AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG017400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG017400 MtrunA17_Chr3g0139951 97.000 400 12 0 1 400 1 400 0.0 806
MsaG017400 MtrunA17_Chr6g0485811 45.376 465 225 10 125 570 107 561 7.44e-117 360
MsaG017400 MtrunA17_Chr8g0390351 44.662 459 228 11 109 549 44 494 4.37e-114 352
MsaG017400 MtrunA17_Chr3g0139941 78.125 192 9 2 402 593 1 159 6.66e-96 290
MsaG017400 MtrunA17_Chr1g0149101 44.604 139 73 4 148 282 498 636 1.09e-28 121
MsaG017400 MtrunA17_Chr5g0394661 48.800 125 60 4 148 269 488 611 4.10e-27 116
MsaG017400 MtrunA17_Chr1g0205031 36.719 128 68 5 143 267 409 526 6.65e-14 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG017400 AT4G29000.1 40.433 554 243 18 13 533 24 523 4.00e-112 348
MsaG017400 AT2G20110.3 40.883 521 247 14 84 590 66 539 9.66e-106 329
MsaG017400 AT2G20110.1 41.352 503 240 13 84 572 66 527 8.30e-105 328
MsaG017400 AT2G20110.2 40.588 510 241 13 84 572 66 534 7.51e-103 323
MsaG017400 AT5G25790.1 36.722 482 248 15 49 524 11 441 8.10e-83 267
MsaG017400 AT5G25790.2 35.714 504 267 15 49 546 11 463 1.69e-82 268
MsaG017400 AT5G25790.3 36.515 482 245 16 49 524 11 437 4.08e-82 265
MsaG017400 AT3G16160.1 44.737 152 80 2 116 266 34 182 3.13e-32 128
MsaG017400 AT3G22760.2 41.401 157 87 3 126 280 186 339 1.50e-28 119
MsaG017400 AT3G22760.1 41.401 157 87 3 126 280 309 462 2.41e-28 120
MsaG017400 AT4G14770.1 46.774 124 64 2 148 269 375 498 4.68e-28 119
MsaG017400 AT4G14770.2 46.774 124 64 2 148 269 355 478 6.93e-28 119
MsaG017400 AT4G14770.3 46.774 124 64 2 148 269 356 479 6.95e-28 119
MsaG017400 AT3G22780.1 42.029 138 78 2 148 283 401 538 1.07e-27 118
MsaG017400 AT3G04850.1 45.968 124 65 2 148 269 453 576 5.20e-27 116

Find 126 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACATCAATTTAAGTGTTTC+TGG 0.101248 3:+108766133 None:intergenic
GCTAAAGTACTTACAATTTA+AGG 0.107021 3:+108767980 None:intergenic
TTCTCTTCTTGGGTGTTATA+TGG 0.169921 3:+108767280 None:intergenic
ATTATTATTGGTAGCATTAA+AGG 0.183098 3:-108765938 MsaT017400.1:intron
CATTCCAATTGCCTCCTTTC+GGG 0.215507 3:+108767786 None:intergenic
ATTTGTCTTTGCAGCTTCTT+TGG 0.243681 3:+108766611 None:intergenic
GCAACTAATGCTGCCATTAA+TGG 0.244194 3:-108767336 MsaT017400.1:CDS
TCAAAATAAAGCAGGGTTAA+AGG 0.248253 3:-108768052 MsaT017400.1:CDS
TACTTACAATTTAAGGCATT+TGG 0.284828 3:+108767987 None:intergenic
TCTCTTCTTGGGTGTTATAT+GGG 0.286069 3:+108767281 None:intergenic
AAAATCACATACCTGAATTT+AGG 0.297536 3:+108766788 None:intergenic
CTTGGTGAACTGATTATTAT+TGG 0.298905 3:-108765950 MsaT017400.1:CDS
TCATTCCAATTGCCTCCTTT+CGG 0.299863 3:+108767785 None:intergenic
AAGTCCAACTGCTCCATTAA+TGG 0.310344 3:+108767323 None:intergenic
TTGATATTGACATTCATAAT+AGG 0.314713 3:-108766165 MsaT017400.1:CDS
GTGTCTGAAATTCAATTAAT+AGG 0.329611 3:-108767537 MsaT017400.1:CDS
GGCTTATCCTGACCAAGTTC+AGG 0.337443 3:-108765979 MsaT017400.1:CDS
TCGGAAATTTGCGCGGCAAT+TGG 0.338947 3:-108769582 MsaT017400.1:CDS
TCCTCCGGCGCAAATGCATT+TGG 0.349311 3:-108769453 MsaT017400.1:CDS
AATAGAAGCTTCATATTTCT+CGG 0.353823 3:+108766276 None:intergenic
CTACTAACCATAGAAACTTC+TGG 0.357925 3:+108767706 None:intergenic
TTTGCATGATTCTCCGAAAC+AGG 0.382385 3:+108766208 None:intergenic
ACCAAGTTCAGGGATGTTCT+TGG 0.382968 3:-108765968 MsaT017400.1:CDS
AACCTCTTCACCGGAAGCTT+TGG 0.384541 3:+108769281 None:intergenic
AGATGTTGCCAAGCCTGTTT+CGG 0.392240 3:-108766221 MsaT017400.1:CDS
TTCGGTAATGGTTCTGCAAA+TGG 0.394963 3:-108766088 MsaT017400.1:CDS
AACACTCACAATACTTCTTA+AGG 0.401328 3:+108767478 None:intergenic
TTAATAGGAAGGCACAATAA+AGG 0.404131 3:-108767522 MsaT017400.1:CDS
TAATTTCAAGACCTAAATTC+AGG 0.410173 3:-108766799 MsaT017400.1:intron
GCGTCGGTGGCGACAATGTC+AGG 0.412454 3:+108769528 None:intergenic
TGTTTCCACGGCCGTCTCAC+TGG 0.412786 3:+108769419 None:intergenic
GGACTTGGACCCTCCATCTC+TGG 0.418333 3:-108767306 MsaT017400.1:CDS
ATTAATGGAGCAGTTGGACT+TGG 0.419842 3:-108767321 MsaT017400.1:CDS
GCTACCTATGCAAGAACTAA+TGG 0.420530 3:-108764253 MsaT017400.1:CDS
TAAATTGATGTGTGATGAAC+AGG 0.421391 3:-108766122 MsaT017400.1:CDS
AGCCACTGGGATGGAGCAAT+TGG 0.435821 3:+108764273 None:intergenic
GTACTCCACACCAAAGCTTC+CGG 0.447922 3:-108769291 MsaT017400.1:CDS
TACTGTGAGTGCTATGCAGC+TGG 0.448205 3:-108767868 MsaT017400.1:CDS
AAAGGAAGCTGACAGGGATA+AGG 0.448296 3:+108766844 None:intergenic
TTCAAATTTCCAGAAATGAG+AGG 0.459036 3:-108766322 MsaT017400.1:intron
CATGACTGCTCAACACCAAC+AGG 0.463692 3:-108767208 MsaT017400.1:intron
ACCAAGAACATCCCTGAACT+TGG 0.469962 3:+108765967 None:intergenic
TGATAGTGGTGCTGAAACTA+AGG 0.471033 3:-108764320 MsaT017400.1:CDS
TCTTTCGTTGAGGTTGCTCA+TGG 0.471035 3:-108764215 MsaT017400.1:CDS
CACTGCTGTTTATGCAGAGC+AGG 0.471249 3:-108766005 MsaT017400.1:CDS
CTGTTTATGCAGAGCAGGAA+AGG 0.476553 3:-108766000 MsaT017400.1:CDS
AAGGAAGCTGACAGGGATAA+GGG 0.478405 3:+108766845 None:intergenic
TCACAGCCTCAAAATAAAGC+AGG 0.479128 3:-108768060 MsaT017400.1:CDS
GCTGCCCGAAAGGAGGCAAT+TGG 0.479529 3:-108767790 MsaT017400.1:CDS
GTTCTTGCATAGGTAGCCAC+TGG 0.479534 3:+108764259 None:intergenic
GATAAGGGAGATGAAGCTAT+AGG 0.479560 3:+108766860 None:intergenic
GAACATCCCTGAACTTGGTC+AGG 0.480468 3:+108765972 None:intergenic
GATTGAAAATGCGGCATCAC+CGG 0.492928 3:+108769353 None:intergenic
GGAGAAGAGCGAAACGACGC+TGG 0.493971 3:-108769615 MsaT017400.1:CDS
CGGAAACAAAGGAAGCTGAC+AGG 0.494375 3:+108766837 None:intergenic
TGTTATATGGGTTCCAGAGA+TGG 0.499612 3:+108767293 None:intergenic
TGAGGCTGTGATCTAGGGCT+AGG 0.501431 3:+108768072 None:intergenic
CGACGCTGGATTTAGCTAAT+CGG 0.509373 3:-108769601 MsaT017400.1:CDS
AAAGGATGTCACTGCAAGAA+AGG 0.510127 3:-108767504 MsaT017400.1:CDS
TTGGATTTCGCCGCCGCATG+TGG 0.510164 3:-108769563 MsaT017400.1:CDS
ATCGAAACTAACTGCGGGCG+CGG 0.513160 3:+108769329 None:intergenic
TCAAATTTCCAGAAATGAGA+GGG 0.516415 3:-108766321 MsaT017400.1:intron
CTGAAATTCAATTAATAGGA+AGG 0.519135 3:-108767533 MsaT017400.1:CDS
GCTTATCCTGACCAAGTTCA+GGG 0.520596 3:-108765978 MsaT017400.1:CDS
CAAAAGTCTTCCAACTCTGA+TGG 0.520619 3:-108766031 MsaT017400.1:CDS
ATGATTCTCCGAAACAGGCT+TGG 0.524373 3:+108766213 None:intergenic
AAATGCATTTGCGCCGGAGG+AGG 0.526333 3:+108769455 None:intergenic
GCTGCCATTAATGGAGCAGT+TGG 0.529615 3:-108767327 MsaT017400.1:CDS
CAGAGCAGAGGACGTTGGCA+TGG 0.529760 3:+108767454 None:intergenic
AGTCACCAGTGAGACGGCCG+TGG 0.538539 3:-108769424 MsaT017400.1:CDS
CACCAAAGCTTCCGGTGAAG+AGG 0.538599 3:-108769283 MsaT017400.1:CDS
GAAGCTGCAAAGACAAATGC+AGG 0.539292 3:-108766606 MsaT017400.1:intron
TGTGACAGTGACTGCGGCGT+CGG 0.541888 3:+108769512 None:intergenic
TGTGGTGGTGATTGTTTCCA+CGG 0.542299 3:+108769407 None:intergenic
AGCGCTTGAAACCTCTTCAC+CGG 0.544016 3:+108769272 None:intergenic
TTCATGTTGAAGGTCTGTGT+TGG 0.547492 3:-108766691 MsaT017400.1:intron
GGAAGCTTTGGTGTGGAGTA+CGG 0.547715 3:+108769293 None:intergenic
TCCAAATGCATTTGCGCCGG+AGG 0.550391 3:+108769452 None:intergenic
CTCTGCTGCTGCCACTGTGG+TGG 0.557444 3:+108769392 None:intergenic
ACCGTCGGATTTGCCTCCTC+CGG 0.560178 3:-108769468 MsaT017400.1:CDS
GGAGGCAAATCCGACGGTGT+CGG 0.562332 3:+108769473 None:intergenic
ATAGGCAGTGTCGGAAACAA+AGG 0.562595 3:+108766826 None:intergenic
GAACAATGAGGCTGCCCGAA+AGG 0.567258 3:-108767800 MsaT017400.1:CDS
GAATCATCGAAACTAACTGC+GGG 0.568372 3:+108769324 None:intergenic
TGCATAGGTAGCCACTGGGA+TGG 0.569627 3:+108764264 None:intergenic
ATGTCCATTAGTTCTTGCAT+AGG 0.570734 3:+108764249 None:intergenic
GATTTCGCCGCCGCATGTGG+AGG 0.572850 3:-108769560 MsaT017400.1:CDS
AAATGAGAGGGAAAGCTGCT+AGG 0.574833 3:-108766309 MsaT017400.1:CDS
CGGTGTCGGAGGTCGTAGAA+TGG 0.576418 3:+108769487 None:intergenic
AGCAGTGTATCCATCAGAGT+TGG 0.576661 3:+108766021 None:intergenic
TAGTCTAGTTCAAATCAGAC+AGG 0.581100 3:-108767358 MsaT017400.1:CDS
TTAAGTGTTTCTGGTGACAG+TGG 0.589606 3:+108766142 None:intergenic
GGAGGCAATTGGAATGACAC+TGG 0.589713 3:-108767779 MsaT017400.1:CDS
GACAGTGACTGCGGCGTCGG+TGG 0.593114 3:+108769515 None:intergenic
AAATCCAAATGCATTTGCGC+CGG 0.594109 3:+108769449 None:intergenic
CTTCACCGGAAGCTTTGGTG+TGG 0.594505 3:+108769286 None:intergenic
CAATGAGGCTGCCCGAAAGG+AGG 0.594923 3:-108767797 MsaT017400.1:CDS
CACAGCCTCAAAATAAAGCA+GGG 0.602704 3:-108768059 MsaT017400.1:CDS
GGAAACAAAGGAAGCTGACA+GGG 0.605542 3:+108766838 None:intergenic
GGCAAATCCGACGGTGTCGG+AGG 0.608094 3:+108769476 None:intergenic
TATATGGGTTCCAGAGATGG+AGG 0.609649 3:+108767296 None:intergenic
GCAGCTGGGATCTATTGTGA+TGG 0.610068 3:-108767853 MsaT017400.1:CDS
GAGAACGTCACAGTCTCCGC+CGG 0.610187 3:-108769372 MsaT017400.1:CDS
GGGCGCGGTGATTGAAAATG+CGG 0.613912 3:+108769344 None:intergenic
ACTGTGAGTGCTATGCAGCT+GGG 0.620605 3:-108767867 MsaT017400.1:CDS
TGATGTGTGATGAACAGGAT+GGG 0.620967 3:-108766117 MsaT017400.1:CDS
ATACTACTGATCTTTCGTTG+AGG 0.630168 3:-108764225 MsaT017400.1:CDS
TTCTTGCATAGGTAGCCACT+GGG 0.635007 3:+108764260 None:intergenic
TCATAATAATCTGAACAATG+AGG 0.638704 3:-108767812 MsaT017400.1:CDS
GATAGTGGTGCTGAAACTAA+GGG 0.640097 3:-108764319 MsaT017400.1:CDS
TGAAAATGCGGCATCACCGG+CGG 0.641386 3:+108769356 None:intergenic
GGCGACAATGTCAGGTACGA+CGG 0.643457 3:+108769536 None:intergenic
GCCGGAGGAGGCAAATCCGA+CGG 0.645977 3:+108769467 None:intergenic
TCACTCACAGATCAAACTGT+CGG 0.650466 3:-108767231 MsaT017400.1:CDS
ATATGGGTTCCAGAGATGGA+GGG 0.670217 3:+108767297 None:intergenic
TCTACGACCTCCGACACCGT+CGG 0.672076 3:-108769483 MsaT017400.1:CDS
TTGATGTGTGATGAACAGGA+TGG 0.672796 3:-108766118 MsaT017400.1:CDS
GTTCTCTGCTGCTGCCACTG+TGG 0.675511 3:+108769389 None:intergenic
TAGCTAATCGGAAATTTGCG+CGG 0.681451 3:-108769589 MsaT017400.1:CDS
CGACGGACCTCCACATGCGG+CGG 0.682146 3:+108769553 None:intergenic
GTACGACGGACCTCCACATG+CGG 0.684282 3:+108769550 None:intergenic
TGCCAATTGCTCCATCCCAG+TGG 0.687073 3:-108764275 MsaT017400.1:CDS
ATAGTGGTGCTGAAACTAAG+GGG 0.690161 3:-108764318 MsaT017400.1:CDS
TGAATCATCGAAACTAACTG+CGG 0.719757 3:+108769323 None:intergenic
ATGGTTTGTGACAGTGACTG+CGG 0.730603 3:+108769506 None:intergenic
GGAAACAATCACCACCACAG+TGG 0.761756 3:-108769403 MsaT017400.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 108764210 108769639 108764210 ID=MsaG017400
Chr3 mRNA 108764210 108769639 108764210 ID=MsaT017400.1;Parent=MsaG017400
Chr3 exon 108764210 108764406 108764210 ID=MsaT017400.1.exon8;Parent=MsaT017400.1
Chr3 CDS 108764210 108764406 108764210 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108765939 108766331 108765939 ID=MsaT017400.1.exon7;Parent=MsaT017400.1
Chr3 CDS 108765939 108766331 108765939 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108766607 108766701 108766607 ID=MsaT017400.1.exon6;Parent=MsaT017400.1
Chr3 CDS 108766607 108766701 108766607 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108766800 108766891 108766800 ID=MsaT017400.1.exon5;Parent=MsaT017400.1
Chr3 CDS 108766800 108766891 108766800 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108767209 108767565 108767209 ID=MsaT017400.1.exon4;Parent=MsaT017400.1
Chr3 CDS 108767209 108767565 108767209 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108767714 108767891 108767714 ID=MsaT017400.1.exon3;Parent=MsaT017400.1
Chr3 CDS 108767714 108767891 108767714 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108767994 108768104 108767994 ID=MsaT017400.1.exon2;Parent=MsaT017400.1
Chr3 CDS 108767994 108768104 108767994 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Chr3 exon 108769272 108769639 108769272 ID=MsaT017400.1.exon1;Parent=MsaT017400.1
Chr3 CDS 108769272 108769639 108769272 ID=cds.MsaT017400.1;Parent=MsaT017400.1
Gene Sequence

>MsaT017400.1

ATGGAGAAGAGCGAAACGACGCTGGATTTAGCTAATCGGAAATTTGCGCGGCAATTGGATTTCGCCGCCGCATGTGGAGGTCCGTCGTACCTGACATTGTCGCCACCGACGCCGCAGTCACTGTCACAAACCATTCTACGACCTCCGACACCGTCGGATTTGCCTCCTCCGGCGCAAATGCATTTGGATTTTCAGTCACCAGTGAGACGGCCGTGGAAACAATCACCACCACAGTGGCAGCAGCAGAGAACGTCACAGTCTCCGCCGGTGATGCCGCATTTTCAATCACCGCGCCCGCAGTTAGTTTCGATGATTCATCGATTACCGTACTCCACACCAAAGCTTCCGGTGAAGAGGTTTCAAGCGCTAAACGAGTCTCCTAGCCCTAGATCACAGCCTCAAAATAAAGCAGGGTTAAAGGACAACACTCTAAAGAAGCAAAAACGGTGTAACTGCAAAAATTCCAAATGCCTTAAATTGTACTGTGAGTGCTATGCAGCTGGGATCTATTGTGATGGTTGCAACTGTCAAAATTGTCATAATAATCTGAACAATGAGGCTGCCCGAAAGGAGGCAATTGGAATGACACTGGAAAAAAATCCAAATGCTTTCAGACCAAAAATTGCAAGCAGTCCGCAAAAACCAGAAGTTTCTATGGAGGAAGTGTCTGAAATTCAATTAATAGGAAGGCACAATAAAGGATGTCACTGCAAGAAAGGTTGCCTTAAGAAGTATTGTGAGTGTTTCCATGCCAACGTCCTCTGCTCTGAAAATTGTAAATGCATTGACTGCAAGAATTTTGAAGGAAGTGACGAATGGAGAATAGTTTTACAAGAAGAGTGTAGTCTAGTTCAAATCAGACAGGCAACTAATGCTGCCATTAATGGAGCAGTTGGACTTGGACCCTCCATCTCTGGAACCCATATAACACCCAAGAAGAGAAAAATCCAGGAAAGTTTTTCTGGCAAATCACTCACAGATCAAACTGTCGGCATGACTGCTCAACACCAACAGGAACTTGATCCTATAGCTTCATCTCCCTTATCCCTGTCAGCTTCCTTTGTTTCCGACACTGCCTATAAAATAATTTCAAGACCTAAATTCAGGTCTGTGTTGGCTGATGTCCTCCAGACACAGAATGTGAAAAATCTTTGTTCACTTTTAGTTGTTCTCTCCAAAGAAGCTGCAAAGACAAATGCAGAAATGAGAGGGAAAGCTGCTAGGAAAATAGAGACCGAGAAATATGAAGCTTCTATTGCTTCATCATCTCAATTGCTGCAAGACAGTAGAGATGTTGCCAAGCCTGTTTCGGAGAATCATGCAAATAAAGATGTAGCAGATGCAGTTGATATTGACATTCATAATAGGCCACTGTCACCAGAAACACTTAAATTGATGTGTGATGAACAGGATGGGATGTTTTTCGGTAATGGTTCTGCAAATGGAGTTGCAATTGACAATACTTATCAGAACATGATTCAAAAGTCTTCCAACTCTGATGGATACACTGCTGTTTATGCAGAGCAGGAAAGGCTTATCCTGACCAAGTTCAGGGATGTTCTTGGTGAACTGATTATTATTGGTAGCATTAAAGAAACAATGCACTCTTCATCAGTGAAGAAAGATATGAGTATCGAGAAAACACCTAAAAACAATGGTGATAGTGGTGCTGAAACTAAGGGGATTCTTCTCAACAACTGCACTGCCAATTGCTCCATCCCAGTGGCTACCTATGCAAGAACTAATGGACATGATACTACTGATCTTTCGTTGAGGTTGCTCATGGATTGA

Protein sequence

>MsaT017400.1

MEKSETTLDLANRKFARQLDFAAACGGPSYLTLSPPTPQSLSQTILRPPTPSDLPPPAQMHLDFQSPVRRPWKQSPPQWQQQRTSQSPPVMPHFQSPRPQLVSMIHRLPYSTPKLPVKRFQALNESPSPRSQPQNKAGLKDNTLKKQKRCNCKNSKCLKLYCECYAAGIYCDGCNCQNCHNNLNNEAARKEAIGMTLEKNPNAFRPKIASSPQKPEVSMEEVSEIQLIGRHNKGCHCKKGCLKKYCECFHANVLCSENCKCIDCKNFEGSDEWRIVLQEECSLVQIRQATNAAINGAVGLGPSISGTHITPKKRKIQESFSGKSLTDQTVGMTAQHQQELDPIASSPLSLSASFVSDTAYKIISRPKFRSVLADVLQTQNVKNLCSLLVVLSKEAAKTNAEMRGKAARKIETEKYEASIASSSQLLQDSRDVAKPVSENHANKDVADAVDIDIHNRPLSPETLKLMCDEQDGMFFGNGSANGVAIDNTYQNMIQKSSNSDGYTAVYAEQERLILTKFRDVLGELIIIGSIKETMHSSSVKKDMSIEKTPKNNGDSGAETKGILLNNCTANCSIPVATYARTNGHDTTDLSLRLLMD*