AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0529040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0529040 MtrunA17_Chr7g0223781 85.294 136 20 0 2 137 447 582 1.94e-74 233
Msa0529040 MtrunA17_Chr7g0223681 57.353 136 57 1 2 137 360 494 7.21e-40 140
Msa0529040 MtrunA17_Chr7g0248131 56.618 136 58 1 2 137 452 586 1.02e-39 140
Msa0529040 MtrunA17_Chr7g0223031 52.899 138 64 1 2 139 449 585 7.83e-38 135
Msa0529040 MtrunA17_Chr7g0223751 55.147 136 60 1 2 137 449 583 1.48e-37 134
Msa0529040 MtrunA17_Chr7g0248151 55.147 136 60 1 2 137 450 584 3.62e-37 133
Msa0529040 MtrunA17_Chr7g0223731 54.015 137 62 1 2 138 449 584 2.72e-36 130
Msa0529040 MtrunA17_Chr7g0223541 50.360 139 65 3 2 138 406 542 3.09e-34 125
Msa0529040 MtrunA17_Chr8g0350731 51.471 136 65 1 2 137 477 611 3.57e-34 125
Msa0529040 MtrunA17_Chr2g0298861 49.265 136 69 0 2 137 461 596 2.50e-33 122
Msa0529040 MtrunA17_Chr7g0223621 50.746 134 65 1 2 135 449 581 7.88e-33 121
Msa0529040 MtrunA17_Chr7g0217971 49.630 135 67 1 2 136 425 558 1.08e-32 120
Msa0529040 MtrunA17_Chr5g0427901 48.551 138 71 0 2 139 460 597 1.49e-32 120
Msa0529040 MtrunA17_Chr7g0223801 49.265 136 68 1 1 136 447 581 2.06e-32 120
Msa0529040 MtrunA17_Chr7g0223631 51.471 136 65 1 2 137 435 569 2.51e-32 119
Msa0529040 MtrunA17_Chr7g0223721 48.872 133 68 0 2 134 449 581 2.68e-32 119
Msa0529040 MtrunA17_Chr7g0223701 48.571 140 68 1 2 137 453 592 4.93e-32 119
Msa0529040 MtrunA17_Chr1g0166551 49.624 133 66 1 2 134 334 465 5.02e-32 118
Msa0529040 MtrunA17_Chr7g0223181 51.128 133 64 1 2 133 448 580 5.29e-32 119
Msa0529040 MtrunA17_Chr7g0233311 48.551 138 70 1 2 138 449 586 8.05e-32 118
Msa0529040 MtrunA17_Chr7g0223741 50.725 138 66 2 2 138 449 585 3.18e-31 116
Msa0529040 MtrunA17_Chr7g0223711 50.000 138 65 2 2 137 449 584 1.47e-30 115
Msa0529040 MtrunA17_Chr4g0031301 50.388 129 63 1 2 129 448 576 4.80e-30 113
Msa0529040 MtrunA17_Chr7g0245531 48.529 136 70 0 2 137 146 281 1.09e-29 109
Msa0529040 MtrunA17_Chr7g0262821 50.388 129 63 1 2 129 448 576 1.41e-29 112
Msa0529040 MtrunA17_Chr8g0390821 47.015 134 71 0 2 135 487 620 1.52e-29 112
Msa0529040 MtrunA17_Chr7g0223291 52.066 121 57 1 2 121 448 568 1.94e-29 111
Msa0529040 MtrunA17_Chr4g0031321 49.612 129 64 1 2 129 448 576 2.14e-29 111
Msa0529040 MtrunA17_Chr2g0287631 49.265 136 68 1 2 136 449 584 2.51e-29 111
Msa0529040 MtrunA17_Chr7g0245541 45.588 136 74 0 2 137 33 168 6.94e-29 104
Msa0529040 MtrunA17_Chr2g0298851 48.120 133 68 1 2 134 450 581 7.87e-29 110
Msa0529040 MtrunA17_Chr7g0233301 44.928 138 75 1 2 138 418 555 5.51e-28 107
Msa0529040 MtrunA17_Chr2g0293581 47.761 134 69 1 2 134 450 583 6.10e-28 107
Msa0529040 MtrunA17_Chr4g0073741 48.837 129 65 1 2 129 447 575 7.04e-28 107
Msa0529040 MtrunA17_Chr4g0040931 46.617 133 71 0 2 134 449 581 1.48e-27 106
Msa0529040 MtrunA17_Chr7g0228281 45.865 133 71 1 2 134 466 597 2.15e-27 105
Msa0529040 MtrunA17_Chr1g0152001 46.617 133 70 1 2 134 134 265 4.95e-27 102
Msa0529040 MtrunA17_Chr7g0221661 44.361 133 74 0 2 134 449 581 6.84e-27 104
Msa0529040 MtrunA17_Chr7g0223851 47.015 134 70 1 1 134 458 590 7.02e-27 104
Msa0529040 MtrunA17_Chr7g0215261 46.617 133 71 0 2 134 415 547 6.58e-26 101
Msa0529040 MtrunA17_Chr4g0012541 45.865 133 71 1 2 134 441 572 9.85e-26 101
Msa0529040 MtrunA17_Chr7g0223831 46.512 129 69 0 2 130 421 549 1.65e-25 100
Msa0529040 MtrunA17_Chr7g0225671 44.361 133 73 1 2 134 456 587 1.31e-24 98.2
Msa0529040 MtrunA17_Chr2g0284681 45.299 117 63 1 2 117 453 569 2.59e-22 91.7
Msa0529040 MtrunA17_Chr8g0388671 41.045 134 77 2 2 133 474 607 2.83e-22 91.3
Msa0529040 MtrunA17_Chr8g0388761 41.045 134 77 2 2 133 474 607 3.37e-22 91.3
Msa0529040 MtrunA17_Chr7g0223821 46.617 133 70 1 1 133 450 581 2.31e-21 89.0
Msa0529040 MtrunA17_Chr6g0462601 45.600 125 68 0 2 126 448 572 3.44e-21 88.2
Msa0529040 MtrunA17_Chr1g0188611 45.536 112 61 0 2 113 128 239 1.01e-20 85.1
Msa0529040 MtrunA17_Chr7g0223761 43.119 109 62 0 26 134 194 302 1.34e-20 85.5
Msa0529040 MtrunA17_Chr6g0462681 40.152 132 79 0 2 133 448 579 6.49e-20 84.7
Msa0529040 MtrunA17_Chr6g0462771 44.094 127 71 0 4 130 455 581 8.38e-20 84.3
Msa0529040 MtrunA17_Chr6g0462711 42.308 130 73 2 2 130 455 583 1.49e-19 83.6
Msa0529040 MtrunA17_Chr2g0277021 39.831 118 69 2 2 118 502 618 4.11e-19 82.4
Msa0529040 MtrunA17_Chr6g0462641 41.221 131 73 3 2 130 453 581 4.82e-19 82.0
Msa0529040 MtrunA17_Chr6g0462611 41.085 129 76 0 2 130 396 524 5.19e-19 82.0
Msa0529040 MtrunA17_Chr7g0223791 44.444 90 50 0 35 124 90 179 1.20e-18 77.8
Msa0529040 MtrunA17_Chr2g0279901 39.474 114 67 2 2 114 485 597 2.33e-17 77.4
Msa0529040 MtrunA17_Chr2g0331381 52.055 73 35 0 28 100 410 482 3.31e-17 77.0
Msa0529040 MtrunA17_Chr4g0049501 38.596 114 68 2 2 114 483 595 1.61e-15 72.0
Msa0529040 MtrunA17_Chr2g0299821 47.423 97 41 3 4 92 390 484 1.65e-15 72.0
Msa0529040 MtrunA17_Chr7g0223871 41.758 91 53 0 44 134 7 97 2.90e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0529040 AT3G12580.1 55.263 114 50 1 2 114 448 561 2.78e-30 114
Msa0529040 AT5G02490.1 53.509 114 52 1 2 114 448 561 4.51e-29 111
Msa0529040 AT1G16030.1 48.872 133 67 1 2 133 447 579 4.98e-29 110
Msa0529040 AT3G09440.1 52.632 114 53 1 2 114 448 561 6.02e-29 110
Msa0529040 AT3G09440.4 52.632 114 53 1 2 114 448 561 6.02e-29 110
Msa0529040 AT3G09440.2 52.632 114 53 1 2 114 448 561 6.02e-29 110
Msa0529040 AT3G09440.3 52.632 114 53 1 2 114 448 561 6.02e-29 110
Msa0529040 AT5G02500.1 52.632 114 53 1 2 114 448 561 1.23e-28 110
Msa0529040 AT1G56410.1 48.062 129 64 2 2 129 448 574 5.14e-28 108
Msa0529040 AT5G42020.1 42.308 130 73 2 2 129 473 602 5.48e-22 90.9
Msa0529040 AT5G28540.1 42.308 130 73 2 2 129 473 602 5.59e-22 90.9
Msa0529040 AT5G42020.3 42.308 130 73 2 2 129 478 607 7.00e-22 90.9
Msa0529040 AT4G24280.1 39.831 118 69 2 2 118 511 627 4.64e-19 82.8
Msa0529040 AT5G49910.1 38.983 118 70 2 2 118 511 627 1.21e-18 81.6
Msa0529040 AT5G09590.1 40.179 112 65 2 2 112 489 599 1.03e-16 75.9
Msa0529040 AT4G37910.1 38.596 114 68 2 2 114 484 596 7.85e-16 73.6
Msa0529040 AT4G37910.2 38.596 114 68 2 2 114 484 596 7.85e-16 73.6
Msa0529040 AT1G09080.2 40.833 120 70 1 2 120 477 596 1.08e-13 67.4
Msa0529040 AT1G09080.1 40.833 120 70 1 2 120 487 606 1.25e-13 67.0

Find 30 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACAATATCCTTGTATTAT+TGG 0.140106 4_1:-2060779 None:intergenic
TTGAACTTCATTTCTTCTTC+AGG 0.277701 4_1:-2060958 None:intergenic
TATCCTTGTATTATTGGTTA+TGG 0.304694 4_1:-2060773 None:intergenic
TCACTGCATTAACTTTCTTC+TGG 0.335240 4_1:-2060864 None:intergenic
CAAGATAAACAAGGCTTTGA+AGG 0.356394 4_1:+2060909 Msa0529040:CDS
TTTGTGAGGGTGAGAGGAAA+TGG 0.358539 4_1:+2060596 Msa0529040:CDS
AAGAAGAAATGAAGTTCAAT+TGG 0.384214 4_1:+2060962 Msa0529040:CDS
GGCTAGTGATAACAATTTGT+TGG 0.411065 4_1:+2060618 Msa0529040:CDS
CTTTGAAGGATATTGATAGA+AGG 0.417926 4_1:+2060923 Msa0529040:CDS
GCTAGTGATAACAATTTGTT+GGG 0.433463 4_1:+2060619 Msa0529040:CDS
TTCTTCTTCAGGACGAAGCT+TGG 0.451153 4_1:-2060947 None:intergenic
AGTTAATGCAGTGAATGCTT+TGG 0.464192 4_1:+2060873 Msa0529040:CDS
TTCAATTGGAAAATTTCAAA+GGG 0.465133 4_1:+2060976 Msa0529040:CDS
CAAAATATACATTCAAAGAA+TGG 0.482301 4_1:-2060681 None:intergenic
GTTCAATTGGAAAATTTCAA+AGG 0.484360 4_1:+2060975 Msa0529040:CDS
TTGTGAGGGTGAGAGGAAAT+GGG 0.484675 4_1:+2060597 Msa0529040:CDS
TTATGGTTTGTGAGGGTGAG+AGG 0.504583 4_1:+2060590 None:intergenic
TTTGAAGGATATTGATAGAA+GGG 0.532707 4_1:+2060924 Msa0529040:CDS
TATGCTGAGGAAGAATGTAC+TGG 0.557813 4_1:+2060733 Msa0529040:CDS
AATGGCCTCGAGGATTAGAA+AGG 0.577938 4_1:-2060663 None:intergenic
GAAGCGGAGAAATACAAGGC+TGG 0.585908 4_1:+2060829 Msa0529040:CDS
TATGCGAATGATTCAAGAAG+CGG 0.586070 4_1:+2060813 Msa0529040:CDS
GTCGGGATTATGGTTTGTGA+GGG 0.590502 4_1:+2060583 None:intergenic
TCAAGAAGCGGAGAAATACA+AGG 0.594382 4_1:+2060825 Msa0529040:CDS
TGTCGGGATTATGGTTTGTG+AGG 0.614910 4_1:+2060582 None:intergenic
TTACCATAACCAATAATACA+AGG 0.647129 4_1:+2060770 Msa0529040:CDS
TATCTTAATTGTATATGCTG+AGG 0.648927 4_1:+2060720 Msa0529040:CDS
TTATGTTTACAAGATAAACA+AGG 0.665369 4_1:+2060900 Msa0529040:CDS
TGGAACCTTTCTAATCCTCG+AGG 0.689314 4_1:+2060658 Msa0529040:CDS
ACATTCAAAGAATGGCCTCG+AGG 0.713234 4_1:-2060673 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAAATATACATTCAAAGAA+TGG - chr4_1:2060684-2060703 None:intergenic 20.0%
!! TTATGTTTACAAGATAAACA+AGG + chr4_1:2060900-2060919 Msa0529040:CDS 20.0%
!! TTCAATTGGAAAATTTCAAA+GGG + chr4_1:2060976-2060995 Msa0529040:CDS 20.0%
! TATCTTAATTGTATATGCTG+AGG + chr4_1:2060720-2060739 Msa0529040:CDS 25.0%
! TTACCATAACCAATAATACA+AGG + chr4_1:2060770-2060789 Msa0529040:CDS 25.0%
!! TATCCTTGTATTATTGGTTA+TGG - chr4_1:2060776-2060795 None:intergenic 25.0%
! TGACAATATCCTTGTATTAT+TGG - chr4_1:2060782-2060801 None:intergenic 25.0%
! TTTGAAGGATATTGATAGAA+GGG + chr4_1:2060924-2060943 Msa0529040:CDS 25.0%
! AAGAAGAAATGAAGTTCAAT+TGG + chr4_1:2060962-2060981 Msa0529040:CDS 25.0%
! GTTCAATTGGAAAATTTCAA+AGG + chr4_1:2060975-2060994 Msa0529040:CDS 25.0%
! GCTAGTGATAACAATTTGTT+GGG + chr4_1:2060619-2060638 Msa0529040:CDS 30.0%
!!! TGGGTTTGTTTTATCTTGAT+TGG + chr4_1:2060638-2060657 Msa0529040:CDS 30.0%
!!! TATTTTGACATAGATGCTGA+TGG + chr4_1:2060697-2060716 Msa0529040:CDS 30.0%
! CTTTGAAGGATATTGATAGA+AGG + chr4_1:2060923-2060942 Msa0529040:CDS 30.0%
TTGAACTTCATTTCTTCTTC+AGG - chr4_1:2060961-2060980 None:intergenic 30.0%
GGCTAGTGATAACAATTTGT+TGG + chr4_1:2060618-2060637 Msa0529040:CDS 35.0%
TATGCGAATGATTCAAGAAG+CGG + chr4_1:2060813-2060832 Msa0529040:CDS 35.0%
TCACTGCATTAACTTTCTTC+TGG - chr4_1:2060867-2060886 None:intergenic 35.0%
AGTTAATGCAGTGAATGCTT+TGG + chr4_1:2060873-2060892 Msa0529040:CDS 35.0%
! CAAGATAAACAAGGCTTTGA+AGG + chr4_1:2060909-2060928 Msa0529040:CDS 35.0%
TATGCTGAGGAAGAATGTAC+TGG + chr4_1:2060733-2060752 Msa0529040:CDS 40.0%
TCAAGAAGCGGAGAAATACA+AGG + chr4_1:2060825-2060844 Msa0529040:CDS 40.0%
TTTGTGAGGGTGAGAGGAAA+TGG + chr4_1:2060596-2060615 Msa0529040:CDS 45.0%
TTGTGAGGGTGAGAGGAAAT+GGG + chr4_1:2060597-2060616 Msa0529040:CDS 45.0%
TGGAACCTTTCTAATCCTCG+AGG + chr4_1:2060658-2060677 Msa0529040:CDS 45.0%
AATGGCCTCGAGGATTAGAA+AGG - chr4_1:2060666-2060685 None:intergenic 45.0%
ACATTCAAAGAATGGCCTCG+AGG - chr4_1:2060676-2060695 None:intergenic 45.0%
TTCTTCTTCAGGACGAAGCT+TGG - chr4_1:2060950-2060969 None:intergenic 45.0%
GAAGCGGAGAAATACAAGGC+TGG + chr4_1:2060829-2060848 Msa0529040:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 2060592 2061014 2060592 ID=Msa0529040;Name=Msa0529040
chr4_1 mRNA 2060592 2061014 2060592 ID=Msa0529040-mRNA-1;Parent=Msa0529040;Name=Msa0529040-mRNA-1;_AED=0.19;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|140
chr4_1 exon 2060592 2061014 2060592 ID=Msa0529040-mRNA-1:exon:640;Parent=Msa0529040-mRNA-1
chr4_1 CDS 2060592 2061014 2060592 ID=Msa0529040-mRNA-1:cds;Parent=Msa0529040-mRNA-1
Gene Sequence

>Msa0529040

ATGGTTTGTGAGGGTGAGAGGAAATGGGCTAGTGATAACAATTTGTTGGGTTTGTTTTATCTTGATTGGAACCTTTCTAATCCTCGAGGCCATTCTTTGAATGTATATTTTGACATAGATGCTGATGGTATCTTAATTGTATATGCTGAGGAAGAATGTACTGGAAATAAGAAAGAGATTACCATAACCAATAATACAAGGATATTGTCAACTGAGCAGATTATGCGAATGATTCAAGAAGCGGAGAAATACAAGGCTGGAGATGAAGAGTACCAGAAGAAAGTTAATGCAGTGAATGCTTTGGATGATTATGTTTACAAGATAAACAAGGCTTTGAAGGATATTGATAGAAGGGCCAAGCTTCGTCCTGAAGAAGAAATGAAGTTCAATTGGAAAATTTCAAAGGGCAAAAAGTATACTTGA

Protein sequence

>Msa0529040

MVCEGERKWASDNNLLGLFYLDWNLSNPRGHSLNVYFDIDADGILIVYAEEECTGNKKEITITNNTRILSTEQIMRMIQEAEKYKAGDEEYQKKVNAVNALDDYVYKINKALKDIDRRAKLRPEEEMKFNWKISKGKKYT*