68e-22 91.3
Msa0527590 AT2G31400.1 31.061 132 77 1 6 123 426 557 7.23e-16 73.2
Msa0527590 AT2G31400.2 31.061 132 77 1 6 123 426 557 1.01e-15 72.8
Msa0527590 AT5G02860.1 29.545 132 79 1 5 122 400 531 4.73e-15 70.9
Msa0527590 AT5G02860.1 27.941 136 83 3 5 125 189 324 2.78e-12 63.2
Msa0527590 AT5G02860.1 39.506 81 49 0 46 126 315 395 2.43e-11 60.5
Msa0527590 AT5G02860.1 32.530 83 56 0 43 125 697 779 4.73e-11 59.3
Msa0527590 AT5G02860.4 29.545 132 79 1 5 122 400 531 4.73e-15 70.9
Msa0527590 AT5G02860.4 27.941 136 83 3 5 125 189 324 2.78e-12 63.2
Msa0527590 AT5G02860.4 39.506 81 49 0 46 126 315 395 2.43e-11 60.5
Msa0527590 AT5G02860.4 32.530 83 56 0 43 125 697 779 4.73e-11 59.3
Msa0527590 AT5G02860.2 29.545 132 79 1 5 122 400 531 4.73e-15 70.9
Msa0527590 AT5G02860.2 27.941 136 83 3 5 125 189 324 2.78e-12 63.2
Msa0527590 AT5G02860.2 39.506 81 49 0 46 126 315 395 2.43e-11 60.5
Msa0527590 AT5G02860.2 32.530 83 56 0 43 125 697 779 4.73e-11 59.3
Msa0527590 AT5G02860.5 29.545 132 79 1 5 122 400 531 4.73e-15 70.9
Msa0527590 AT5G02860.5 27.941 136 83 3 5 125 189 324 2.78e-12 63.2
Msa0527590 AT5G02860.5 39.506 81 49 0 46 126 315 395 2.43e-11 60.5
Msa0527590 AT5G02860.5 32.530 83 56 0 43 125 697 779 4.73e-11 59.3
Msa0527590 AT5G02860.3 29.545 132 79 1 5 122 400 531 4.73e-15 70.9
Msa0527590 AT5G02860.3 27.941 136 83 3 5 125 189 324 2.78e-12 63.2
Msa0527590 AT5G02860.3 39.506 81 49 0 46 126 315 395 2.43e-11 60.5
Msa0527590 AT5G02860.3 32.530 83 56 0 43 125 697 779 4.73e-11 59.3
Msa0527590 AT4G20090.2 37.037 81 51 0 43 123 395 475 3.63e-13 65.5
Msa0527590 AT4G20090.1 37.037 81 51 0 43 123 395 475 3.63e-13 65.5
Msa0527590 AT1G11710.2 37.113 97 61 0 26 122 243 339 2.88e-12 62.8
Msa0527590 AT1G11710.1 37.113 97 61 0 26 122 272 368 2.93e-12 62.8
Msa0527590 AT2G41720.2 29.104 134 79 2 8 125 170 303 6.96e-12 62.0
Msa0527590 AT2G41720.3 29.104 134 79 2 8 125 302 435 7.10e-12 62.0
Msa0527590 AT5G39980.1 34.940 83 54 0 43 125 258 340 7.23e-12 61.6
Msa0527590 AT2G41720.1 29.104 134 79 2 8 125 302 435 7.61e-12 61.6
Msa0527590 AT1G77360.2 33.696 92 59 2 34 124 155 245 1.56e-11 60.8
Msa0527590 AT1G77360.1 33.696 92 59 2 34 124 191 281 1.58e-11 60.8
Msa0527590 AT1G79490.1 27.737 137 81 3 5 125 329 463 2.08e-11 60.5
Msa0527590 AT1G74750.2 30.769 91 63 0 43 133 392 482 2.44e-11 60.5
Msa0527590 AT1G74750.1 30.769 91 63 0 43 133 392 482 2.44e-11 60.5
Msa0527590 AT1G74750.4 30.769 91 63 0 43 133 392 482 2.44e-11 60.5
Msa0527590 AT1G74750.3 30.769 91 63 0 43 133 392 482 2.44e-11 60.5
Msa0527590 AT5G12100.1 28.058 139 84 2 1 123 224 362 2.89e-11 60.1
Msa0527590 AT1G51965.1 24.427 131 85 1 5 121 496 626 2.95e-11 60.1
Msa0527590 AT2G02150.1 25.899 139 87 2 1 123 272 410 3.68e-11 59.7
Msa0527590 AT2G02150.2 25.899 139 87 2 1 123 272 410 3.68e-11 59.7
Msa0527590 AT3G22670.1 23.134 134 89 1 3 122 287 420 5.97e-11 58.9
Msa0527590 AT3G18110.1 29.630 135 80 3 4 123 312 446 7.12e-11 58.9
Msa0527590 AT3G18110.1 24.627 134 87 1 6 125 279 412 9.61e-11 58.5
Msa0527590 AT3G06920.2 26.515 132 83 1 5 122 652 783 7.43e-11 58.9
Msa0527590 AT3G06920.3 26.515 132 83 1 5 122 652 783 7.43e-11 58.9
Msa0527590 AT3G06920.1 26.515 132 83 1 5 122 638 769 7.64e-11 58.9
Msa0527590 AT4G19440.4 29.927 137 78 3 5 125 289 423 8.14e-11 58.9
Msa0527590 AT4G19440.2 29.927 137 78 3 5 125 289 423 8.14e-11 58.9
Msa0527590 AT4G19440.3 29.927 137 78 3 5 125 289 423 8.14e-11 58.9
Msa0527590 AT4G19440.1 29.927 137 78 3 5 125 289 423 8.14e-11 58.9

Find 34 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTAAGATGTATGGGATAT+TGG 0.176636 3_4:+82054153 Msa0527590:CDS
ATTAAGATGTATGGGATATT+GGG 0.252748 3_4:+82054154 Msa0527590:CDS
GGGAACGTATGCAGCTCTTT+TGG 0.292517 3_4:+82054345 Msa0527590:CDS
TCTTGGTGTTAGGCCGAATA+TGG 0.299116 3_4:+82054219 Msa0527590:intron
AAAATGAGAAATGGGTTATT+AGG 0.337583 3_4:+82054110 Msa0527590:CDS
AGAAGCGTTGAGTGTGTATA+AGG 0.365785 3_4:+82054396 Msa0527590:CDS
AGAATGGATTTGTACCGAAC+TGG 0.376470 3_4:+82054323 Msa0527590:CDS
GCATTATACAAAACCATATT+CGG 0.387706 3_4:-82054232 None:intergenic
TCGGCTTTGATTAAGATGTA+TGG 0.388766 3_4:+82054145 Msa0527590:CDS
GGGATATTGGGGAATTATGA+TGG 0.405598 3_4:+82054166 Msa0527590:CDS
TGGGGAGAGCTAAGAGGGCT+AGG 0.405827 3_4:+82054269 Msa0527590:CDS
GAGAACAGGTAATGTTGATA+TGG 0.439246 3_4:+82054063 Msa0527590:intron
ATCAAAGCCGAAAACGCAAC+TGG 0.442434 3_4:-82054133 None:intergenic
TAATGCTTTGTTGTATGCTA+TGG 0.445887 3_4:+82054249 Msa0527590:CDS
TATAAGGAAATGAAGGAAAA+GGG 0.447588 3_4:+82054412 Msa0527590:CDS
CGGCTTTGATTAAGATGTAT+GGG 0.473408 3_4:+82054146 Msa0527590:CDS
AATGCTTTGTTGTATGCTAT+GGG 0.489162 3_4:+82054250 Msa0527590:CDS
GGATGCTAAGGGTGTGTACC+AGG 0.490310 3_4:+82054291 Msa0527590:CDS
GTATAAGGAAATGAAGGAAA+AGG 0.490358 3_4:+82054411 Msa0527590:CDS
GAATGGATTTGTACCGAACT+GGG 0.498906 3_4:+82054324 Msa0527590:CDS
TAAGAGGGCTAGGGATGCTA+AGG 0.514521 3_4:+82054279 Msa0527590:CDS
GCTGCATACGTTCCCCAGTT+CGG 0.517673 3_4:-82054337 None:intergenic
ATGCTATGGGGAGAGCTAAG+AGG 0.526400 3_4:+82054263 Msa0527590:CDS
GAGTGTGTATAAGGAAATGA+AGG 0.541603 3_4:+82054405 Msa0527590:CDS
TGTATATGCAATTGTCAGGC+TGG 0.541985 3_4:-82054546 None:intergenic
TGCTATGGGGAGAGCTAAGA+GGG 0.552045 3_4:+82054264 Msa0527590:CDS
TGGAAGCTTATTCGAGAGGA+CGG 0.561160 3_4:+82054365 Msa0527590:CDS
TTAAGATGTATGGGATATTG+GGG 0.561755 3_4:+82054155 Msa0527590:CDS
GGGGAGAGCTAAGAGGGCTA+GGG 0.569487 3_4:+82054270 Msa0527590:CDS
ATTGTCAGGCTGGCAAGTCA+CGG 0.579708 3_4:-82054536 None:intergenic
GGATATTGGGGAATTATGAT+GGG 0.583755 3_4:+82054167 Msa0527590:CDS
AATGGATTTGTACCGAACTG+GGG 0.693984 3_4:+82054325 Msa0527590:CDS
AAGAGGGCTAGGGATGCTAA+GGG 0.711520 3_4:+82054280 Msa0527590:CDS
ATGCTTTGTTGTATGCTATG+GGG 0.732710 3_4:+82054251 Msa0527590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAATGATATGAAAGTTCT+TGG + chr3_4:82054202-82054221 Msa0527590:intron 20.0%
!!! AAAATGAGAAATGGGTTATT+AGG + chr3_4:82054110-82054129 Msa0527590:CDS 25.0%
! ATTAAGATGTATGGGATATT+GGG + chr3_4:82054154-82054173 Msa0527590:CDS 25.0%
! GCATTATACAAAACCATATT+CGG - chr3_4:82054235-82054254 None:intergenic 25.0%
! TATAAGGAAATGAAGGAAAA+GGG + chr3_4:82054412-82054431 Msa0527590:CDS 25.0%
ATTTATGTTTATGCGAGAAC+AGG + chr3_4:82054049-82054068 Msa0527590:intron 30.0%
ATAGTGCGAAAAATGAGAAA+TGG + chr3_4:82054101-82054120 Msa0527590:CDS 30.0%
TAGTGCGAAAAATGAGAAAT+GGG + chr3_4:82054102-82054121 Msa0527590:CDS 30.0%
GATTAAGATGTATGGGATAT+TGG + chr3_4:82054153-82054172 Msa0527590:CDS 30.0%
TTAAGATGTATGGGATATTG+GGG + chr3_4:82054155-82054174 Msa0527590:CDS 30.0%
!! ATATGAAAGTTCTTGGTGTT+AGG + chr3_4:82054209-82054228 Msa0527590:intron 30.0%
! TAATGCTTTGTTGTATGCTA+TGG + chr3_4:82054249-82054268 Msa0527590:CDS 30.0%
! AATGCTTTGTTGTATGCTAT+GGG + chr3_4:82054250-82054269 Msa0527590:CDS 30.0%
GTATAAGGAAATGAAGGAAA+AGG + chr3_4:82054411-82054430 Msa0527590:CDS 30.0%
GAGAACAGGTAATGTTGATA+TGG + chr3_4:82054063-82054082 Msa0527590:intron 35.0%
! TCGGCTTTGATTAAGATGTA+TGG + chr3_4:82054145-82054164 Msa0527590:CDS 35.0%
! CGGCTTTGATTAAGATGTAT+GGG + chr3_4:82054146-82054165 Msa0527590:CDS 35.0%
GGATATTGGGGAATTATGAT+GGG + chr3_4:82054167-82054186 Msa0527590:CDS 35.0%
! ATGCTTTGTTGTATGCTATG+GGG + chr3_4:82054251-82054270 Msa0527590:CDS 35.0%
TACCAGGAGATGAAAAAGAA+TGG + chr3_4:82054307-82054326 Msa0527590:CDS 35.0%
!! ATCCATTCTTTTTCATCTCC+TGG - chr3_4:82054312-82054331 None:intergenic 35.0%
GAGTGTGTATAAGGAAATGA+AGG + chr3_4:82054405-82054424 Msa0527590:CDS 35.0%
! TATTAGGCCAGTTGCGTTTT+CGG + chr3_4:82054126-82054145 Msa0527590:CDS 40.0%
GGGATATTGGGGAATTATGA+TGG + chr3_4:82054166-82054185 Msa0527590:CDS 40.0%
! AGAATGGATTTGTACCGAAC+TGG + chr3_4:82054323-82054342 Msa0527590:CDS 40.0%
! GAATGGATTTGTACCGAACT+GGG + chr3_4:82054324-82054343 Msa0527590:CDS 40.0%
! AATGGATTTGTACCGAACTG+GGG + chr3_4:82054325-82054344 Msa0527590:CDS 40.0%
!! CTTTTGGAAGCTTATTCGAG+AGG + chr3_4:82054361-82054380 Msa0527590:CDS 40.0%
!! AGAAGCGTTGAGTGTGTATA+AGG + chr3_4:82054396-82054415 Msa0527590:CDS 40.0%
! TTGACATGTGTGCTGATGTT+GGG + chr3_4:82054470-82054489 Msa0527590:intron 40.0%
ATCAAAGCCGAAAACGCAAC+TGG - chr3_4:82054136-82054155 None:intergenic 45.0%
!! TCTTGGTGTTAGGCCGAATA+TGG + chr3_4:82054219-82054238 Msa0527590:intron 45.0%
TGGAAGCTTATTCGAGAGGA+CGG + chr3_4:82054365-82054384 Msa0527590:CDS 45.0%
! CTTGACATGTGTGCTGATGT+TGG + chr3_4:82054469-82054488 Msa0527590:intron 45.0%
ATGCTATGGGGAGAGCTAAG+AGG + chr3_4:82054263-82054282 Msa0527590:CDS 50.0%
TGCTATGGGGAGAGCTAAGA+GGG + chr3_4:82054264-82054283 Msa0527590:CDS 50.0%
TAAGAGGGCTAGGGATGCTA+AGG + chr3_4:82054279-82054298 Msa0527590:CDS 50.0%
AAGAGGGCTAGGGATGCTAA+GGG + chr3_4:82054280-82054299 Msa0527590:CDS 50.0%
! GGGAACGTATGCAGCTCTTT+TGG + chr3_4:82054345-82054364 Msa0527590:CDS 50.0%
! GGATGCTAAGGGTGTGTACC+AGG + chr3_4:82054291-82054310 Msa0527590:CDS 55.0%
GCTGCATACGTTCCCCAGTT+CGG - chr3_4:82054340-82054359 None:intergenic 55.0%
TGGGGAGAGCTAAGAGGGCT+AGG + chr3_4:82054269-82054288 Msa0527590:CDS 60.0%
GGGGAGAGCTAAGAGGGCTA+GGG + chr3_4:82054270-82054289 Msa0527590:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 82054032 82054554 82054032 ID=Msa0527590;Name=Msa0527590
chr3_4 mRNA 82054032 82054554 82054032 ID=Msa0527590-mRNA-1;Parent=Msa0527590;Name=Msa0527590-mRNA-1;_AED=0.47;_eAED=0.52;_QI=0|0|0|1|0|0|4|0|133
chr3_4 exon 82054032 82054038 82054032 ID=Msa0527590-mRNA-1:exon:24835;Parent=Msa0527590-mRNA-1
chr3_4 exon 82054071 82054188 82054071 ID=Msa0527590-mRNA-1:exon:24836;Parent=Msa0527590-mRNA-1
chr3_4 exon 82054231 82054476 82054231 ID=Msa0527590-mRNA-1:exon:24837;Parent=Msa0527590-mRNA-1
chr3_4 exon 82054524 82054554 82054524 ID=Msa0527590-mRNA-1:exon:24838;Parent=Msa0527590-mRNA-1
chr3_4 CDS 82054032 82054038 82054032 ID=Msa0527590-mRNA-1:cds;Parent=Msa0527590-mRNA-1
chr3_4 CDS 82054071 82054188 82054071 ID=Msa0527590-mRNA-1:cds;Parent=Msa0527590-mRNA-1
chr3_4 CDS 82054231 82054476 82054231 ID=Msa0527590-mRNA-1:cds;Parent=Msa0527590-mRNA-1
chr3_4 CDS 82054524 82054554 82054524 ID=Msa0527590-mRNA-1:cds;Parent=Msa0527590-mRNA-1
Gene Sequence

>Msa0527590

ATGTGTCGTAATGTTGATATGGCTTTGAAATTGTATGATAGTGCGAAAAATGAGAAATGGGTTATTAGGCCAGTTGCGTTTTCGGCTTTGATTAAGATGTATGGGATATTGGGGAATTATGATGGGCCGAATATGGTTTTGTATAATGCTTTGTTGTATGCTATGGGGAGAGCTAAGAGGGCTAGGGATGCTAAGGGTGTGTACCAGGAGATGAAAAAGAATGGATTTGTACCGAACTGGGGAACGTATGCAGCTCTTTTGGAAGCTTATTCGAGAGGACGGTTGAGTAAAGAAGCGTTGAGTGTGTATAAGGAAATGAAGGAAAAGGGAATGAGTATGAATAAAGTTCTTTATAGTATGCTTCTTGACATATATGAAGCGTTCCGTGACTTGCCAGCCTGA

Protein sequence

>Msa0527590

MCRNVDMALKLYDSAKNEKWVIRPVAFSALIKMYGILGNYDGPNMVLYNALLYAMGRAKRARDAKGVYQEMKKNGFVPNWGTYAALLEAYSRGRLSKEALSVYKEMKEKGMSMNKVLYSMLLDIYEAFRDLPA*