AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene04115

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04115.t1 MTR_3g061330 85.987 157 21 1 1 157 1 156 4.48e-94 273
MS.gene04115.t1 MTR_3g061350 84.076 157 25 0 1 157 1 157 4.52e-93 271
MS.gene04115.t1 MTR_3g061370 82.166 157 25 1 1 157 1 154 1.73e-90 265
MS.gene04115.t1 MTR_3g061320 77.707 157 34 1 1 157 1 156 1.18e-85 252
MS.gene04115.t1 MTR_3g061290 77.707 157 34 1 1 157 1 156 3.75e-85 248
MS.gene04115.t1 MTR_3g061310 76.923 156 35 1 1 156 1 155 7.60e-83 245
MS.gene04115.t1 MTR_3g061340 73.418 158 30 4 1 157 1 147 1.21e-74 224
MS.gene04115.t1 MTR_3g061220 67.424 132 28 3 1 132 1 117 3.16e-55 169
MS.gene04115.t1 MTR_7g050710 49.524 105 51 1 7 109 8 112 1.03e-32 118
MS.gene04115.t1 MTR_1g035460 43.182 132 74 1 27 157 3 134 1.56e-32 119
MS.gene04115.t1 MTR_7g050560 51.961 102 47 1 9 108 10 111 6.75e-32 116
MS.gene04115.t1 MTR_7g050720 39.103 156 88 3 4 155 2 154 7.23e-30 110
MS.gene04115.t1 MTR_8g103940 38.255 149 82 2 10 156 37 177 1.18e-29 112
MS.gene04115.t1 MTR_7g050580 46.903 113 57 2 1 110 1 113 2.63e-29 109
MS.gene04115.t1 MTR_3g098790 47.059 102 52 1 9 108 10 111 5.57e-28 106
MS.gene04115.t1 MTR_5g044670 35.256 156 84 3 12 157 16 164 6.24e-26 100
MS.gene04115.t1 MTR_1g108780 37.226 137 76 2 21 157 10 136 4.35e-24 97.1
MS.gene04115.t1 MTR_7g050590 48.780 82 42 0 27 108 3 84 3.18e-23 92.8
MS.gene04115.t1 MTR_4g119990 38.760 129 73 4 10 135 13 138 4.97e-23 93.6
MS.gene04115.t1 MTR_1g035640 37.903 124 71 3 12 135 9 126 1.12e-22 93.2
MS.gene04115.t1 MTR_4g068320 36.364 132 75 2 12 134 6 137 3.36e-22 91.7
MS.gene04115.t1 MTR_3g005480 34.483 145 90 4 12 152 21 164 8.16e-21 85.9
MS.gene04115.t1 MTR_1g034240 34.091 132 78 2 12 134 7 138 1.34e-20 87.4
MS.gene04115.t1 MTR_1g035650 33.333 156 89 4 9 157 6 153 2.49e-20 83.6
MS.gene04115.t1 MTR_7g050640 40.625 96 55 1 10 103 11 106 6.65e-20 80.1
MS.gene04115.t1 MTR_5g070440 35.862 145 87 3 12 152 21 163 1.42e-19 82.8
MS.gene04115.t1 MTR_3g005490 35.172 145 87 4 12 149 21 165 1.74e-19 82.4
MS.gene04115.t1 MTR_1g035620 32.394 142 90 3 9 148 6 143 2.08e-19 84.0
MS.gene04115.t1 MTR_1g033740 33.117 154 94 4 2 149 12 162 7.49e-19 79.3
MS.gene04115.t1 MTR_1g035570 32.773 119 71 3 12 130 9 118 1.42e-18 81.6
MS.gene04115.t1 MTR_1g035440 40.196 102 58 2 10 108 13 114 3.82e-18 78.6
MS.gene04115.t1 MTR_1g050845 30.935 139 84 3 9 145 6 134 4.96e-18 80.5
MS.gene04115.t1 MTR_1g035480 33.333 141 84 4 2 135 7 144 5.44e-18 76.6
MS.gene04115.t1 MTR_1g034210 37.719 114 66 3 6 117 2 112 6.79e-18 79.0
MS.gene04115.t1 MTR_1g034210 37.719 114 66 3 6 117 2 112 1.01e-17 79.0
MS.gene04115.t1 MTR_1g035510 37.391 115 64 4 25 135 1 111 1.27e-17 76.6
MS.gene04115.t1 MTR_6g043890 38.182 110 64 3 10 116 13 121 4.33e-17 77.0
MS.gene04115.t1 MTR_6g061070 36.842 133 78 4 2 132 8 136 2.68e-16 75.1
MS.gene04115.t1 MTR_1g035470 38.596 114 61 4 27 135 3 112 7.50e-16 70.1
MS.gene04115.t1 MTR_3g005495 38.636 88 54 0 21 108 24 111 1.72e-15 72.8
MS.gene04115.t1 MTR_3g005495 41.414 99 56 1 12 108 243 341 2.30e-15 72.4
MS.gene04115.t1 MTR_3g005440 34.188 117 76 1 13 128 23 139 1.92e-15 72.8
MS.gene04115.t1 MTR_3g005440 36.842 95 58 1 16 108 246 340 4.75e-13 65.9
MS.gene04115.t1 MTR_1g035500 30.380 158 100 4 2 152 15 169 2.19e-15 70.1
MS.gene04115.t1 MTR_3g005460 39.394 99 58 1 12 108 25 123 2.58e-15 72.4
MS.gene04115.t1 MTR_3g005460 36.275 102 62 2 10 108 260 361 2.54e-13 66.6
MS.gene04115.t1 MTR_3g005420 32.168 143 95 1 12 152 289 431 5.37e-15 71.6
MS.gene04115.t1 MTR_3g005420 35.644 101 62 2 12 109 40 140 2.60e-12 63.9
MS.gene04115.t1 MTR_1g035520 38.182 110 62 4 15 124 79 182 6.67e-13 65.5
MS.gene04115.t1 MTR_3g005420 35.644 101 62 2 12 109 21 121 2.44e-12 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04115.t1 AT1G49475 37.143 140 73 4 11 137 33 170 7.39e-20 82.0
MS.gene04115.t1 AT3G18990 31.343 134 84 3 8 133 1 134 2.02e-17 77.8
MS.gene04115.t1 AT3G18990 31.343 134 84 3 8 133 1 134 3.32e-17 77.4
MS.gene04115.t1 AT4G01580 30.065 153 93 5 2 149 19 162 1.09e-16 73.6
MS.gene04115.t1 AT3G18960 34.545 110 69 2 2 108 19 128 1.72e-16 73.6
MS.gene04115.t1 AT3G18960 34.545 110 69 2 2 108 19 128 2.40e-16 72.8
MS.gene04115.t1 AT3G18960 38.095 84 52 0 25 108 8 91 1.02e-13 65.5

Find 38 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATGAATCAGTTGAGATTT+TGG 0.207341 3.2:+52533374 MS.gene04115:CDS
GCTCTAAATGGAAAGTTTAT+TGG 0.210456 3.2:+52533142 MS.gene04115:CDS
CTCTCTTGGACATGGCTCTT+TGG 0.220059 3.2:+52533224 MS.gene04115:CDS
CAATCCTATGAAGATTAGTT+TGG 0.289306 3.2:-52532758 None:intergenic
AGCCTCCTGATGGCTCTAAA+TGG 0.306763 3.2:+52533130 MS.gene04115:CDS
AGTCTATTTCTACTGCATTC+TGG 0.324981 3.2:-52533296 None:intergenic
TCTTTGGTTGTATTTGAATA+TGG 0.328557 3.2:+52533240 MS.gene04115:CDS
TTTACTGAAAATTACTCTCT+TGG 0.354240 3.2:+52533210 MS.gene04115:CDS
TGGTGAGATTTGGTTTGAAA+AGG 0.373936 3.2:+52533176 MS.gene04115:CDS
AGTAAGTTTACAAGGAGATA+TGG 0.410176 3.2:+52533078 MS.gene04115:CDS
TATCTCCTTGTAAACTTACT+TGG 0.436135 3.2:-52533075 None:intergenic
ACTTTCCATTTAGAGCCATC+AGG 0.456300 3.2:-52533135 None:intergenic
TCCTCCAAACTAATCTTCAT+AGG 0.457688 3.2:+52532754 MS.gene04115:CDS
AGATTTGGTTTGAAAAGGGT+TGG 0.470784 3.2:+52533181 MS.gene04115:CDS
AAGTTTGATGTACACATACT+TGG 0.471543 3.2:+52533273 MS.gene04115:CDS
GGAGGATGATCTTGAAGAAA+CGG 0.484427 3.2:-52532737 None:intergenic
GGTGAGATTTGGTTTGAAAA+GGG 0.495938 3.2:+52533177 MS.gene04115:CDS
TCCTATGAAGATTAGTTTGG+AGG 0.495980 3.2:-52532755 None:intergenic
TTGGTTGTATTTGAATATGG+AGG 0.544853 3.2:+52533243 MS.gene04115:CDS
CAGACTTTCTTATGTGGTCG+AGG 0.545112 3.2:-52533447 None:intergenic
GGGAAGGATAGGATTTCCTC+TGG 0.551524 3.2:-52532712 None:intergenic
AAGAAACGGATGGGAAGGAT+AGG 0.554094 3.2:-52532723 None:intergenic
AAGTATGTGTACATCAAACT+TGG 0.555627 3.2:-52533271 None:intergenic
AAACACCAAGTAAGTTTACA+AGG 0.556474 3.2:+52533070 MS.gene04115:CDS
TCAGGAGGCTCGATCAACAC+TGG 0.566183 3.2:-52533117 None:intergenic
GTGTTGATCGAGCCTCCTGA+TGG 0.575886 3.2:+52533120 MS.gene04115:CDS
AAACCTCAGACTTTCTTATG+TGG 0.581200 3.2:-52533453 None:intergenic
TGAATGGCTTAATCGGAAGA+AGG 0.588393 3.2:+52533398 MS.gene04115:CDS
TCTTGAAGAAACGGATGGGA+AGG 0.589415 3.2:-52532728 None:intergenic
GATGATCTTGAAGAAACGGA+TGG 0.597527 3.2:-52532733 None:intergenic
AATGATGAAAATGACAATGT+TGG 0.613196 3.2:+52533339 MS.gene04115:CDS
TTTACAAGGAGATATGGAGT+TGG 0.615306 3.2:+52533084 MS.gene04115:CDS
ATGATCTTGAAGAAACGGAT+GGG 0.618403 3.2:-52532732 None:intergenic
CGACCACATAAGAAAGTCTG+AGG 0.627469 3.2:+52533450 MS.gene04115:CDS
GAAAATTACTCTCTTGGACA+TGG 0.632483 3.2:+52533216 MS.gene04115:CDS
ACTCTTTCATTCATGGCCAG+AGG 0.635124 3.2:+52532696 None:intergenic
TTCCATTTAGAGCCATCAGG+AGG 0.635302 3.2:-52533132 None:intergenic
TGTGGTCGAGGAGAATCAGA+AGG 0.646974 3.2:-52533435 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTAAACTAAATAGTACTAAT+AGG - chr3.2:52532796-52532815 None:intergenic 20.0%
!! GTTTATTGGAAAAAAATCAA+TGG + chr3.2:52533156-52533175 MS.gene04115:CDS 20.0%
! AAAAAATCAATGGTGAGATT+TGG + chr3.2:52533166-52533185 MS.gene04115:CDS 25.0%
! AATGATGAAAATGACAATGT+TGG + chr3.2:52533339-52533358 MS.gene04115:CDS 25.0%
! TCAAAACAAAATATTAGCAC+TGG + chr3.2:52532917-52532936 MS.gene04115:intron 25.0%
! TCTTTGGTTGTATTTGAATA+TGG + chr3.2:52533240-52533259 MS.gene04115:CDS 25.0%
! TTTACTGAAAATTACTCTCT+TGG + chr3.2:52533210-52533229 MS.gene04115:CDS 25.0%
AAACACCAAGTAAGTTTACA+AGG + chr3.2:52533070-52533089 MS.gene04115:CDS 30.0%
AACTATCACTGTTGTATTTC+TGG + chr3.2:52532985-52533004 MS.gene04115:intron 30.0%
AAGTATGTGTACATCAAACT+TGG - chr3.2:52533274-52533293 None:intergenic 30.0%
AAGTTTGATGTACACATACT+TGG + chr3.2:52533273-52533292 MS.gene04115:CDS 30.0%
AGTAAGTTTACAAGGAGATA+TGG + chr3.2:52533078-52533097 MS.gene04115:CDS 30.0%
TATCTCCTTGTAAACTTACT+TGG - chr3.2:52533078-52533097 None:intergenic 30.0%
TTGGTTGTATTTGAATATGG+AGG + chr3.2:52533243-52533262 MS.gene04115:CDS 30.0%
! CAATCCTATGAAGATTAGTT+TGG - chr3.2:52532761-52532780 None:intergenic 30.0%
! GCTCTAAATGGAAAGTTTAT+TGG + chr3.2:52533142-52533161 MS.gene04115:CDS 30.0%
! TGATGAATCAGTTGAGATTT+TGG + chr3.2:52533374-52533393 MS.gene04115:CDS 30.0%
! TTTTGGATGAATGGCTTAAT+CGG + chr3.2:52533391-52533410 MS.gene04115:CDS 30.0%
!!! AGCACTGGCAAATTTTATTA+TGG + chr3.2:52532932-52532951 MS.gene04115:intron 30.0%
ATGATCTTGAAGAAACGGAT+GGG - chr3.2:52532735-52532754 None:intergenic 35.0%
GAAAATTACTCTCTTGGACA+TGG + chr3.2:52533216-52533235 MS.gene04115:CDS 35.0%
TCCTCCAAACTAATCTTCAT+AGG + chr3.2:52532754-52532773 MS.gene04115:CDS 35.0%
TTTACAAGGAGATATGGAGT+TGG + chr3.2:52533084-52533103 MS.gene04115:CDS 35.0%
! ACCTTTTGCTTAGTGACTAA+CGG + chr3.2:52533028-52533047 MS.gene04115:intron 35.0%
! CAGTTGAGATTTTGGATGAA+TGG + chr3.2:52533382-52533401 MS.gene04115:CDS 35.0%
!! AGATTTGGTTTGAAAAGGGT+TGG + chr3.2:52533181-52533200 MS.gene04115:CDS 35.0%
!! AGTCTATTTCTACTGCATTC+TGG - chr3.2:52533299-52533318 None:intergenic 35.0%
!! ATCACTGTTGTATTTCTGGA+AGG + chr3.2:52532989-52533008 MS.gene04115:intron 35.0%
!! GGTGAGATTTGGTTTGAAAA+GGG + chr3.2:52533177-52533196 MS.gene04115:CDS 35.0%
!! TCCTATGAAGATTAGTTTGG+AGG - chr3.2:52532758-52532777 None:intergenic 35.0%
!! TGGTGAGATTTGGTTTGAAA+AGG + chr3.2:52533176-52533195 MS.gene04115:CDS 35.0%
GATGATCTTGAAGAAACGGA+TGG - chr3.2:52532736-52532755 None:intergenic 40.0%
GGAGGATGATCTTGAAGAAA+CGG - chr3.2:52532740-52532759 None:intergenic 40.0%
TGAATGGCTTAATCGGAAGA+AGG + chr3.2:52533398-52533417 MS.gene04115:CDS 40.0%
! ACTTTCCATTTAGAGCCATC+AGG - chr3.2:52533138-52533157 None:intergenic 40.0%
! CCTTTTGCTTAGTGACTAAC+GGG + chr3.2:52533029-52533048 MS.gene04115:intron 40.0%
! CTTTTGCTTAGTGACTAACG+GGG + chr3.2:52533030-52533049 MS.gene04115:intron 40.0%
AAGAAACGGATGGGAAGGAT+AGG - chr3.2:52532726-52532745 None:intergenic 45.0%
CAGACTTTCTTATGTGGTCG+AGG - chr3.2:52533450-52533469 None:intergenic 45.0%
CATGTTGCATGAGTGATGTG+TGG - chr3.2:52532835-52532854 None:intergenic 45.0%
CCCGTTAGTCACTAAGCAAA+AGG - chr3.2:52533032-52533051 None:intergenic 45.0%
TCTTGAAGAAACGGATGGGA+AGG - chr3.2:52532731-52532750 None:intergenic 45.0%
! TTCCATTTAGAGCCATCAGG+AGG - chr3.2:52533135-52533154 None:intergenic 45.0%
CTCTCTTGGACATGGCTCTT+TGG + chr3.2:52533224-52533243 MS.gene04115:CDS 50.0%
GGGAAGGATAGGATTTCCTC+TGG - chr3.2:52532715-52532734 None:intergenic 50.0%
TGTGGTCGAGGAGAATCAGA+AGG - chr3.2:52533438-52533457 None:intergenic 50.0%
!! AGCCTCCTGATGGCTCTAAA+TGG + chr3.2:52533130-52533149 MS.gene04115:CDS 50.0%
TCAGGAGGCTCGATCAACAC+TGG - chr3.2:52533120-52533139 None:intergenic 55.0%
! GTGTTGATCGAGCCTCCTGA+TGG + chr3.2:52533120-52533139 MS.gene04115:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 52532708 52533470 52532708 ID=MS.gene04115
chr3.2 mRNA 52532708 52533470 52532708 ID=MS.gene04115.t1;Parent=MS.gene04115
chr3.2 exon 52532708 52532779 52532708 ID=MS.gene04115.t1.exon1;Parent=MS.gene04115.t1
chr3.2 CDS 52532708 52532779 52532708 ID=cds.MS.gene04115.t1;Parent=MS.gene04115.t1
chr3.2 exon 52533069 52533470 52533069 ID=MS.gene04115.t1.exon2;Parent=MS.gene04115.t1
chr3.2 CDS 52533069 52533470 52533069 ID=cds.MS.gene04115.t1;Parent=MS.gene04115.t1
Gene Sequence

>MS.gene04115

ATGGCCAGAGGAAATCCTATCCTTCCCATCCGTTTCTTCAAGATCATCCTCCAAACTAATCTTCATAGGATTGTAAGCTAGCATTCCTATTAGTACTATTTAGTTTAGATTTCTTAGTATGTAACCACACATCACTCATGCAACATGTTATATATGCATTGAGCATTTCACATATTTTCTGTTTACAATATTAGCACTAGAACTTTTCATCAAAACAAAATATTAGCACTGGCAAATTTTATTATGGATACACACACATAACACATGAATATTGTTTAACTATCACTGTTGTATTTCTGGAAGGAATATTTATATTTGACACCTTTTGCTTAGTGACTAACGGGGTTCTTTAATTTTACAGCAAACACCAAGTAAGTTTACAAGGAGATATGGAGTTGGTCTATCAAATCCAGTGTTGATCGAGCCTCCTGATGGCTCTAAATGGAAAGTTTATTGGAAAAAAATCAATGGTGAGATTTGGTTTGAAAAGGGTTGGAAAACTTTTACTGAAAATTACTCTCTTGGACATGGCTCTTTGGTTGTATTTGAATATGGAGGAACTTCCAAGTTTGATGTACACATACTTGGCCAGAATGCAGTAGAAATAGACTATGATTCTTTAAGTGATACTAATGATGAAAATGACAATGTTGGTCATAGTGATGATGATGAATCAGTTGAGATTTTGGATGAATGGCTTAATCGGAAGAAGGCTAAACAAAGATCACCTTCTGATTCTCCTCGACCACATAAGAAAGTCTGA
Protein sequence

>MS.gene04115.t1

MARGNPILPIRFFKIILQTNLHRIQTPSKFTRRYGVGLSNPVLIEPPDGSKWKVYWKKINGEIWFEKGWKTFTENYSLGHGSLVVFEYGGTSKFDVHILGQNAVEIDYDSLSDTNDENDNVGHSDDDESVEILDEWLNRKKAKQRSPSDSPRPHKKV