AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene33310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33310.t1 MTR_3g089055 97.248 109 3 0 72 180 388 496 1.31e-69 221
MS.gene33310.t1 MTR_3g089055 85.246 61 9 0 1 61 222 282 1.03e-26 105
MS.gene33310.t1 MTR_3g089055 97.248 109 3 0 72 180 383 491 1.51e-69 221
MS.gene33310.t1 MTR_3g089055 85.246 61 9 0 1 61 217 277 1.32e-26 105
MS.gene33310.t1 MTR_1g029420 91.667 108 9 0 73 180 411 518 5.16e-65 209
MS.gene33310.t1 MTR_1g029420 72.131 61 17 0 1 61 244 304 2.03e-21 90.9
MS.gene33310.t1 MTR_5g097480 69.811 106 32 0 75 180 365 470 1.47e-46 160
MS.gene33310.t1 MTR_5g097480 49.180 61 31 0 1 61 196 256 1.87e-12 65.1
MS.gene33310.t1 MTR_2g082090 66.355 107 36 0 74 180 399 505 2.12e-43 152
MS.gene33310.t1 MTR_3g056110 62.264 106 40 0 75 180 363 468 2.19e-41 146
MS.gene33310.t1 MTR_4g133660 51.370 146 53 4 52 180 325 469 5.94e-41 145
MS.gene33310.t1 MTR_2g026250 65.000 100 35 0 81 180 423 522 1.36e-39 142
MS.gene33310.t1 MTR_5g094450 57.025 121 47 2 65 180 338 458 6.79e-39 139
MS.gene33310.t1 MTR_6g047750 47.664 107 50 2 74 180 482 582 3.21e-26 104
MS.gene33310.t1 MTR_7g057230 49.057 106 53 1 75 180 480 584 3.08e-25 102
MS.gene33310.t1 MTR_7g027190 41.406 128 67 2 55 180 477 598 1.35e-20 88.6
MS.gene33310.t1 MTR_8g442410 45.283 106 55 1 75 180 350 452 6.49e-20 86.7
MS.gene33310.t1 MTR_4g077760 38.655 119 64 3 69 181 369 484 1.25e-16 77.0
MS.gene33310.t1 MTR_4g104020 40.000 100 57 1 81 180 350 446 4.18e-16 75.5
MS.gene33310.t1 MTR_3g065980 35.417 144 69 5 28 153 288 425 8.40e-16 74.7
MS.gene33310.t1 MTR_7g074650 42.991 107 54 3 75 181 620 719 3.39e-15 73.2
MS.gene33310.t1 MTR_4g076020 41.667 108 54 4 75 181 257 356 5.83e-14 69.3
MS.gene33310.t1 MTR_3g072710 36.364 110 66 2 71 180 320 425 7.88e-14 68.9
MS.gene33310.t1 MTR_5g015950 31.304 115 63 2 81 180 259 372 2.93e-13 67.4
MS.gene33310.t1 MTR_3g053270 31.304 115 63 2 81 180 259 372 2.93e-13 67.4
MS.gene33310.t1 MTR_1g069725 37.615 109 61 2 73 181 287 388 3.10e-13 67.4
MS.gene33310.t1 MTR_2g097467 27.742 155 99 3 28 180 436 579 3.66e-13 67.0
MS.gene33310.t1 MTR_4g064200 36.634 101 63 1 81 180 475 575 8.81e-13 65.9
MS.gene33310.t1 MTR_4g064160 33.019 106 71 0 75 180 504 609 1.38e-12 65.5
MS.gene33310.t1 MTR_4g064150 31.132 106 73 0 75 180 553 658 3.12e-12 64.3
MS.gene33310.t1 MTR_2g097410 33.333 108 68 3 75 180 561 666 4.37e-12 63.9
MS.gene33310.t1 MTR_4g064180 30.189 106 74 0 75 180 446 551 4.61e-12 63.9
MS.gene33310.t1 MTR_2g097463 31.000 100 69 0 81 180 481 580 8.73e-12 63.2
MS.gene33310.t1 MTR_1g096030 29.101 189 105 7 14 175 176 362 1.31e-11 62.4
MS.gene33310.t1 MTR_4g076140 38.667 75 46 0 106 180 320 394 1.42e-11 62.4
MS.gene33310.t1 MTR_2g089100 31.034 116 78 2 67 181 256 370 1.95e-11 62.0
MS.gene33310.t1 MTR_4g064120 29.245 106 75 0 75 180 446 551 2.12e-11 62.0
MS.gene33310.t1 MTR_2g097473 27.273 154 97 5 30 180 438 579 2.69e-11 61.6
MS.gene33310.t1 MTR_4g102790 39.450 109 60 5 74 180 478 582 8.02e-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
MS.gene33310.t1 AT1G21450 81.250 112 20 1 69 180 408 518 2.68e-59 194
MS.gene33310.t1 AT1G21450 44.068 118 52 2 1 115 244 350 1.08e-20 89.0
MS.gene33310.t1 AT5G48150 68.868 106 33 0 75 180 311 416 5.95e-46 157
MS.gene33310.t1 AT5G48150 68.868 106 33 0 75 180 311 416 5.95e-46 157
MS.gene33310.t1 AT5G48150 68.868 106 33 0 75 180 311 416 5.95e-46 157
MS.gene33310.t1 AT5G48150 68.868 106 33 0 75 180 311 416 5.95e-46 157
MS.gene33310.t1 AT2G04890 64.151 106 38 0 75 180 234 339 3.02e-45 154
MS.gene33310.t1 AT1G50600 64.151 106 38 0 75 180 347 452 5.59e-41 144
MS.gene33310.t1 AT1G50600 49.180 61 31 0 1 61 178 238 1.08e-11 62.8
MS.gene33310.t1 AT1G50600 64.151 106 38 0 75 180 418 523 1.04e-40 145
MS.gene33310.t1 AT1G50600 49.180 61 31 0 1 61 249 309 8.96e-12 63.2
MS.gene33310.t1 AT1G50600 64.151 106 38 0 75 180 422 527 1.05e-40 145
MS.gene33310.t1 AT1G50600 49.180 61 31 0 1 61 253 313 9.50e-12 63.2
MS.gene33310.t1 AT4G17230 55.833 120 43 1 61 180 342 451 7.13e-40 142
MS.gene33310.t1 AT4G17230 55.833 120 43 1 61 180 342 451 7.13e-40 142
MS.gene33310.t1 AT5G52510 50.943 106 51 1 75 180 462 566 4.89e-27 107
MS.gene33310.t1 AT5G66770 46.316 95 48 1 81 175 410 501 3.01e-18 81.6
MS.gene33310.t1 AT3G50650 40.708 113 64 1 67 179 350 459 3.91e-17 78.6
MS.gene33310.t1 AT3G03450 46.000 100 49 2 81 180 375 469 3.15e-16 75.9
MS.gene33310.t1 AT2G29065 36.449 107 67 1 75 180 446 552 8.86e-16 74.7
MS.gene33310.t1 AT1G07530 38.679 106 65 0 75 180 585 690 1.67e-15 73.9
MS.gene33310.t1 AT5G17490 46.000 100 49 2 81 180 346 440 4.39e-15 72.8
MS.gene33310.t1 AT1G66350 41.667 108 54 4 74 180 331 430 8.95e-15 71.6
MS.gene33310.t1 AT3G54220 42.593 108 53 4 75 181 478 577 9.17e-15 71.6
MS.gene33310.t1 AT1G55580 34.653 101 63 1 80 180 272 369 1.05e-14 71.6
MS.gene33310.t1 AT5G41920 39.450 109 59 2 73 180 228 330 2.78e-14 70.1
MS.gene33310.t1 AT3G46600 36.634 101 64 0 80 180 196 296 5.82e-14 69.3
MS.gene33310.t1 AT3G46600 36.634 101 64 0 80 180 372 472 6.84e-14 69.3
MS.gene33310.t1 AT3G46600 36.634 101 64 0 80 180 404 504 7.64e-14 68.9
MS.gene33310.t1 AT5G59450 35.922 103 64 1 80 180 421 523 1.10e-13 68.6
MS.gene33310.t1 AT2G37650 33.019 106 71 0 75 180 533 638 1.07e-12 65.9
MS.gene33310.t1 AT2G37650 33.019 106 71 0 75 180 521 626 1.15e-12 65.9
MS.gene33310.t1 AT2G01570 33.871 186 94 10 16 180 328 505 3.78e-12 64.3
MS.gene33310.t1 AT1G50420 34.667 75 49 0 106 180 330 404 1.29e-11 62.8
MS.gene33310.t1 AT1G14920 32.558 172 89 9 28 180 290 453 2.54e-11 61.6
MS.gene33310.t1 AT2G29060 31.132 106 73 0 75 180 511 616 4.13e-11 61.2
MS.gene33310.t1 AT2G29060 31.132 106 73 0 75 180 474 579 4.45e-11 61.2
MS.gene33310.t1 AT5G67411 34.653 101 64 2 80 180 89 187 5.02e-11 59.3

Find 36 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACGACCGTTACAAGTTT+TGG 0.308347 3.3:+75223470 None:intergenic
CATGTAGGCTGCAATTCTTT+TGG 0.335860 3.3:+75224062 None:intergenic
TCGATGCTTGATTGTCGAAT+TGG 0.379071 3.3:-75223602 MS.gene33310:CDS
GCCGCTCGCCTCGCTGAATC+CGG 0.387906 3.3:-75224028 MS.gene33310:CDS
GGCAAGGGATATTGTTAATA+CGG 0.423892 3.3:-75223306 MS.gene33310:CDS
ATGCAAGGAACCTCCTTCTT+CGG 0.450058 3.3:-75223981 MS.gene33310:CDS
CAAAAGAATTGCAGCCTACA+TGG 0.454180 3.3:-75224061 MS.gene33310:CDS
ACAGTTGAAACGCTCTCGTC+AGG 0.461394 3.3:+75223536 None:intergenic
TACTCTTCCTAGAGAGAGCC+AGG 0.477900 3.3:-75223357 MS.gene33310:CDS
CGTCAGGCATGTGATGAAGC+TGG 0.484030 3.3:+75223552 None:intergenic
TCTCAACATTCATCCTATCC+TGG 0.491515 3.3:+75223339 None:intergenic
AGCGATGCAGATACTGTTCG+AGG 0.503528 3.3:-75223948 MS.gene33310:intron
ACGAGACCAACTTCTTCGCT+TGG 0.503960 3.3:-75223507 MS.gene33310:CDS
GAATGTTGAGAGGCAATGTC+TGG 0.507684 3.3:-75223327 MS.gene33310:CDS
ATCCTATCCTGGCTCTCTCT+AGG 0.512100 3.3:+75223350 None:intergenic
TCTTTACCAAGCGAAGAAGT+TGG 0.520115 3.3:+75223501 None:intergenic
GCTGCTAGACGGTCCGAAGA+AGG 0.532544 3.3:+75223968 None:intergenic
TCCAAAACTTGTAACGGTCG+TGG 0.541218 3.3:-75223471 MS.gene33310:CDS
TTATAGAGCTTTGAAATGCA+AGG 0.546542 3.3:-75223996 MS.gene33310:CDS
TTTGAATCCAAAACTTGTAA+CGG 0.552516 3.3:-75223477 MS.gene33310:CDS
TTGAGAGGCAATGTCTGGCA+AGG 0.566022 3.3:-75223322 MS.gene33310:CDS
CGACGAATTGTCTCAAGTCA+AGG 0.571474 3.3:-75224094 MS.gene33310:CDS
GAATTGCAGCCTACATGGTG+AGG 0.589095 3.3:-75224056 MS.gene33310:CDS
TCCGGATTCAGCGAGGCGAG+CGG 0.592435 3.3:+75224027 None:intergenic
CGACAATCAAGCATCGATGA+CGG 0.603447 3.3:+75223608 None:intergenic
GTATCTGCATCGCTGCTAGA+CGG 0.609923 3.3:+75223957 None:intergenic
CGGCGAGTCCCTCACCATGT+AGG 0.609983 3.3:+75224047 None:intergenic
TTCCTAGAGAGAGCCAGGAT+AGG 0.625909 3.3:-75223352 MS.gene33310:CDS
TCGAATTGGAGAAGCTCTTG+TGG 0.628740 3.3:-75223588 MS.gene33310:CDS
TGAGAGGCAATGTCTGGCAA+GGG 0.635494 3.3:-75223321 MS.gene33310:CDS
TTAATACGGTTGCAATGTGA+AGG 0.636823 3.3:-75223292 None:intergenic
AATTGCAGCCTACATGGTGA+GGG 0.638850 3.3:-75224055 MS.gene33310:CDS
CTTGACTTGAGACAATTCGT+CGG 0.653570 3.3:+75224095 None:intergenic
GCTAGACGGTCCGAAGAAGG+AGG 0.655079 3.3:+75223971 None:intergenic
AGGATAGGATGAATGTTGAG+AGG 0.660140 3.3:-75223337 MS.gene33310:CDS
AATTTCGAGCGGTCTCATCG+AGG 0.679065 3.3:-75223644 MS.gene33310:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAGATTTTGATATCAATCA+AGG - chr3.3:75223565-75223584 MS.gene33310:CDS 20.0%
! TTTGAATCCAAAACTTGTAA+CGG - chr3.3:75223927-75223946 MS.gene33310:intron 25.0%
!!! AGCTCTATAAATACTTTTTC+CGG + chr3.3:75223398-75223417 None:intergenic 25.0%
TAAACCCGAATTTAGAAACA+CGG + chr3.3:75223487-75223506 None:intergenic 30.0%
TAACTATGCAATAACAGAAG+CGG - chr3.3:75223515-75223534 MS.gene33310:CDS 30.0%
TCAACAAATCTCTGCAAAAA+CGG + chr3.3:75223985-75224004 None:intergenic 30.0%
! ATTGTCATTTGAATTTCGAG+CGG - chr3.3:75223749-75223768 MS.gene33310:intron 30.0%
! TTTGTCCGTGTTTCTAAATT+CGG - chr3.3:75223479-75223498 MS.gene33310:CDS 30.0%
!! TTATAGAGCTTTGAAATGCA+AGG - chr3.3:75223408-75223427 MS.gene33310:CDS 30.0%
AACAAATCTCTGCAAAAACG+GGG + chr3.3:75223983-75224002 None:intergenic 35.0%
CAACAAATCTCTGCAAAAAC+GGG + chr3.3:75223984-75224003 None:intergenic 35.0%
GAAGCAAGTGTTTGAATTCA+GGG + chr3.3:75223605-75223624 None:intergenic 35.0%
GGCAAGGGATATTGTTAATA+CGG - chr3.3:75224098-75224117 MS.gene33310:CDS 35.0%
TATGATCTTTAGTCCTCCAA+CGG + chr3.3:75223693-75223712 None:intergenic 35.0%
! TTGTCCGTGTTTCTAAATTC+GGG - chr3.3:75223480-75223499 MS.gene33310:CDS 35.0%
AGGATAGGATGAATGTTGAG+AGG - chr3.3:75224067-75224086 MS.gene33310:CDS 40.0%
CAAAAGAATTGCAGCCTACA+TGG - chr3.3:75223343-75223362 MS.gene33310:CDS 40.0%
CATCACATGTTAGATTGACC+GGG - chr3.3:75223639-75223658 MS.gene33310:intron 40.0%
CCATCACATGTTAGATTGAC+CGG - chr3.3:75223638-75223657 MS.gene33310:CDS 40.0%
CGAAGCAAGTGTTTGAATTC+AGG + chr3.3:75223606-75223625 None:intergenic 40.0%
GAACAACTAGCAGAAACACT+TGG - chr3.3:75223726-75223745 MS.gene33310:intron 40.0%
GAATTCAAACACTTGCTTCG+AGG - chr3.3:75223606-75223625 MS.gene33310:CDS 40.0%
GTTGGAGGACTAAAGATCAT+AGG - chr3.3:75223692-75223711 MS.gene33310:intron 40.0%
TCGATGCTTGATTGTCGAAT+TGG - chr3.3:75223802-75223821 MS.gene33310:intron 40.0%
TCTCAACATTCATCCTATCC+TGG + chr3.3:75224068-75224087 None:intergenic 40.0%
TCTTTACCAAGCGAAGAAGT+TGG + chr3.3:75223906-75223925 None:intergenic 40.0%
! CATGTAGGCTGCAATTCTTT+TGG + chr3.3:75223345-75223364 None:intergenic 40.0%
! CTTGACTTGAGACAATTCGT+CGG + chr3.3:75223312-75223331 None:intergenic 40.0%
!! AGGCTGCAATTCTTTTGGAA+CGG + chr3.3:75223340-75223359 None:intergenic 40.0%
AAATCTCTGCAAAAACGGGG+CGG + chr3.3:75223980-75223999 None:intergenic 45.0%
AATTGCAGCCTACATGGTGA+GGG - chr3.3:75223349-75223368 MS.gene33310:CDS 45.0%
AGACACAGGATCATCAATCC+CGG + chr3.3:75223660-75223679 None:intergenic 45.0%
ATGCAAGGAACCTCCTTCTT+CGG - chr3.3:75223423-75223442 MS.gene33310:CDS 45.0%
CCGGTCAATCTAACATGTGA+TGG + chr3.3:75223641-75223660 None:intergenic 45.0%
CGACGAATTGTCTCAAGTCA+AGG - chr3.3:75223310-75223329 MS.gene33310:CDS 45.0%
GAATGTTGAGAGGCAATGTC+TGG - chr3.3:75224077-75224096 MS.gene33310:CDS 45.0%
TCCAAAACTTGTAACGGTCG+TGG - chr3.3:75223933-75223952 MS.gene33310:intron 45.0%
TCGAATTGGAGAAGCTCTTG+TGG - chr3.3:75223816-75223835 MS.gene33310:intron 45.0%
! TCCACGACCGTTACAAGTTT+TGG + chr3.3:75223937-75223956 None:intergenic 45.0%
!! CGACAATCAAGCATCGATGA+CGG + chr3.3:75223799-75223818 None:intergenic 45.0%
!!! TACTTTTTCCGGATTCAGCG+AGG + chr3.3:75223387-75223406 None:intergenic 45.0%
AATTTCGAGCGGTCTCATCG+AGG - chr3.3:75223760-75223779 MS.gene33310:intron 50.0%
ACAGTTGAAACGCTCTCGTC+AGG + chr3.3:75223871-75223890 None:intergenic 50.0%
ACGAGACCAACTTCTTCGCT+TGG - chr3.3:75223897-75223916 MS.gene33310:intron 50.0%
AGCGATGCAGATACTGTTCG+AGG - chr3.3:75223456-75223475 MS.gene33310:CDS 50.0%
GAATTGCAGCCTACATGGTG+AGG - chr3.3:75223348-75223367 MS.gene33310:CDS 50.0%
GTATCTGCATCGCTGCTAGA+CGG + chr3.3:75223450-75223469 None:intergenic 50.0%
TACTCTTCCTAGAGAGAGCC+AGG - chr3.3:75224047-75224066 MS.gene33310:CDS 50.0%
TGAGAGGCAATGTCTGGCAA+GGG - chr3.3:75224083-75224102 MS.gene33310:CDS 50.0%
TTCCTAGAGAGAGCCAGGAT+AGG - chr3.3:75224052-75224071 MS.gene33310:CDS 50.0%
TTGAGAGGCAATGTCTGGCA+AGG - chr3.3:75224082-75224101 MS.gene33310:CDS 50.0%
! ATCCTATCCTGGCTCTCTCT+AGG + chr3.3:75224057-75224076 None:intergenic 50.0%
CGTCAGGCATGTGATGAAGC+TGG + chr3.3:75223855-75223874 None:intergenic 55.0%
CTGCAAAAACGGGGCGGTAT+TGG + chr3.3:75223974-75223993 None:intergenic 55.0%
ACGGATCGCTGCACAGACAC+AGG + chr3.3:75223674-75223693 None:intergenic 60.0%
GCTAGACGGTCCGAAGAAGG+AGG + chr3.3:75223436-75223455 None:intergenic 60.0%
GCTGCTAGACGGTCCGAAGA+AGG + chr3.3:75223439-75223458 None:intergenic 60.0%
GTGTCTGTGCAGCGATCCGT+TGG - chr3.3:75223674-75223693 MS.gene33310:intron 60.0%
TCTGTGCAGCGATCCGTTGG+AGG - chr3.3:75223677-75223696 MS.gene33310:intron 60.0%
CGGCGAGTCCCTCACCATGT+AGG + chr3.3:75223360-75223379 None:intergenic 65.0%
TCCGGATTCAGCGAGGCGAG+CGG + chr3.3:75223380-75223399 None:intergenic 65.0%
GCCGCTCGCCTCGCTGAATC+CGG - chr3.3:75223376-75223395 MS.gene33310:CDS 70.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 75223295 75224131 75223295 ID=MS.gene33310
chr3.3 mRNA 75223295 75224131 75223295 ID=MS.gene33310.t1;Parent=MS.gene33310
chr3.3 exon 75223949 75224131 75223949 ID=MS.gene33310.t1.exon1;Parent=MS.gene33310.t1
chr3.3 CDS 75223949 75224131 75223949 ID=cds.MS.gene33310.t1;Parent=MS.gene33310.t1
chr3.3 exon 75223295 75223657 75223295 ID=MS.gene33310.t1.exon2;Parent=MS.gene33310.t1
chr3.3 CDS 75223295 75223657 75223295 ID=cds.MS.gene33310.t1;Parent=MS.gene33310.t1
Gene Sequence

>MS.gene33310

ATGATAAACAATCTCCGACGAATTGTCTCAAGTCAAGGAGAGCCGTTCCAAAAGAATTGCAGCCTACATGGTGAGGGACTCGCCGCTCGCCTCGCTGAATCCGGAAAAAGTATTTATAGAGCTTTGAAATGCAAGGAACCTCCTTCTTCGGACCGTCTAGCAGCGATGCAGATACTGTTCGAGGTTTGTCCGTGTTTCTAAATTCGGGTTTATTGCAAGCTAACTATGCAATAACAGAAGCGGTTTAAAGATGAAATGAAGATTCATATAATAGATTTTGATATCAATCAAGGAAGTCAGTACATAACCCTGAATTCAAACACTTGCTTCGAGGTCTTGTAAGCCATCACATGTTAGATTGACCGGGATTGATGATCCTGTGTCTGTGCAGCGATCCGTTGGAGGACTAAAGATCATAGGACAAGAGACTTGAACAACTAGCAGAAACACTTGGATTGTCATTTGAATTTCGAGCGGTCTCATCGAGGACTTCAATTGTCACCGTCATCGATGCTTGATTGTCGAATTGGAGAAGCTCTTGTGGTGAACTTTGCATTCCAGCTTCATCACATGCCTGACGAGAGCGTTTCAACTGTGAACGAACGAGACCAACTTCTTCGCTTGGTAAAGAGTTTGAATCCAAAACTTGTAACGGTCGTGGAGCAAGATGTAAACACCAATACCGCCCCGTTTTTGCAGAGATTTGTTGAAGCTTACAATTACTACTCTGCTGTGTTTGAGTCACTTGATGTTACTCTTCCTAGAGAGAGCCAGGATAGGATGAATGTTGAGAGGCAATGTCTGGCAAGGGATATTGTTAATACGGTTGCAATGTGA
Protein sequence

>MS.gene33310.t1

MINNLRRIVSSQGEPFQKNCSLHGEGLAARLAESGKSIYRALKCKEPPSSDRLAAMQILFERSHRGLQLSPSSMLDCRIGEALVVNFAFQLHHMPDESVSTVNERDQLLRLVKSLNPKLVTVVEQDVNTNTAPFLQRFVEAYNYYSAVFESLDVTLPRESQDRMNVERQCLARDIVNTVAM