AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene023033

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023033.t1 MTR_7g011950 93.082 159 11 0 1 159 1 159 2.87e-101 288
MS.gene023033.t1 MTR_4g028720 92.453 159 12 0 1 159 1 159 6.77e-99 281
MS.gene023033.t1 MTR_1g077320 85.535 159 23 0 1 159 1 159 8.67e-92 263
MS.gene023033.t1 MTR_5g047580 71.795 156 44 0 1 156 1 156 3.82e-78 229
MS.gene023033.t1 MTR_1g077390 70.701 157 46 0 1 157 1 157 3.31e-77 226
MS.gene023033.t1 MTR_1g084950 76.923 156 36 0 1 156 1 156 5.19e-77 226
MS.gene023033.t1 MTR_1g077300 75.472 159 37 1 1 159 1 157 4.06e-74 219
MS.gene023033.t1 MTR_5g047560 61.538 156 44 1 1 156 1 140 1.65e-60 184
MS.gene023033.t1 MTR_1g090783 56.863 153 66 0 3 155 2 154 1.61e-58 179
MS.gene023033.t1 MTR_1g090697 54.839 155 70 0 1 155 1 155 1.74e-58 179
MS.gene023033.t1 MTR_1g090710 51.923 156 74 1 1 155 1 156 4.77e-55 171
MS.gene023033.t1 MTR_3g466980 45.752 153 82 1 1 152 1 153 3.67e-41 137
MS.gene023033.t1 MTR_4g032620 40.645 155 90 2 1 153 1 155 7.67e-41 137
MS.gene023033.t1 MTR_3g065100 47.771 157 81 1 1 156 1 157 8.24e-39 132
MS.gene023033.t1 MTR_4g063790 38.365 159 96 2 1 157 1 159 2.30e-34 118
MS.gene023033.t1 MTR_8g036130 40.252 159 91 2 1 155 1 159 2.62e-34 120
MS.gene023033.t1 MTR_5g075380 36.538 156 98 1 1 155 1 156 6.37e-34 117
MS.gene023033.t1 MTR_3g466830 41.401 157 91 1 3 158 2 158 5.98e-33 114
MS.gene023033.t1 MTR_3g466890 39.610 154 92 1 3 155 2 155 7.24e-30 107
MS.gene023033.t1 MTR_4g031910 40.667 150 87 2 1 148 1 150 1.13e-29 108
MS.gene023033.t1 MTR_3g467080 34.591 159 102 2 1 157 1 159 3.22e-29 105
MS.gene023033.t1 MTR_2g016210 38.365 159 96 2 1 157 1 159 4.57e-29 107
MS.gene023033.t1 MTR_3g031240 35.849 159 100 2 1 157 1 159 6.83e-29 105
MS.gene023033.t1 MTR_4g032260 40.000 160 94 2 1 158 1 160 2.73e-28 102
MS.gene023033.t1 MTR_4g032290 37.888 161 98 2 1 159 1 161 3.51e-26 99.4
MS.gene023033.t1 MTR_3g031100 36.076 158 97 3 1 155 1 157 7.86e-26 99.0
MS.gene023033.t1 MTR_2g035610 41.525 118 68 1 1 117 1 118 2.09e-25 94.4
MS.gene023033.t1 MTR_2g035580 34.194 155 101 1 1 154 1 155 1.25e-23 90.9
MS.gene023033.t1 MTR_3g465410 35.115 131 83 2 29 157 1 131 3.75e-21 84.0
MS.gene023033.t1 MTR_4g028800 47.945 73 36 1 1 73 1 71 4.94e-21 81.6
MS.gene023033.t1 MTR_3g466900 38.400 125 76 1 32 155 2 126 7.55e-21 82.8
MS.gene023033.t1 MTR_3g466930 36.000 125 79 1 32 155 2 126 7.59e-19 77.8
MS.gene023033.t1 MTR_4g019670 34.091 132 83 2 1 128 1 132 4.11e-17 77.8
MS.gene023033.t1 MTR_7g106510 34.259 108 70 1 3 109 6 113 6.02e-16 74.3
MS.gene023033.t1 MTR_7g055800 33.913 115 49 2 1 115 1 88 1.16e-14 65.9
MS.gene023033.t1 MTR_1g033370 45.745 94 50 1 64 156 28 121 1.27e-14 66.6
MS.gene023033.t1 MTR_1g033930 41.837 98 56 1 62 158 20 117 1.96e-14 66.2
MS.gene023033.t1 MTR_1g033790 38.938 113 62 2 53 158 5 117 2.17e-13 63.2
MS.gene023033.t1 MTR_7g055790 36.697 109 52 2 1 109 59 150 7.97e-13 62.8
MS.gene023033.t1 MTR_7g055940 34.615 104 41 3 1 104 1 77 5.49e-12 58.5
MS.gene023033.t1 MTR_6g005450 32.031 128 74 5 1 115 1 128 6.75e-12 62.4
MS.gene023033.t1 MTR_3g093900 32.292 96 63 1 3 98 6 99 3.09e-11 60.8
MS.gene023033.t1 MTR_6g018920 32.500 80 48 3 1 74 1 80 4.18e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023033.t1 AT5G48670 46.405 153 81 1 1 152 1 153 1.45e-34 123
MS.gene023033.t1 AT3G05860 39.597 149 89 1 1 148 1 149 2.67e-32 114
MS.gene023033.t1 AT3G05860 39.597 149 89 1 1 148 1 149 1.29e-31 114
MS.gene023033.t1 AT3G05860 39.597 149 89 1 1 148 1 149 2.15e-31 113
MS.gene023033.t1 AT5G26630 38.750 160 97 1 1 159 1 160 3.17e-29 107
MS.gene023033.t1 AT1G65300 36.620 142 89 1 3 143 2 143 9.71e-28 104
MS.gene023033.t1 AT1G65330 36.735 147 92 1 3 148 2 148 3.83e-27 103
MS.gene023033.t1 AT5G26650 34.641 153 99 1 4 155 2 154 4.50e-25 99.0
MS.gene023033.t1 AT5G27960 33.987 153 100 1 4 155 2 154 8.44e-24 95.1
MS.gene023033.t1 AT1G31630 29.677 155 107 2 3 156 2 155 6.47e-22 90.1
MS.gene023033.t1 AT2G28700 33.557 149 98 1 1 148 1 149 6.95e-22 90.1
MS.gene023033.t1 AT5G27810 43.750 96 53 1 29 123 1 96 4.54e-21 83.2
MS.gene023033.t1 AT1G22590 29.012 162 99 3 1 155 1 153 2.66e-20 82.4
MS.gene023033.t1 AT1G31640 32.000 150 100 2 3 151 2 150 4.15e-19 83.2
MS.gene023033.t1 AT5G26580 32.258 155 92 1 1 155 1 142 1.09e-17 78.6
MS.gene023033.t1 AT2G40210 37.815 119 69 2 1 116 1 117 4.09e-15 71.6
MS.gene023033.t1 AT5G06500 30.818 159 106 3 1 157 1 157 1.01e-14 69.3
MS.gene023033.t1 AT5G58890 35.417 96 55 2 1 89 1 96 7.39e-13 65.1

Find 28 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCTTTCTTGTTGAATCAT+TGG 0.233760 7.2:-50194978 None:intergenic
TGTTGAATCATTGGAAATAA+AGG 0.251603 7.2:-50194969 None:intergenic
TTTGCAAAAGGAAACTTTCT+TGG 0.282244 7.2:-50195195 None:intergenic
ACCTTTCCTCCTCCTCTTGT+AGG 0.282788 7.2:-50195002 None:intergenic
AGTTGAACATTCTTATGTTT+TGG 0.291264 7.2:+50195275 MS.gene023033:CDS
TGTTTGGCTTCCTTTAGATT+TGG 0.353502 7.2:-50195118 None:intergenic
ATACCTCTCAATCACCTGTT+TGG 0.354870 7.2:-50195134 None:intergenic
TTCCAATGATTCAACAAGAA+AGG 0.389550 7.2:+50194976 MS.gene023033:CDS
TCAGAAACAGTCACATCATC+TGG 0.393115 7.2:-50195319 None:intergenic
AAATCTAAAGGAAGCCAAAC+AGG 0.425294 7.2:+50195120 MS.gene023033:CDS
CTTTAGTAATCATTTGCAAA+AGG 0.447168 7.2:-50195207 None:intergenic
TGTTTCTGATTTGAAAGACT+TGG 0.473410 7.2:+50195333 MS.gene023033:CDS
TGCAAATGATTACTAAAGCT+AGG 0.481563 7.2:+50195212 MS.gene023033:CDS
TTTCACCTTCTTCCTAGTCA+TGG 0.490416 7.2:-50194942 None:intergenic
GCAAATGATTACTAAAGCTA+GGG 0.492435 7.2:+50195213 MS.gene023033:CDS
ACCTCTGTTTCAGAATCAAA+AGG 0.516061 7.2:-50195091 None:intergenic
ACCTACAAGAGGAGGAGGAA+AGG 0.522508 7.2:+50195001 MS.gene023033:CDS
AGAGGTGTGGCCAAATCTAA+AGG 0.522555 7.2:+50195108 MS.gene023033:CDS
AGAGAACTCACTATTCTTTG+TGG 0.526508 7.2:+50195040 MS.gene023033:CDS
CAAAGCCATGACTAGGAAGA+AGG 0.543154 7.2:+50194937 None:intergenic
AGGAGACCTACAAGAGGAGG+AGG 0.545154 7.2:+50194996 MS.gene023033:CDS
GAAGGAAATTGATGACAAGA+TGG 0.549956 7.2:+50195378 MS.gene023033:CDS
GAAAGGAGACCTACAAGAGG+AGG 0.592612 7.2:+50194993 MS.gene023033:CDS
TACATTGCAAAGCCATGACT+AGG 0.609749 7.2:+50194930 None:intergenic
GAGGAAAGGTATCATCAAGA+AGG 0.620547 7.2:+50195015 MS.gene023033:CDS
TTGATTCTGAAACAGAGGTG+TGG 0.630350 7.2:+50195095 MS.gene023033:CDS
AAGCCAAACAGGTGATTGAG+AGG 0.637552 7.2:+50195131 MS.gene023033:CDS
CAAGAAAGGAGACCTACAAG+AGG 0.685284 7.2:+50194990 MS.gene023033:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTAATTGAAAAAAATATGA+AGG + chr7.2:50195360-50195379 MS.gene023033:CDS 15.0%
! CTTTAGTAATCATTTGCAAA+AGG - chr7.2:50195210-50195229 None:intergenic 25.0%
! TGTTGAATCATTGGAAATAA+AGG - chr7.2:50194972-50194991 None:intergenic 25.0%
!! AGTTGAACATTCTTATGTTT+TGG + chr7.2:50195275-50195294 MS.gene023033:CDS 25.0%
GCAAATGATTACTAAAGCTA+GGG + chr7.2:50195213-50195232 MS.gene023033:CDS 30.0%
TGCAAATGATTACTAAAGCT+AGG + chr7.2:50195212-50195231 MS.gene023033:CDS 30.0%
TTCCAATGATTCAACAAGAA+AGG + chr7.2:50194976-50194995 MS.gene023033:CDS 30.0%
TTTGCAAAAGGAAACTTTCT+TGG - chr7.2:50195198-50195217 None:intergenic 30.0%
! TGTTTCTGATTTGAAAGACT+TGG + chr7.2:50195333-50195352 MS.gene023033:CDS 30.0%
AAATCTAAAGGAAGCCAAAC+AGG + chr7.2:50195120-50195139 MS.gene023033:CDS 35.0%
ACCTCTGTTTCAGAATCAAA+AGG - chr7.2:50195094-50195113 None:intergenic 35.0%
AGAGAACTCACTATTCTTTG+TGG + chr7.2:50195040-50195059 MS.gene023033:CDS 35.0%
CTCCTTTCTTGTTGAATCAT+TGG - chr7.2:50194981-50195000 None:intergenic 35.0%
! GAAGGAAATTGATGACAAGA+TGG + chr7.2:50195378-50195397 MS.gene023033:CDS 35.0%
! TGTTTGGCTTCCTTTAGATT+TGG - chr7.2:50195121-50195140 None:intergenic 35.0%
!!! TCCTTTTGATTCTGAAACAG+AGG + chr7.2:50195090-50195109 MS.gene023033:CDS 35.0%
ATACCTCTCAATCACCTGTT+TGG - chr7.2:50195137-50195156 None:intergenic 40.0%
TCAGAAACAGTCACATCATC+TGG - chr7.2:50195322-50195341 None:intergenic 40.0%
!! GAGGAAAGGTATCATCAAGA+AGG + chr7.2:50195015-50195034 MS.gene023033:CDS 40.0%
!! TTGATTCTGAAACAGAGGTG+TGG + chr7.2:50195095-50195114 MS.gene023033:CDS 40.0%
AAGCCAAACAGGTGATTGAG+AGG + chr7.2:50195131-50195150 MS.gene023033:CDS 45.0%
CAAGAAAGGAGACCTACAAG+AGG + chr7.2:50194990-50195009 MS.gene023033:CDS 45.0%
! AGAGGTGTGGCCAAATCTAA+AGG + chr7.2:50195108-50195127 MS.gene023033:CDS 45.0%
ACCTACAAGAGGAGGAGGAA+AGG + chr7.2:50195001-50195020 MS.gene023033:CDS 50.0%
ACCTTTCCTCCTCCTCTTGT+AGG - chr7.2:50195005-50195024 None:intergenic 50.0%
GAAAGGAGACCTACAAGAGG+AGG + chr7.2:50194993-50195012 MS.gene023033:CDS 50.0%
AGGAGACCTACAAGAGGAGG+AGG + chr7.2:50194996-50195015 MS.gene023033:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 50194944 50195423 50194944 ID=MS.gene023033
chr7.2 mRNA 50194944 50195423 50194944 ID=MS.gene023033.t1;Parent=MS.gene023033
chr7.2 exon 50194944 50195423 50194944 ID=MS.gene023033.t1.exon1;Parent=MS.gene023033.t1
chr7.2 CDS 50194944 50195423 50194944 ID=cds.MS.gene023033.t1;Parent=MS.gene023033.t1
Gene Sequence

>MS.gene023033

ATGACTAGGAAGAAGGTGAAACTCGCCTTTATTTCCAATGATTCAACAAGAAAGGAGACCTACAAGAGGAGGAGGAAAGGTATCATCAAGAAGGTGAGAGAACTCACTATTCTTTGTGGTATTTCAGCATGTGCTATAATTTCTGATCCTTTTGATTCTGAAACAGAGGTGTGGCCAAATCTAAAGGAAGCCAAACAGGTGATTGAGAGGTATCAAAACTCATATATGAAAGATGAGAGAAAAAATGTGAACCAAGAAAGTTTCCTTTTGCAAATGATTACTAAAGCTAGGGAACAACTGAGAATGCAAAGACACGACAATCATGAGAATGAGTTGAACATTCTTATGTTTTGGTACATGCAAAACAACAAGCTTCCAGATGATGTGACTGTTTCTGATTTGAAAGACTTGGATAAGTTAATTGAAAAAAATATGAAGGAAATTGATGACAAGATGGCTTCACTTAGTTTATCAAACTGA
Protein sequence

>MS.gene023033.t1

MTRKKVKLAFISNDSTRKETYKRRRKGIIKKVRELTILCGISACAIISDPFDSETEVWPNLKEAKQVIERYQNSYMKDERKNVNQESFLLQMITKAREQLRMQRHDNHENELNILMFWYMQNNKLPDDVTVSDLKDLDKLIEKNMKEIDDKMASLSLSN