AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004942

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004942.t1 MTR_1g077390 92.357 157 12 0 1 157 1 157 1.01e-105 298
MS.gene004942.t1 MTR_1g077320 75.796 157 38 0 1 157 1 157 2.23e-78 229
MS.gene004942.t1 MTR_5g047580 69.872 156 47 0 1 156 1 156 5.97e-77 226
MS.gene004942.t1 MTR_7g011950 74.522 157 40 0 1 157 1 157 5.77e-75 221
MS.gene004942.t1 MTR_4g028720 72.611 157 43 0 1 157 1 157 6.15e-74 218
MS.gene004942.t1 MTR_1g084950 70.513 156 46 0 1 156 1 156 2.85e-69 206
MS.gene004942.t1 MTR_1g077300 70.701 157 44 1 1 157 1 155 9.28e-68 202
MS.gene004942.t1 MTR_1g090783 57.516 153 65 0 3 155 2 154 1.47e-57 177
MS.gene004942.t1 MTR_1g090710 55.128 156 69 1 1 155 1 156 1.49e-56 174
MS.gene004942.t1 MTR_5g047560 57.692 156 50 1 1 156 1 140 7.84e-56 172
MS.gene004942.t1 MTR_1g090697 54.839 155 70 0 1 155 1 155 8.69e-56 172
MS.gene004942.t1 MTR_3g065100 48.408 157 80 1 1 156 1 157 6.46e-37 127
MS.gene004942.t1 MTR_3g466980 43.137 153 86 1 1 152 1 153 7.99e-35 121
MS.gene004942.t1 MTR_4g032620 37.662 154 94 2 1 152 1 154 1.28e-34 121
MS.gene004942.t1 MTR_5g075380 36.538 156 98 1 1 155 1 156 4.84e-34 117
MS.gene004942.t1 MTR_4g031910 43.590 156 86 2 1 154 1 156 1.01e-32 116
MS.gene004942.t1 MTR_4g063790 38.994 159 95 2 1 157 1 159 1.09e-32 114
MS.gene004942.t1 MTR_3g466830 42.667 150 85 1 3 151 2 151 4.02e-32 112
MS.gene004942.t1 MTR_8g036130 38.365 159 94 2 1 155 1 159 1.75e-30 110
MS.gene004942.t1 MTR_3g031240 34.591 159 102 2 1 157 1 159 3.57e-29 105
MS.gene004942.t1 MTR_2g016210 39.735 151 89 2 1 149 1 151 1.77e-28 105
MS.gene004942.t1 MTR_3g466890 39.073 151 91 1 3 152 2 152 1.86e-27 100
MS.gene004942.t1 MTR_3g031100 37.342 158 95 3 1 155 1 157 6.65e-27 101
MS.gene004942.t1 MTR_4g032260 42.138 159 90 2 1 157 1 159 1.10e-26 98.6
MS.gene004942.t1 MTR_2g035610 44.628 121 66 1 1 120 1 121 1.24e-26 97.4
MS.gene004942.t1 MTR_4g032290 41.667 156 89 2 1 154 1 156 1.23e-25 97.8
MS.gene004942.t1 MTR_3g467080 36.420 162 95 4 1 157 1 159 4.09e-25 94.7
MS.gene004942.t1 MTR_4g028800 53.425 73 32 1 1 73 1 71 2.54e-22 85.1
MS.gene004942.t1 MTR_3g465410 36.364 132 80 3 29 157 1 131 5.89e-20 80.9
MS.gene004942.t1 MTR_2g035580 31.373 153 104 1 1 152 1 153 3.82e-19 79.3
MS.gene004942.t1 MTR_4g019670 29.814 161 94 5 1 157 1 146 5.53e-18 80.1
MS.gene004942.t1 MTR_7g106510 28.571 161 96 5 1 157 1 146 8.29e-17 76.6
MS.gene004942.t1 MTR_3g466930 34.426 122 79 1 32 152 2 123 1.87e-15 68.9
MS.gene004942.t1 MTR_3g466900 33.607 122 80 1 32 152 2 123 4.76e-15 67.8
MS.gene004942.t1 MTR_7g055800 33.051 118 52 2 1 118 1 91 2.48e-14 65.1
MS.gene004942.t1 MTR_7g055790 38.182 110 49 2 1 109 59 150 1.39e-13 64.7
MS.gene004942.t1 MTR_1g033790 39.362 94 56 1 64 156 22 115 1.07e-12 61.6
MS.gene004942.t1 MTR_1g033930 37.234 94 58 1 64 156 22 115 1.86e-12 60.8
MS.gene004942.t1 MTR_1g033370 38.298 94 57 1 64 156 28 121 3.44e-12 60.1
MS.gene004942.t1 MTR_7g055940 33.333 105 43 2 1 105 1 78 5.76e-12 58.5
MS.gene004942.t1 MTR_6g005450 31.858 113 69 3 1 106 1 112 1.83e-11 61.2
MS.gene004942.t1 MTR_3g093900 25.926 162 112 3 3 156 6 167 3.59e-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.gene004942.t1 AT5G26630 42.484 153 87 1 1 152 1 153 4.68e-32 114
MS.gene004942.t1 AT3G05860 40.940 149 87 1 1 148 1 149 4.88e-31 111
MS.gene004942.t1 AT5G48670 46.753 154 79 3 1 152 1 153 7.19e-31 113
MS.gene004942.t1 AT3G05860 40.940 149 87 1 1 148 1 149 3.50e-30 110
MS.gene004942.t1 AT3G05860 40.940 149 87 1 1 148 1 149 5.68e-30 109
MS.gene004942.t1 AT1G65330 38.776 147 89 1 3 148 2 148 4.91e-29 107
MS.gene004942.t1 AT1G65300 36.424 151 95 1 3 152 2 152 1.50e-28 106
MS.gene004942.t1 AT5G26650 36.667 150 94 1 4 152 2 151 1.40e-25 100
MS.gene004942.t1 AT5G27960 43.925 107 59 1 4 109 2 108 2.28e-24 96.3
MS.gene004942.t1 AT1G31630 30.323 155 106 2 3 156 2 155 2.34e-22 91.3
MS.gene004942.t1 AT1G22590 30.128 156 105 2 1 155 1 153 1.82e-20 82.8
MS.gene004942.t1 AT1G31640 34.014 147 95 2 3 148 2 147 4.66e-20 85.9
MS.gene004942.t1 AT5G27810 44.086 93 51 1 29 120 1 93 3.40e-19 78.2
MS.gene004942.t1 AT2G28700 38.182 110 67 1 1 109 1 110 2.10e-18 80.5
MS.gene004942.t1 AT5G26580 39.450 109 53 1 1 109 1 96 1.38e-17 78.2
MS.gene004942.t1 AT2G40210 36.923 130 77 2 1 127 1 128 6.38e-15 71.2
MS.gene004942.t1 AT5G06500 34.965 143 86 4 1 141 1 138 1.86e-14 68.6

Find 27 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGCAAAAGAAAACTTTCT+TGG 0.221526 1.4:+63386243 None:intergenic
AGCCTTTCTTGCCGAATCAT+TGG 0.368149 1.4:+63386460 None:intergenic
TGTATGGCTCCCTCTAGATT+TGG 0.415378 1.4:+63386320 None:intergenic
CTCCAATGATTCGGCAAGAA+AGG 0.422860 1.4:-63386462 MS.gene004942:CDS
TCAAATCATCAGGCAACTCT+TGG 0.451496 1.4:+63386129 None:intergenic
AGAGAGCTCTCTATTCTTTG+TGG 0.458868 1.4:-63386398 MS.gene004942:CDS
AAATCTAGAGGGAGCCATAC+AGG 0.466931 1.4:-63386318 MS.gene004942:CDS
TCTGTAACAGTCAAATCATC+AGG 0.472686 1.4:+63386119 None:intergenic
TTTCACCTTCTTCCTAGTCA+TGG 0.474514 1.4:+63386496 None:intergenic
AAAGAAGGGTATCATTAAGA+AGG 0.475254 1.4:-63386423 MS.gene004942:CDS
TGTTATAGAATCAAACGGAT+TGG 0.483520 1.4:+63386352 None:intergenic
ATACCTCTCAATCACCTGTA+TGG 0.492173 1.4:+63386304 None:intergenic
GCAGCAGATTACTAAAACCA+GGG 0.508508 1.4:-63386225 MS.gene004942:CDS
GAATGAGCTGGACATTCATA+TGG 0.511354 1.4:-63386168 MS.gene004942:CDS
TGCAGCAGATTACTAAAACC+AGG 0.515480 1.4:-63386226 MS.gene004942:CDS
TAGCTACAACAAGAGAAAGA+AGG 0.531524 1.4:-63386438 MS.gene004942:CDS
ACCTCTGTTATAGAATCAAA+CGG 0.538136 1.4:+63386347 None:intergenic
CGGATTGGAAATTATAGCAC+AGG 0.556765 1.4:+63386367 None:intergenic
AGCTACAACAAGAGAAAGAA+GGG 0.560386 1.4:-63386437 MS.gene004942:CDS
TCCGTTTGATTCTATAACAG+AGG 0.561391 1.4:-63386348 MS.gene004942:CDS
ACAGAATAATGAGAATGAGC+TGG 0.567812 1.4:-63386180 MS.gene004942:CDS
TTGGAAATTATAGCACAGGC+TGG 0.567823 1.4:+63386371 None:intergenic
AGAGGTGTGGCCAAATCTAG+AGG 0.598360 1.4:-63386330 MS.gene004942:CDS
AGCTGGACATTCATATGGTT+AGG 0.635359 1.4:-63386163 MS.gene004942:CDS
GAGCCATACAGGTGATTGAG+AGG 0.637552 1.4:-63386307 MS.gene004942:CDS
GAGGTGTGGCCAAATCTAGA+GGG 0.655326 1.4:-63386329 MS.gene004942:CDS
TTGATTCTATAACAGAGGTG+TGG 0.661112 1.4:-63386343 MS.gene004942:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACCTCTGTTATAGAATCAAA+CGG + chr1.4:63386193-63386212 None:intergenic 30.0%
GAAAAAGATGAAGGAAATTG+AGG - chr1.4:63386468-63386487 MS.gene004942:CDS 30.0%
GCTAATTGAGAAAAAGATGA+AGG - chr1.4:63386459-63386478 MS.gene004942:CDS 30.0%
TGTTATAGAATCAAACGGAT+TGG + chr1.4:63386188-63386207 None:intergenic 30.0%
! TGCTTTTATCTCCAATGATT+CGG - chr1.4:63386066-63386085 MS.gene004942:CDS 30.0%
!! AAAGAAGGGTATCATTAAGA+AGG - chr1.4:63386114-63386133 MS.gene004942:CDS 30.0%
ACAGAATAATGAGAATGAGC+TGG - chr1.4:63386357-63386376 MS.gene004942:CDS 35.0%
AGCTACAACAAGAGAAAGAA+GGG - chr1.4:63386100-63386119 MS.gene004942:CDS 35.0%
GCTGCAAAAGAAAACTTTCT+TGG + chr1.4:63386297-63386316 None:intergenic 35.0%
TAGCTACAACAAGAGAAAGA+AGG - chr1.4:63386099-63386118 MS.gene004942:CDS 35.0%
TCCGTTTGATTCTATAACAG+AGG - chr1.4:63386189-63386208 MS.gene004942:CDS 35.0%
TCTGTAACAGTCAAATCATC+AGG + chr1.4:63386421-63386440 None:intergenic 35.0%
TTGATTCTATAACAGAGGTG+TGG - chr1.4:63386194-63386213 MS.gene004942:CDS 35.0%
AGAGAGCTCTCTATTCTTTG+TGG - chr1.4:63386139-63386158 MS.gene004942:CDS 40.0%
AGCTGGACATTCATATGGTT+AGG - chr1.4:63386374-63386393 MS.gene004942:CDS 40.0%
ATACCTCTCAATCACCTGTA+TGG + chr1.4:63386236-63386255 None:intergenic 40.0%
GAATGAGCTGGACATTCATA+TGG - chr1.4:63386369-63386388 MS.gene004942:CDS 40.0%
GCAGCAGATTACTAAAACCA+GGG - chr1.4:63386312-63386331 MS.gene004942:CDS 40.0%
TCAAATCATCAGGCAACTCT+TGG + chr1.4:63386411-63386430 None:intergenic 40.0%
TGCAGCAGATTACTAAAACC+AGG - chr1.4:63386311-63386330 MS.gene004942:CDS 40.0%
TTGGAAATTATAGCACAGGC+TGG + chr1.4:63386169-63386188 None:intergenic 40.0%
! CGGATTGGAAATTATAGCAC+AGG + chr1.4:63386173-63386192 None:intergenic 40.0%
!!! TTGCTTTTCTAGTTGTTCCC+TGG + chr1.4:63386332-63386351 None:intergenic 40.0%
AAATCTAGAGGGAGCCATAC+AGG - chr1.4:63386219-63386238 MS.gene004942:CDS 45.0%
AGCCTTTCTTGCCGAATCAT+TGG + chr1.4:63386080-63386099 None:intergenic 45.0%
TGTATGGCTCCCTCTAGATT+TGG + chr1.4:63386220-63386239 None:intergenic 45.0%
! CTCCAATGATTCGGCAAGAA+AGG - chr1.4:63386075-63386094 MS.gene004942:CDS 45.0%
GAGCCATACAGGTGATTGAG+AGG - chr1.4:63386230-63386249 MS.gene004942:CDS 50.0%
GAGGTGTGGCCAAATCTAGA+GGG - chr1.4:63386208-63386227 MS.gene004942:CDS 50.0%
! AGAGGTGTGGCCAAATCTAG+AGG - chr1.4:63386207-63386226 MS.gene004942:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 63386043 63386516 63386043 ID=MS.gene004942
chr1.4 mRNA 63386043 63386516 63386043 ID=MS.gene004942.t1;Parent=MS.gene004942
chr1.4 exon 63386043 63386516 63386043 ID=MS.gene004942.t1.exon1;Parent=MS.gene004942.t1
chr1.4 CDS 63386043 63386516 63386043 ID=cds.MS.gene004942.t1;Parent=MS.gene004942.t1
Gene Sequence

>MS.gene004942

ATGACTAGGAAGAAGGTGAAACTTGCTTTTATCTCCAATGATTCGGCAAGAAAGGCTAGCTACAACAAGAGAAAGAAGGGTATCATTAAGAAGGTGAGAGAGCTCTCTATTCTTTGTGGTATTCCAGCCTGTGCTATAATTTCCAATCCGTTTGATTCTATAACAGAGGTGTGGCCAAATCTAGAGGGAGCCATACAGGTGATTGAGAGGTATCAAAATGCATATATCAAACACAAGAAAAATAATGTGAACCAAGAAAGTTTTCTTTTGCAGCAGATTACTAAAACCAGGGAACAACTAGAAAAGCAAAGACAACAGAATAATGAGAATGAGCTGGACATTCATATGGTTAGGCACTTGCAAAACCAAGAGTTGCCTGATGATTTGACTGTTACAGATTTAAGAGATTATGATAAGCTAATTGAGAAAAAGATGAAGGAAATTGAGGACAAGATTGTTGCACTCAGTTTATGA
Protein sequence

>MS.gene004942.t1

MTRKKVKLAFISNDSARKASYNKRKKGIIKKVRELSILCGIPACAIISNPFDSITEVWPNLEGAIQVIERYQNAYIKHKKNNVNQESFLLQQITKTREQLEKQRQQNNENELDIHMVRHLQNQELPDDLTVTDLRDYDKLIEKKMKEIEDKIVALSL