AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073499

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073499.t1 MTR_4g021760 88.021 192 22 1 1 191 1 192 1.18e-121 346
MS.gene073499.t1 MTR_4g021845 79.581 191 39 0 1 191 1 191 2.34e-113 322
MS.gene073499.t1 MTR_4g021855 76.440 191 45 0 1 191 1 191 5.78e-107 308
MS.gene073499.t1 MTR_4g021790 74.346 191 49 0 1 191 1 191 1.16e-101 294
MS.gene073499.t1 MTR_5g055260 59.474 190 67 2 1 190 1 180 2.15e-76 229
MS.gene073499.t1 MTR_4g023980 76.642 137 32 0 55 191 35 171 1.71e-75 224
MS.gene073499.t1 MTR_1g032570 41.905 210 91 3 13 191 14 223 9.22e-51 172
MS.gene073499.t1 MTR_8g093040 48.864 176 82 4 1 171 1 173 1.03e-45 152
MS.gene073499.t1 MTR_6g045327 45.685 197 99 4 1 191 1 195 1.14e-43 149
MS.gene073499.t1 MTR_3g086100 37.681 207 101 4 13 191 16 222 4.07e-43 151
MS.gene073499.t1 MTR_8g079940 35.407 209 109 2 9 191 24 232 6.83e-43 150
MS.gene073499.t1 MTR_8g105600 40.513 195 96 2 14 188 13 207 7.18e-41 145
MS.gene073499.t1 MTR_2g034960 38.424 203 101 2 13 191 32 234 1.84e-40 144
MS.gene073499.t1 MTR_6g016850 42.767 159 88 2 14 169 13 171 1.90e-40 135
MS.gene073499.t1 MTR_4g121020 37.561 205 102 3 13 191 34 238 2.13e-40 145
MS.gene073499.t1 MTR_4g121020 37.561 205 102 3 13 191 34 238 2.21e-40 145
MS.gene073499.t1 MTR_4g131600 34.653 202 109 4 13 191 23 224 8.96e-35 129
MS.gene073499.t1 MTR_1g013170 35.749 207 105 3 13 191 8 214 1.35e-34 127
MS.gene073499.t1 MTR_7g117705 33.816 207 109 4 13 191 8 214 1.82e-33 124
MS.gene073499.t1 MTR_3g106220 35.071 211 105 3 13 191 11 221 2.17e-33 125
MS.gene073499.t1 MTR_1g013180 34.300 207 108 4 13 191 159 365 3.54e-32 122
MS.gene073499.t1 MTR_3g102590 37.569 181 86 4 13 191 11 166 2.96e-31 112
MS.gene073499.t1 MTR_3g102590 37.569 181 86 4 13 191 11 166 7.64e-31 112
MS.gene073499.t1 MTR_4g131570 31.401 207 114 4 13 191 20 226 1.40e-29 114
MS.gene073499.t1 MTR_1g032570 37.662 154 66 2 68 191 1 154 7.22e-29 112
MS.gene073499.t1 MTR_4g131580 30.882 204 116 4 13 191 20 223 1.55e-28 111
MS.gene073499.t1 MTR_3g102600 32.804 189 89 3 4 191 4 155 3.18e-27 102
MS.gene073499.t1 MTR_3g102600 32.804 189 89 3 4 191 4 155 4.95e-27 102
MS.gene073499.t1 MTR_2g450070 30.093 216 114 4 13 191 21 236 1.69e-26 105
MS.gene073499.t1 MTR_2g450070 30.556 216 113 3 13 191 21 236 1.70e-26 105
MS.gene073499.t1 MTR_3g086100 35.099 151 71 3 68 191 1 151 6.30e-25 100
MS.gene073499.t1 MTR_3g102600 30.435 138 61 1 54 191 4 106 2.03e-19 80.5
MS.gene073499.t1 MTR_3g102600 30.435 138 61 1 54 191 4 106 2.52e-19 81.3
MS.gene073499.t1 MTR_1g013160 33.108 148 72 2 71 191 1 148 1.58e-18 78.6
MS.gene073499.t1 MTR_0450s0040 26.984 189 121 3 14 190 8 191 2.09e-18 81.6
MS.gene073499.t1 MTR_4g121020 34.109 129 60 2 88 191 6 134 2.58e-16 76.6
MS.gene073499.t1 MTR_7g026400 28.931 159 82 3 54 191 32 180 3.01e-16 76.3
MS.gene073499.t1 MTR_8g024260 28.226 124 85 2 12 131 34 157 2.32e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073499.t1 AT1G67710 37.681 207 101 3 13 191 10 216 9.75e-41 144
MS.gene073499.t1 AT2G01760 36.111 216 99 5 13 191 10 223 1.40e-38 136
MS.gene073499.t1 AT3G16857 34.667 225 101 5 13 191 36 260 5.90e-34 127
MS.gene073499.t1 AT3G16857 34.667 225 101 5 13 191 36 260 7.82e-34 126
MS.gene073499.t1 AT2G01760 31.967 244 99 6 13 191 10 251 7.85e-33 121
MS.gene073499.t1 AT2G25180 34.314 204 108 5 13 191 16 218 1.69e-31 120
MS.gene073499.t1 AT4G31920 35.417 192 110 4 13 191 16 206 4.05e-31 118
MS.gene073499.t1 AT5G58080 33.824 204 107 5 13 191 17 217 3.27e-26 105
MS.gene073499.t1 AT3G16857 32.275 189 82 5 49 191 2 190 5.88e-23 95.9
MS.gene073499.t1 AT1G67710 35.762 151 70 2 68 191 1 151 3.67e-22 93.2
MS.gene073499.t1 AT2G01760 32.500 160 70 4 68 191 1 158 1.62e-21 90.1
MS.gene073499.t1 AT1G49190 27.861 201 118 3 16 189 36 236 3.81e-21 89.7
MS.gene073499.t1 AT5G49240 25.352 213 126 3 9 191 37 246 4.07e-19 83.2
MS.gene073499.t1 AT3G62670 25.521 192 121 4 16 189 45 232 1.39e-17 80.1
MS.gene073499.t1 AT1G49190 31.933 119 80 1 16 133 36 154 1.98e-15 73.9
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 3.07e-12 64.7
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 4.48e-12 64.3
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 4.48e-12 64.3
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 4.48e-12 64.3
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 6.17e-12 63.9
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 6.17e-12 63.9
MS.gene073499.t1 AT5G60100 30.894 123 79 3 14 131 64 185 6.17e-12 63.9
MS.gene073499.t1 AT5G24470 27.778 126 81 3 13 131 49 171 1.95e-11 62.4

Find 37 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGTAATCGATGCAATTATA+AGG 0.312923 4.1:-76392561 MS.gene073499:CDS
ACATCTCCTCGACGAAATTA+AGG 0.321564 4.1:+76392582 None:intergenic
TGAGTTGTAGGGTAACATTT+TGG 0.373812 4.1:+76392321 None:intergenic
CGAATATTGGACCAAGCCTT+TGG 0.374007 4.1:-76392132 MS.gene073499:CDS
AATGTGGGGCTTGCGAATAT+TGG 0.387677 4.1:-76392145 MS.gene073499:CDS
ATCAGAAGCCATGCTACATT+TGG 0.418312 4.1:+76392430 None:intergenic
CAAAGAAGGCCCGTTTGTCT+TGG 0.418636 4.1:-76391962 MS.gene073499:CDS
GTTTCAAGAAAATAGAAAAC+GGG 0.418887 4.1:-76392021 MS.gene073499:CDS
CTTTCTTTCCAACATGTTGA+AGG 0.419409 4.1:+76392406 None:intergenic
TGGCAACATGTTATAAGAAA+AGG 0.422808 4.1:-76392086 MS.gene073499:CDS
TGATGGTTTGTCGGTGAAAA+GGG 0.427097 4.1:+76392652 None:intergenic
ATATGAAATTGTTGGAAGCT+TGG 0.446291 4.1:-76392045 MS.gene073499:CDS
AAAAGAAACACTTGCAAAGA+AGG 0.446990 4.1:-76391976 MS.gene073499:CDS
ATGATGGTTTGTCGGTGAAA+AGG 0.455733 4.1:+76392651 None:intergenic
CTTCAACATGTTGGAAAGAA+AGG 0.459586 4.1:-76392405 MS.gene073499:CDS
AATAAATTCTTACTAATGAC+AGG 0.461511 4.1:+76392293 None:intergenic
TTCTCGCGACCAAGACAAAC+GGG 0.470376 4.1:+76391953 None:intergenic
TGTAATCGATGCAATTATAA+GGG 0.476930 4.1:-76392560 MS.gene073499:intron
TTGAGACCTTCTGATAATGA+TGG 0.479264 4.1:+76392635 None:intergenic
TTCTGATAATGATGGTTTGT+CGG 0.493949 4.1:+76392643 None:intergenic
AAGTCGTAAACATCCATGTT+TGG 0.494866 4.1:+76392347 None:intergenic
TGTTTCAAGAAAATAGAAAA+CGG 0.510078 4.1:-76392022 MS.gene073499:CDS
AGGAAAGAATCATACTATCA+AGG 0.510494 4.1:+76391892 None:intergenic
ATTATGAAGTCTATTGAATG+TGG 0.513075 4.1:-76392161 MS.gene073499:CDS
TTCTGATGCCTTCAACATGT+TGG 0.527887 4.1:-76392414 MS.gene073499:CDS
TTATGAAGTCTATTGAATGT+GGG 0.532174 4.1:-76392160 MS.gene073499:CDS
TTCAGTTACCAAATGTAGCA+TGG 0.538628 4.1:-76392438 MS.gene073499:intron
ATTCTCGCGACCAAGACAAA+CGG 0.543227 4.1:+76391952 None:intergenic
CTACGTGCAGTCAATCAACT+AGG 0.547867 4.1:-76391915 MS.gene073499:CDS
ATCATTATCAGAAGGTCTCA+AGG 0.582734 4.1:-76392633 MS.gene073499:CDS
AGAACTTTCTGCAGAATCAA+CGG 0.593830 4.1:+76392184 None:intergenic
TCTTATAACATGTTGCCACA+TGG 0.594344 4.1:+76392091 None:intergenic
TATGAAGTCTATTGAATGTG+GGG 0.598969 4.1:-76392159 MS.gene073499:CDS
TGATGCTCATATGCCAAACA+TGG 0.604750 4.1:-76392360 MS.gene073499:CDS
CACTCTCCTTAATTTCGTCG+AGG 0.625060 4.1:-76392588 MS.gene073499:CDS
GACAAACCATCATTATCAGA+AGG 0.636966 4.1:-76392641 MS.gene073499:CDS
TTTCAAGAAAATAGAAAACG+GGG 0.722642 4.1:-76392020 MS.gene073499:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAAAATATGAAATTGT+TGG - chr4.1:76392510-76392529 MS.gene073499:intron 15.0%
!! AATAAATTCTTACTAATGAC+AGG + chr4.1:76392273-76392292 None:intergenic 20.0%
!! ATAGATGAAAACTTTGAATA+AGG + chr4.1:76392046-76392065 None:intergenic 20.0%
!! TGTTTCAAGAAAATAGAAAA+CGG - chr4.1:76392541-76392560 MS.gene073499:intron 20.0%
!!! TTATTTCTTTTTTGTAGTGA+TGG - chr4.1:76392356-76392375 MS.gene073499:CDS 20.0%
!!! TTCAAAGTTTTCATCTATTT+TGG - chr4.1:76392048-76392067 MS.gene073499:CDS 20.0%
! ATTATGAAGTCTATTGAATG+TGG - chr4.1:76392402-76392421 MS.gene073499:CDS 25.0%
! GTTTCAAGAAAATAGAAAAC+GGG - chr4.1:76392542-76392561 MS.gene073499:intron 25.0%
! TGTAATCGATGCAATTATAA+GGG - chr4.1:76392003-76392022 MS.gene073499:CDS 25.0%
! TTATGAAGTCTATTGAATGT+GGG - chr4.1:76392403-76392422 MS.gene073499:CDS 25.0%
! TTTCAAGAAAATAGAAAACG+GGG - chr4.1:76392543-76392562 MS.gene073499:intron 25.0%
AAAAGAAACACTTGCAAAGA+AGG - chr4.1:76392587-76392606 MS.gene073499:CDS 30.0%
ATATGAAATTGTTGGAAGCT+TGG - chr4.1:76392518-76392537 MS.gene073499:intron 30.0%
GTGTAATCGATGCAATTATA+AGG - chr4.1:76392002-76392021 MS.gene073499:CDS 30.0%
TATGAAGTCTATTGAATGTG+GGG - chr4.1:76392404-76392423 MS.gene073499:CDS 30.0%
TGGCAACATGTTATAAGAAA+AGG - chr4.1:76392477-76392496 MS.gene073499:intron 30.0%
! CTTTGCAAGTGTTTCTTTTA+AGG + chr4.1:76392586-76392605 None:intergenic 30.0%
! TTCTGATAATGATGGTTTGT+CGG + chr4.1:76391923-76391942 None:intergenic 30.0%
!! TTGAACTGTTTTTCAACCAA+AGG + chr4.1:76392450-76392469 None:intergenic 30.0%
AAAAACAGTTCAAGACCATG+TGG - chr4.1:76392457-76392476 MS.gene073499:intron 35.0%
AAGTCGTAAACATCCATGTT+TGG + chr4.1:76392219-76392238 None:intergenic 35.0%
AGAACTTTCTGCAGAATCAA+CGG + chr4.1:76392382-76392401 None:intergenic 35.0%
ATCATTATCAGAAGGTCTCA+AGG - chr4.1:76391930-76391949 MS.gene073499:CDS 35.0%
CTTCAACATGTTGGAAAGAA+AGG - chr4.1:76392158-76392177 MS.gene073499:CDS 35.0%
CTTTCTTTCCAACATGTTGA+AGG + chr4.1:76392160-76392179 None:intergenic 35.0%
GACAAACCATCATTATCAGA+AGG - chr4.1:76391922-76391941 MS.gene073499:CDS 35.0%
TCTTATAACATGTTGCCACA+TGG + chr4.1:76392475-76392494 None:intergenic 35.0%
TTCAGTTACCAAATGTAGCA+TGG - chr4.1:76392125-76392144 MS.gene073499:CDS 35.0%
! TGAGTTGTAGGGTAACATTT+TGG + chr4.1:76392245-76392264 None:intergenic 35.0%
! TTGAGACCTTCTGATAATGA+TGG + chr4.1:76391931-76391950 None:intergenic 35.0%
!!! GACAGGAATTTTGAGTTGTA+GGG + chr4.1:76392256-76392275 None:intergenic 35.0%
!!! TGACAGGAATTTTGAGTTGT+AGG + chr4.1:76392257-76392276 None:intergenic 35.0%
ACATCTCCTCGACGAAATTA+AGG + chr4.1:76391984-76392003 None:intergenic 40.0%
ATCAGAAGCCATGCTACATT+TGG + chr4.1:76392136-76392155 None:intergenic 40.0%
TGATGCTCATATGCCAAACA+TGG - chr4.1:76392203-76392222 MS.gene073499:intron 40.0%
TTCTGATGCCTTCAACATGT+TGG - chr4.1:76392149-76392168 MS.gene073499:CDS 40.0%
! ATGATGGTTTGTCGGTGAAA+AGG + chr4.1:76391915-76391934 None:intergenic 40.0%
! TGATGGTTTGTCGGTGAAAA+GGG + chr4.1:76391914-76391933 None:intergenic 40.0%
!! CTGTTTTTCAACCAAAGGCT+TGG + chr4.1:76392445-76392464 None:intergenic 40.0%
AATGTGGGGCTTGCGAATAT+TGG - chr4.1:76392418-76392437 MS.gene073499:CDS 45.0%
ATTCTCGCGACCAAGACAAA+CGG + chr4.1:76392614-76392633 None:intergenic 45.0%
CACTCTCCTTAATTTCGTCG+AGG - chr4.1:76391975-76391994 MS.gene073499:CDS 45.0%
CGAATATTGGACCAAGCCTT+TGG - chr4.1:76392431-76392450 MS.gene073499:CDS 45.0%
CTACGTGCAGTCAATCAACT+AGG - chr4.1:76392648-76392667 MS.gene073499:CDS 45.0%
CAAAGAAGGCCCGTTTGTCT+TGG - chr4.1:76392601-76392620 MS.gene073499:CDS 50.0%
TTCTCGCGACCAAGACAAAC+GGG + chr4.1:76392613-76392632 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 76391907 76392678 76391907 ID=MS.gene073499
chr4.1 mRNA 76391907 76392678 76391907 ID=MS.gene073499.t1;Parent=MS.gene073499
chr4.1 exon 76392561 76392678 76392561 ID=MS.gene073499.t1.exon1;Parent=MS.gene073499.t1
chr4.1 CDS 76392561 76392678 76392561 ID=cds.MS.gene073499.t1;Parent=MS.gene073499.t1
chr4.1 exon 76392306 76392455 76392306 ID=MS.gene073499.t1.exon2;Parent=MS.gene073499.t1
chr4.1 CDS 76392306 76392455 76392306 ID=cds.MS.gene073499.t1;Parent=MS.gene073499.t1
chr4.1 exon 76391907 76392212 76391907 ID=MS.gene073499.t1.exon3;Parent=MS.gene073499.t1
chr4.1 CDS 76391907 76392212 76391907 ID=cds.MS.gene073499.t1;Parent=MS.gene073499.t1
Gene Sequence

>MS.gene073499

ATGGCCCTTTTCACCGACAAACCATCATTATCAGAAGGTCTCAAGGTTCTTGCAATTGATCATGACATCACTCTCCTTAATTTCGTCGAGGAGATGTGTAATCGATGCAATTATAAGGGTTAGTAACTGAATCACACCTTATTCAAAGTTTTCATCTATTTTGGTAAAAATTCTGACTTTTATATGTTTTCATGTTTGCTTATTCTGATATTGTTTATTTCAGTTACCAAATGTAGCATGGCTTCTGATGCCTTCAACATGTTGGAAAGAAAGGACTGTTTCGATGTAATGTTGATTGATGCTCATATGCCAAACATGGATGTTTACGACTTTGTCCAAAATGTTACCCTACAACTCAAAATTCCTGTCATTAGTAAGAATTTATTCAACTTTGCACAATTCAAATGATTCATTCATATTATGTACTTAATAAGTGTGAACTTACATTATTATTTCTTTTTTGTAGTGATGGCCGTTGATTCTGCAGAAAGTTCTATTATGAAGTCTATTGAATGTGGGGCTTGCGAATATTGGACCAAGCCTTTGGTTGAAAAACAGTTCAAGACCATGTGGCAACATGTTATAAGAAAAGGTTTGACTCAAAACAAAAAATATGAAATTGTTGGAAGCTTGGTGTTTCAAGAAAATAGAAAACGGGGTAGAGAAGATGCTAATGCCTTAAAAGAAACACTTGCAAAGAAGGCCCGTTTGTCTTGGTCGCGAGAATTGCATCAGCAGTTTCTACGTGCAGTCAATCAACTAGGCCTTGATA
Protein sequence

>MS.gene073499.t1

MALFTDKPSLSEGLKVLAIDHDITLLNFVEEMCNRCNYKVTKCSMASDAFNMLERKDCFDVMLIDAHMPNMDVYDFVQNVTLQLKIPVIMMAVDSAESSIMKSIECGACEYWTKPLVEKQFKTMWQHVIRKGLTQNKKYEIVGSLVFQENRKRGREDANALKETLAKKARLSWSRELHQQFLRAVNQLGLD