AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054728

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054728.t1 MTR_3g101810 96.721 122 4 0 1 122 117 238 9.05e-83 243
MS.gene054728.t1 MTR_8g093500 76.923 91 21 0 28 118 87 177 4.13e-47 152
MS.gene054728.t1 MTR_5g017210 81.443 97 18 0 23 119 105 201 1.18e-46 150
MS.gene054728.t1 MTR_2g100490 57.273 110 44 2 12 118 244 353 9.14e-28 105
MS.gene054728.t1 MTR_8g015450 59.375 96 35 1 27 118 296 391 1.16e-27 105
MS.gene054728.t1 MTR_7g069590 68.519 54 17 0 61 114 32 85 1.11e-22 87.0
MS.gene054728.t1 MTR_5g079500 62.500 56 21 0 62 117 225 280 1.63e-19 82.0
MS.gene054728.t1 MTR_1g018090 62.963 54 20 0 64 117 283 336 3.51e-19 81.6
MS.gene054728.t1 MTR_1g106460 50.746 67 33 0 51 117 234 300 2.06e-18 79.0
MS.gene054728.t1 MTR_5g005110 61.111 54 21 0 64 117 233 286 3.75e-18 78.6
MS.gene054728.t1 MTR_1g106470 62.963 54 20 0 64 117 205 258 1.19e-17 76.6
MS.gene054728.t1 MTR_3g103030 53.968 63 29 0 55 117 229 291 4.04e-17 75.5
MS.gene054728.t1 MTR_4g131160 58.929 56 23 0 62 117 203 258 3.87e-15 70.5
MS.gene054728.t1 MTR_4g131160 58.929 56 23 0 62 117 206 261 4.01e-15 70.5
MS.gene054728.t1 MTR_1g106480 62.222 45 17 0 73 117 87 131 1.35e-14 66.2
MS.gene054728.t1 MTR_1g080890 48.571 70 36 0 48 117 186 255 1.94e-14 68.2
MS.gene054728.t1 MTR_2g067000 49.333 75 31 1 51 118 146 220 3.00e-14 67.4
MS.gene054728.t1 MTR_1g060700 57.407 54 23 0 65 118 357 410 2.89e-13 65.1
MS.gene054728.t1 MTR_4g033295 56.140 57 24 1 65 120 128 184 9.66e-13 62.0
MS.gene054728.t1 MTR_2g089070 51.852 54 26 0 65 118 146 199 1.69e-12 62.4
MS.gene054728.t1 MTR_7g110810 49.153 59 26 1 57 115 208 262 1.15e-11 60.5
MS.gene054728.t1 MTR_1g052470 41.573 89 47 2 33 120 280 364 2.02e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054728.t1 AT5G67060 86.170 94 13 0 28 121 83 176 8.83e-47 150
MS.gene054728.t1 AT5G67060 86.170 94 13 0 28 121 95 188 1.41e-46 150
MS.gene054728.t1 AT3G50330 76.724 116 16 3 16 121 71 185 1.54e-46 150
MS.gene054728.t1 AT4G00120 69.663 89 27 0 30 118 87 175 2.46e-38 128
MS.gene054728.t1 AT3G21330 64.130 92 33 0 27 118 241 332 3.92e-37 129
MS.gene054728.t1 AT5G09750 71.579 95 27 0 28 122 92 186 1.02e-35 122
MS.gene054728.t1 AT5G01305 67.797 59 19 0 56 114 38 96 9.50e-23 87.8
MS.gene054728.t1 AT5G43175 52.174 69 33 0 49 117 126 194 3.70e-20 82.0
MS.gene054728.t1 AT4G33880 64.815 54 19 0 64 117 275 328 1.37e-19 82.4
MS.gene054728.t1 AT1G27740 52.941 68 32 0 50 117 162 229 2.15e-19 80.9
MS.gene054728.t1 AT5G37800 53.333 75 28 1 50 117 189 263 3.75e-19 80.9
MS.gene054728.t1 AT1G66470 63.636 55 20 0 63 117 203 257 8.78e-19 79.7
MS.gene054728.t1 AT2G14760 62.963 54 20 0 64 117 246 299 2.06e-18 79.0
MS.gene054728.t1 AT2G24260 54.930 71 25 2 53 117 28 97 9.17e-17 73.6
MS.gene054728.t1 AT2G24260 54.930 71 25 2 53 117 131 200 3.97e-16 73.2
MS.gene054728.t1 AT4G30980 55.224 67 30 0 51 117 126 192 5.21e-16 72.4
MS.gene054728.t1 AT4G30980 55.224 67 30 0 51 117 174 240 7.87e-16 72.4
MS.gene054728.t1 AT2G14760 50.746 67 20 1 64 117 246 312 5.51e-15 69.7
MS.gene054728.t1 AT5G58010 53.030 66 31 0 52 117 96 161 2.00e-14 67.8

Find 19 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTGACGTTTCTTCTCTT+TGG 0.218574 5.3:+33073952 None:intergenic
CGTTTCTCTGATGGCGATGC+AGG 0.384416 5.3:+33074060 None:intergenic
GCTCCGAATGCGAACCATTA+CGG 0.409587 5.3:-33074084 MS.gene054728:CDS
TTGACGTTTCTTCTCTTTGG+TGG 0.422338 5.3:+33073955 None:intergenic
ATCGAGTTTCGTTTCTCTGA+TGG 0.446419 5.3:+33074051 None:intergenic
GGACCGTAATGGTTCGCATT+CGG 0.478513 5.3:+33074081 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 5.3:-33073872 MS.gene054728:CDS
GGTACCAGGTGGAACTAAGA+TGG 0.521420 5.3:-33073851 MS.gene054728:CDS
AAACTCGATGGCGGCGATGA+GGG 0.543464 5.3:-33074037 MS.gene054728:CDS
ATGGCGATGCAGGACCGTAA+TGG 0.551664 5.3:+33074070 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 5.3:-33073833 MS.gene054728:CDS
GACACAACTTAAGTCACTGC+AGG 0.578655 5.3:-33073779 MS.gene054728:CDS
GAAACTCGATGGCGGCGATG+AGG 0.602988 5.3:-33074038 MS.gene054728:CDS
ATCAGAGAAACGAAACTCGA+TGG 0.615534 5.3:-33074049 MS.gene054728:CDS
TGTCTAGCTGCTATACTCTG+AGG 0.634069 5.3:+33073919 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 5.3:+33073847 None:intergenic
ATACTGCAAAGAATGGTACC+AGG 0.680757 5.3:-33073865 MS.gene054728:CDS
AGAGAAACGAAACTCGATGG+CGG 0.700467 5.3:-33074046 MS.gene054728:CDS
CTGCAAAGAATGGTACCAGG+TGG 0.704915 5.3:-33073862 MS.gene054728:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAGAATACTGCAAAGAA+TGG - chr5.3:33074004-33074023 MS.gene054728:CDS 25.0%
!! GATTTTGGGTCTATGTAAAT+TGG + chr5.3:33073894-33073913 None:intergenic 30.0%
!!! TTGGTGGTTTTACTGATTTT+GGG + chr5.3:33073908-33073927 None:intergenic 30.0%
!!! TTTGGTGGTTTTACTGATTT+TGG + chr5.3:33073909-33073928 None:intergenic 30.0%
ATCTTGACGTTTCTTCTCTT+TGG + chr5.3:33073927-33073946 None:intergenic 35.0%
ATACTGCAAAGAATGGTACC+AGG - chr5.3:33074011-33074030 MS.gene054728:CDS 40.0%
ATCAGAGAAACGAAACTCGA+TGG - chr5.3:33073827-33073846 MS.gene054728:CDS 40.0%
ATCGAGTTTCGTTTCTCTGA+TGG + chr5.3:33073828-33073847 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr5.3:33074043-33074062 MS.gene054728:CDS 40.0%
TTGACGTTTCTTCTCTTTGG+TGG + chr5.3:33073924-33073943 None:intergenic 40.0%
AGAGAAACGAAACTCGATGG+CGG - chr5.3:33073830-33073849 MS.gene054728:CDS 45.0%
GACACAACTTAAGTCACTGC+AGG - chr5.3:33074097-33074116 MS.gene054728:CDS 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr5.3:33074032-33074051 None:intergenic 45.0%
TGTCTAGCTGCTATACTCTG+AGG + chr5.3:33073960-33073979 None:intergenic 45.0%
CTGCAAAGAATGGTACCAGG+TGG - chr5.3:33074014-33074033 MS.gene054728:CDS 50.0%
GCTCCGAATGCGAACCATTA+CGG - chr5.3:33073792-33073811 MS.gene054728:CDS 50.0%
GGACCGTAATGGTTCGCATT+CGG + chr5.3:33073798-33073817 None:intergenic 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr5.3:33074025-33074044 MS.gene054728:CDS 50.0%
ATGGCGATGCAGGACCGTAA+TGG + chr5.3:33073809-33073828 None:intergenic 55.0%
! AAACTCGATGGCGGCGATGA+GGG - chr5.3:33073839-33073858 MS.gene054728:CDS 55.0%
! CGTTTCTCTGATGGCGATGC+AGG + chr5.3:33073819-33073838 None:intergenic 55.0%
! GAAACTCGATGGCGGCGATG+AGG - chr5.3:33073838-33073857 MS.gene054728:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 33073765 33074133 33073765 ID=MS.gene054728
chr5.3 mRNA 33073765 33074133 33073765 ID=MS.gene054728.t1;Parent=MS.gene054728
chr5.3 exon 33073765 33074133 33073765 ID=MS.gene054728.t1.exon1;Parent=MS.gene054728.t1
chr5.3 CDS 33073765 33074133 33073765 ID=cds.MS.gene054728.t1;Parent=MS.gene054728.t1
Gene Sequence

>MS.gene054728

ATGTTTTCAAATTCGAGAAACGAGATTGCTCCGAATGCGAACCATTACGGTCCTGCATCGCCATCAGAGAAACGAAACTCGATGGCGGCGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAAAATCAGTAAAACCACCAAAGAGAAGAAACGTCAAGATTTCAAAAGATCCTCAGAGTATAGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCATGA
Protein sequence

>MS.gene054728.t1

MFSNSRNEIAPNANHYGPASPSEKRNSMAAMREMIFRIAAMQPIYIDPKSVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERAS