AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG004380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG004380 MtrunA17_Chr1g0196071 98.756 402 5 0 1 402 1 402 0.0 831
MsaG004380 MtrunA17_Chr2g0286441 68.490 384 118 3 21 402 11 393 0.0 555
MsaG004380 MtrunA17_Chr2g0278511 53.009 432 168 10 1 402 1 427 9.39e-153 438
MsaG004380 MtrunA17_Chr5g0404321 52.246 423 174 7 1 402 1 416 3.73e-144 416
MsaG004380 MtrunA17_Chr1g0201891 50.572 437 175 10 1 402 1 431 7.41e-143 413
MsaG004380 MtrunA17_Chr8g0373001 51.429 420 178 6 1 402 1 412 3.41e-141 408
MsaG004380 MtrunA17_Chr1g0155301 55.153 359 149 6 50 402 70 422 6.24e-133 387
MsaG004380 MtrunA17_Chr2g0315641 50.279 358 145 5 50 402 42 371 4.95e-119 350
MsaG004380 MtrunA17_Chr2g0315651 43.733 375 173 8 36 402 23 367 5.16e-95 289
MsaG004380 MtrunA17_Chr8g0373361 41.247 417 201 17 1 395 11 405 5.63e-82 257
MsaG004380 MtrunA17_Chr8g0373331 33.911 404 198 10 1 393 1 346 1.57e-60 199
MsaG004380 MtrunA17_Chr8g0373341 33.333 399 180 13 1 392 1 320 7.79e-47 163
MsaG004380 MtrunA17_Chr1g0156151 53.521 142 62 1 65 202 66 207 4.93e-45 155
MsaG004380 MtrunA17_Chr8g0373351 35.275 309 121 9 99 394 44 286 1.06e-43 154
MsaG004380 MtrunA17_Chr3g0091401 38.776 98 54 1 92 189 8 99 5.67e-14 67.8
MsaG004380 MtrunA17_Chr2g0334041 50.000 62 24 1 340 401 305 359 1.70e-12 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG004380 AT2G47900.2 71.913 413 98 6 1 402 1 406 0.0 586
MsaG004380 AT2G47900.1 71.913 413 98 6 1 402 1 406 0.0 586
MsaG004380 AT2G47900.3 71.739 414 98 6 1 402 1 407 0.0 585
MsaG004380 AT3G06380.1 56.049 405 150 9 1 402 1 380 3.24e-147 423
MsaG004380 AT5G18680.1 58.470 366 124 8 50 402 39 389 7.14e-147 422
MsaG004380 AT1G43640.1 48.747 439 178 11 1 402 1 429 2.06e-140 407
MsaG004380 AT1G76900.2 47.380 458 182 9 1 402 1 455 1.48e-137 401
MsaG004380 AT1G76900.1 47.380 458 182 9 1 402 1 455 1.48e-137 401
MsaG004380 AT1G76900.3 47.380 458 182 9 1 402 1 455 1.48e-137 401
MsaG004380 AT1G25280.1 48.438 448 182 7 1 402 1 445 4.12e-136 397
MsaG004380 AT2G18280.2 50.990 404 185 6 1 402 1 393 5.56e-134 390
MsaG004380 AT2G18280.1 50.990 404 185 6 1 402 1 393 5.56e-134 390
MsaG004380 AT1G47270.3 52.846 369 150 5 42 402 36 388 3.51e-132 385
MsaG004380 AT1G47270.1 52.846 369 150 5 42 402 61 413 4.30e-132 385
MsaG004380 AT1G47270.2 52.846 369 150 5 42 402 60 412 5.17e-132 385
MsaG004380 AT1G43640.2 51.359 368 147 7 62 402 1 363 6.59e-130 378
MsaG004380 AT5G18680.2 58.497 306 100 7 109 402 7 297 1.03e-115 339
MsaG004380 AT3G06380.2 59.589 292 108 5 113 402 5 288 3.76e-113 333
MsaG004380 AT1G53320.1 49.036 363 152 6 48 402 42 379 6.49e-113 335
MsaG004380 AT1G25280.3 50.741 270 94 5 169 402 1 267 6.71e-83 254
MsaG004380 AT1G25280.2 50.741 270 94 5 169 402 1 267 6.71e-83 254
MsaG004380 AT1G61940.2 70.930 86 25 0 53 138 1 86 4.87e-40 144
MsaG004380 AT1G61940.1 72.131 61 17 0 53 113 1 61 1.51e-24 101
MsaG004380 AT1G61940.1 48.000 100 28 5 248 346 102 178 1.22e-12 67.8

Find 108 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATATCATTTCTCTAAATT+TGG 0.095614 1:-69088727 MsaT004380.1:CDS
TTGTAACAGATCAAACTTTC+TGG 0.178818 1:-69088582 MsaT004380.1:intron
GATGCACACCCTCCAATTTA+TGG 0.187148 1:-69088539 MsaT004380.1:CDS
GCAAATCTGTCTCCATAAAT+TGG 0.193737 1:+69088527 None:intergenic
CTCATATGATCTGAATGTTT+TGG 0.268134 1:-69088426 MsaT004380.1:CDS
TTAGGTTAACGATGTCATTT+AGG 0.284142 1:-69090654 None:intergenic
TCGCGTGCGCCGGTGTTTGC+AGG 0.297366 1:-69090408 MsaT004380.1:CDS
AAGGGATTTGACGTGAAATT+CGG 0.342997 1:-69090613 MsaT004380.1:CDS
GAAAATGTCATTCTGCAGTT+TGG 0.348950 1:-69087846 MsaT004380.1:CDS
TGCATCATACACTGTAAATT+TGG 0.359668 1:+69088556 None:intergenic
CAATCACTCACAAGCAATCT+TGG 0.389643 1:+69087734 None:intergenic
TAGGATTATGCAATGTGTTA+TGG 0.402541 1:-69088183 MsaT004380.1:CDS
TGTAACAGATCAAACTTTCT+GGG 0.411602 1:-69088581 MsaT004380.1:intron
CCTGCCTCAGCTGTTGAACC+TGG 0.411820 1:-69088152 MsaT004380.1:CDS
GACAGGGAATGTCAACTTGC+TGG 0.412110 1:+69090339 None:intergenic
AGGGATTTGACGTGAAATTC+GGG 0.417694 1:-69090612 MsaT004380.1:CDS
GATCTGAAGAACGGGATAGA+TGG 0.420581 1:+69088077 None:intergenic
GACAAGTGCTACCTGCTTCA+AGG 0.422783 1:+69090315 None:intergenic
ATGGGTTGAGTCGGAGTTGT+TGG 0.422794 1:-69090516 MsaT004380.1:CDS
TAGTTTCCTGCAGGAACTCT+TGG 0.422898 1:+69088464 None:intergenic
TGCGTCGGGGCCACACCTCC+AGG 0.436166 1:+69088134 None:intergenic
TTATCAAAGGTGCTGCTGAT+TGG 0.436264 1:+69088030 None:intergenic
GCGCCGGTGTTTGCAGGAGT+TGG 0.436346 1:-69090402 MsaT004380.1:CDS
TGTTATTGCCAATGGTGCTT+TGG 0.443517 1:-69090548 MsaT004380.1:CDS
GAAGAAATTGAGTCTGCGTC+GGG 0.444561 1:+69088120 None:intergenic
TTGAGGTTTCAGATGATACT+TGG 0.450054 1:-69090450 MsaT004380.1:CDS
ATAACACATTGCATAATCCT+AGG 0.454350 1:+69088185 None:intergenic
GGTGCTTTGGTGATTGATGA+TGG 0.458578 1:-69090535 MsaT004380.1:CDS
AATGCTTCAAAGGCAGAGAT+TGG 0.458777 1:+69087783 None:intergenic
TGCTGGTGTTTGAACTTCAA+TGG 0.466360 1:-69087945 MsaT004380.1:CDS
GCTACCTGCTTCAAGGAGAC+AGG 0.468323 1:+69090322 None:intergenic
GAGACTTAGCCTGGTGGTGC+GGG 0.471988 1:+69088499 None:intergenic
CCAGGTTCAACAGCTGAGGC+AGG 0.472095 1:+69088152 None:intergenic
CATCATGCAGCCTGGTCCAA+GGG 0.476151 1:-69089070 MsaT004380.1:intron
GAAGGAGTAGCACCTATGTT+GGG 0.479960 1:-69088692 MsaT004380.1:CDS
GAGTATGATCATGGATAGGA+AGG 0.482584 1:-69090632 MsaT004380.1:CDS
TGAAGTTCAAACACCAGCAT+TGG 0.484021 1:+69087949 None:intergenic
CAAAGGCAGAGATTGGATAC+TGG 0.485873 1:+69087790 None:intergenic
ATCAATCACCAAAGCACCAT+TGG 0.486769 1:+69090540 None:intergenic
GTCATTTAGGAGTATGATCA+TGG 0.487718 1:-69090641 MsaT004380.1:CDS
CACTTGCTTGAGACTTAGCC+TGG 0.491047 1:+69088490 None:intergenic
TGGAGTTTCTGAGGAGGCCC+AGG 0.493680 1:-69087868 MsaT004380.1:CDS
AAGAATGTTGTCGCGTGCGC+CGG 0.493919 1:-69090418 MsaT004380.1:CDS
AGCTGTTGAACCTGGAGGTG+TGG 0.496026 1:-69088144 MsaT004380.1:CDS
ATAAGAGAGCCCCTTGGACC+AGG 0.512782 1:+69089060 None:intergenic
GTGCTTTGGTGATTGATGAT+GGG 0.516000 1:-69090534 MsaT004380.1:CDS
TGGGTTGAGTCGGAGTTGTT+GGG 0.521100 1:-69090515 MsaT004380.1:CDS
AGAAGGAGTAGCACCTATGT+TGG 0.521149 1:-69088693 MsaT004380.1:CDS
TCATCATGCAGCCTGGTCCA+AGG 0.523744 1:-69089071 MsaT004380.1:intron
CTTTGATAAGTCAAAATGAT+GGG 0.523813 1:-69088016 MsaT004380.1:CDS
GCACATCCCTCAAAAGCTCA+TGG 0.537457 1:+69090482 None:intergenic
TTGCAAAGTCCCGCACCACC+AGG 0.537675 1:-69088508 MsaT004380.1:CDS
TTCAACAGCTGAGGCAGGGA+TGG 0.540786 1:+69088157 None:intergenic
ATTCCCTGTCTCCTTGAAGC+AGG 0.548762 1:-69090326 MsaT004380.1:intron
CAGATGATACTTGGCCGACT+CGG 0.549792 1:-69090441 MsaT004380.1:CDS
CACATCCCTCAAAAGCTCAT+GGG 0.551644 1:+69090483 None:intergenic
GCATATTGCAAATGCTTCAA+AGG 0.553851 1:+69087773 None:intergenic
CCTTTGATAAGTCAAAATGA+TGG 0.555873 1:-69088017 MsaT004380.1:CDS
AAAATGTTAACAGGGGCCCT+AGG 0.556228 1:-69088202 MsaT004380.1:intron
GGATGTGCTTATGAGAATTG+AGG 0.557422 1:-69090467 MsaT004380.1:CDS
ATACCTCAACTTCCCAACAT+AGG 0.558903 1:+69088680 None:intergenic
GTCAACTTGCTGGACAATTG+AGG 0.559973 1:+69090349 None:intergenic
TCTTGGTGTCAAAGCTGCTA+AGG 0.561466 1:+69087751 None:intergenic
GAGAAATGATATAGTCAGTG+TGG 0.564360 1:+69088736 None:intergenic
AATCTGTCTCCATAAATTGG+AGG 0.567458 1:+69088530 None:intergenic
CACTGAATAAGAGAGCCCCT+TGG 0.567563 1:+69089054 None:intergenic
TTTGACGTGAAATTCGGGTA+TGG 0.568681 1:-69090607 MsaT004380.1:CDS
TGATTGGAGATTCTCTGAGC+GGG 0.569183 1:+69088046 None:intergenic
GCACCTATGTTGGGAAGTTG+AGG 0.569372 1:-69088683 MsaT004380.1:intron
TGAAGAAATTGAGTCTGCGT+CGG 0.573052 1:+69088119 None:intergenic
ATTCTGCAGTTTGGAAAAGT+CGG 0.574704 1:-69087837 MsaT004380.1:CDS
TCATATGAGACATGCACGAT+GGG 0.577709 1:+69088440 None:intergenic
AAGTCAAAATGATGGGGAGC+TGG 0.581065 1:-69088009 MsaT004380.1:CDS
TGGAGTTGTTCATGCCACCT+AGG 0.583552 1:+69087969 None:intergenic
TTTGCAGCCTCAACTGATGA+CGG 0.583581 1:-69088798 MsaT004380.1:intron
GGCATGAACAACTCCAATGC+TGG 0.585250 1:-69087962 MsaT004380.1:CDS
TGAGACTTAGCCTGGTGGTG+CGG 0.585690 1:+69088498 None:intergenic
ACGATGGGATAGTTTCCTGC+AGG 0.585969 1:+69088455 None:intergenic
GATGTTAATGTTATTGCCAA+TGG 0.594465 1:-69090556 MsaT004380.1:CDS
ATCTGTCTCCATAAATTGGA+GGG 0.597162 1:+69088531 None:intergenic
CTACCTGCTTCAAGGAGACA+GGG 0.598753 1:+69090323 None:intergenic
GTGTCTCCAAGAGTTCCTGC+AGG 0.601279 1:-69088470 MsaT004380.1:CDS
GACACTTGCGTGCAGCAAGA+AGG 0.601304 1:+69088769 None:intergenic
CAGGTTCAACAGCTGAGGCA+GGG 0.604724 1:+69088153 None:intergenic
GAACTTGCCGTCATCAGTTG+AGG 0.606120 1:+69088791 None:intergenic
GATTGGATACTGGTAATCCA+TGG 0.610280 1:+69087800 None:intergenic
AGAAATGATATAGTCAGTGT+GGG 0.610923 1:+69088737 None:intergenic
GCCTCAGCTGTTGAACCTGG+AGG 0.611858 1:-69088149 MsaT004380.1:CDS
TTAGGAGTATGATCATGGAT+AGG 0.615050 1:-69090636 MsaT004380.1:CDS
AACTTGCTGGACAATTGAGG+AGG 0.616449 1:+69090352 None:intergenic
TAACACATTGCATAATCCTA+GGG 0.617287 1:+69088186 None:intergenic
ATCATGCAGCCTGGTCCAAG+GGG 0.619178 1:-69089069 MsaT004380.1:intron
TGATTGATGATGGGTTGAGT+CGG 0.620505 1:-69090525 MsaT004380.1:CDS
ACCTCCAGGTTCAACAGCTG+AGG 0.623409 1:+69088148 None:intergenic
CTGATTGGAGATTCTCTGAG+CGG 0.624740 1:+69088045 None:intergenic
ATCATATGAGACATGCACGA+TGG 0.626290 1:+69088439 None:intergenic
ACATCCCTCAAAAGCTCATG+GGG 0.631071 1:+69090484 None:intergenic
AGTATGATCATGGATAGGAA+GGG 0.631347 1:-69090631 MsaT004380.1:CDS
GCAGTTTGGAAAAGTCGGAA+AGG 0.632984 1:-69087832 MsaT004380.1:CDS
ATTTGGATGATGTATCAAGA+AGG 0.634683 1:-69088710 MsaT004380.1:CDS
CGGAAAGGATGTGTTCACCA+TGG 0.642135 1:-69087817 MsaT004380.1:CDS
TGCTATATTAAACGAAATCG+CGG 0.643232 1:-69089033 MsaT004380.1:CDS
GCGACAACATTCTTCCGAGT+CGG 0.645949 1:+69090427 None:intergenic
TTTGATAAGTCAAAATGATG+GGG 0.648482 1:-69088015 MsaT004380.1:CDS
GAGTTGGAGAGAAATTGTGA+AGG 0.664353 1:-69090386 MsaT004380.1:CDS
TCTCCAACTCCTGCAAACAC+CGG 0.665494 1:+69090399 None:intergenic
AAGAAATTGAGTCTGCGTCG+GGG 0.697436 1:+69088121 None:intergenic
TTGCTTGAGACTTAGCCTGG+TGG 0.709949 1:+69088493 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 69087737 69090665 69087737 ID=MsaG004380
Chr1 mRNA 69087737 69090665 69087737 ID=MsaT004380.1;Parent=MsaG004380
Chr1 exon 69087737 69088211 69087737 ID=MsaT004380.1.exon5;Parent=MsaT004380.1
Chr1 CDS 69087737 69088211 69087737 ID=cds.MsaT004380.1;Parent=MsaT004380.1
Chr1 exon 69088419 69088595 69088419 ID=MsaT004380.1.exon4;Parent=MsaT004380.1
Chr1 CDS 69088419 69088595 69088419 ID=cds.MsaT004380.1;Parent=MsaT004380.1
Chr1 exon 69088684 69088813 69088684 ID=MsaT004380.1.exon3;Parent=MsaT004380.1
Chr1 CDS 69088684 69088813 69088684 ID=cds.MsaT004380.1;Parent=MsaT004380.1
Chr1 exon 69088995 69089082 69088995 ID=MsaT004380.1.exon2;Parent=MsaT004380.1
Chr1 CDS 69088995 69089082 69088995 ID=cds.MsaT004380.1;Parent=MsaT004380.1
Chr1 exon 69090327 69090665 69090327 ID=MsaT004380.1.exon1;Parent=MsaT004380.1
Chr1 CDS 69090327 69090665 69090327 ID=cds.MsaT004380.1;Parent=MsaT004380.1
Gene Sequence

>MsaT004380.1

ATGTCATTTAGGAGTATGATCATGGATAGGAAGGGATTTGACGTGAAATTCGGGTATGGTATGAGATCAAGATCACAGTCACACTGTGATGTTAATGTTATTGCCAATGGTGCTTTGGTGATTGATGATGGGTTGAGTCGGAGTTGTTGGGCTAACATGCCCCATGAGCTTTTGAGGGATGTGCTTATGAGAATTGAGGTTTCAGATGATACTTGGCCGACTCGGAAGAATGTTGTCGCGTGCGCCGGTGTTTGCAGGAGTTGGAGAGAAATTGTGAAGGAACTTGTTAAGCCTCCTCAATTGTCCAGCAAGTTGACATTCCCTGTCTCCTTGAAGCAGCCTGGTCCAAGGGGCTCTCTTATTCAGTGCTATATTAAACGAAATCGCGGCGACCAAATTTATTATCTTTTTCTCAGTTTGAACCAAGCCTCAACTGATGACGGCAAGTTCCTTCTTGCTGCACGCAAGTGTCGACGTGCAACCCACACTGACTATATCATTTCTCTAAATTTGGATGATGTATCAAGAAGGAGTAGCACCTATGTTGGGAAGTTGAGATCAAACTTTCTGGGCACCAAATTTACAGTGTATGATGCACACCCTCCAATTTATGGAGACAGATTTGCAAAGTCCCGCACCACCAGGCTAAGTCTCAAGCAAGTGTCTCCAAGAGTTCCTGCAGGAAACTATCCCATCGTGCATGTCTCATATGATCTGAATGTTTTGGGCTCTAGGGGCCCTAGGATTATGCAATGTGTTATGGATGCCATCCCTGCCTCAGCTGTTGAACCTGGAGGTGTGGCCCCGACGCAGACTCAATTTCTTCATAGCAGAGTTGATACTTCTCCATCTATCCCGTTCTTCAGATCAAAATCAACCCGCTCAGAGAATCTCCAATCAGCAGCACCTTTGATAAGTCAAAATGATGGGGAGCTGGTGTTAAAAAACAAGGCTCCTAGGTGGCATGAACAACTCCAATGCTGGTGTTTGAACTTCAATGGACGTGTGACAGTCGCTTCAGTTAAAAATTTCCAGCTGGTTGCTTCTCCTAAAAATGGAGTTTCTGAGGAGGCCCAGGAAAATGTCATTCTGCAGTTTGGAAAAGTCGGAAAGGATGTGTTCACCATGGATTACCAGTATCCAATCTCTGCCTTTGAAGCATTTGCAATATGCCTTAGCAGCTTTGACACCAAGATTGCTTGTGAGTGA
Protein sequence

>MsaT004380.1

MSFRSMIMDRKGFDVKFGYGMRSRSQSHCDVNVIANGALVIDDGLSRSCWANMPHELLRDVLMRIEVSDDTWPTRKNVVACAGVCRSWREIVKELVKPPQLSSKLTFPVSLKQPGPRGSLIQCYIKRNRGDQIYYLFLSLNQASTDDGKFLLAARKCRRATHTDYIISLNLDDVSRRSSTYVGKLRSNFLGTKFTVYDAHPPIYGDRFAKSRTTRLSLKQVSPRVPAGNYPIVHVSYDLNVLGSRGPRIMQCVMDAIPASAVEPGGVAPTQTQFLHSRVDTSPSIPFFRSKSTRSENLQSAAPLISQNDGELVLKNKAPRWHEQLQCWCLNFNGRVTVASVKNFQLVASPKNGVSEEAQENVILQFGKVGKDVFTMDYQYPISAFEAFAICLSSFDTKIACE*