AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060189

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060189.t1 MTR_2g076400 98.324 179 2 1 1 179 1 178 1.02e-130 363
MS.gene060189.t1 MTR_2g092950 77.707 157 24 1 1 157 1 146 6.13e-89 258
MS.gene060189.t1 MTR_4g079930 86.508 126 17 0 32 157 27 152 1.68e-83 244
MS.gene060189.t1 MTR_2g016110 69.540 174 53 0 2 175 3 176 1.31e-82 242
MS.gene060189.t1 MTR_4g094428 76.296 135 32 0 31 165 43 177 2.58e-77 231
MS.gene060189.t1 MTR_5g072510 74.074 135 35 0 33 167 36 170 6.73e-76 227
MS.gene060189.t1 MTR_8g086350 81.818 132 24 0 26 157 23 154 2.44e-72 216
MS.gene060189.t1 MTR_1g442860 76.000 125 30 0 34 158 65 189 4.40e-70 211
MS.gene060189.t1 MTR_1g075990 73.611 144 38 0 32 175 51 194 1.08e-68 207
MS.gene060189.t1 MTR_3g031830 74.627 134 34 0 34 167 42 175 4.99e-67 204
MS.gene060189.t1 MTR_7g097030 75.758 132 32 0 33 164 63 194 2.71e-65 199
MS.gene060189.t1 MTR_1g069825 75.573 131 32 0 34 164 52 182 1.36e-64 198
MS.gene060189.t1 MTR_7g115700 66.667 135 40 3 32 163 25 157 4.78e-63 192
MS.gene060189.t1 MTR_1g080210 76.000 125 30 0 34 158 40 164 3.43e-61 188
MS.gene060189.t1 MTR_1g114020 68.889 45 14 0 33 77 70 114 4.01e-16 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060189.t1 AT2G42610 85.600 125 18 0 33 157 24 148 8.67e-82 240
MS.gene060189.t1 AT2G42610 85.600 125 18 0 33 157 24 148 8.67e-82 240
MS.gene060189.t1 AT1G78815 72.956 159 40 1 2 157 5 163 2.28e-79 234
MS.gene060189.t1 AT1G07090 77.273 132 30 0 33 164 30 161 1.18e-77 230
MS.gene060189.t1 AT1G16910 67.073 164 38 1 3 166 8 155 3.28e-74 220
MS.gene060189.t1 AT5G58500 77.444 133 29 1 33 164 18 150 4.42e-74 221
MS.gene060189.t1 AT4G18610 69.935 153 40 2 33 179 36 188 3.65e-73 218
MS.gene060189.t1 AT2G31160 75.573 131 32 0 34 164 54 184 2.59e-66 202
MS.gene060189.t1 AT3G23290 78.740 127 27 0 32 158 46 172 5.56e-66 201
MS.gene060189.t1 AT5G28490 75.573 131 32 0 33 163 24 154 6.24e-65 197
MS.gene060189.t1 AT3G04510 74.615 130 33 0 34 163 33 162 6.89e-65 198

Find 35 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAGGTACTTGGATCAATT+TGG 0.186025 2.3:+20658707 MS.gene060189:CDS
GGAAGCCTTGATGCACTTAT+TGG 0.224973 2.3:+20658818 MS.gene060189:CDS
AGAAGAGATTGGAACACTTT+TGG 0.264015 2.3:+20658614 MS.gene060189:CDS
CTAGCAAAAGGATTAGTTTC+AGG 0.303544 2.3:-20658878 None:intergenic
AGAGCTGCTTATGAAGAAAA+TGG 0.368567 2.3:+20658848 MS.gene060189:CDS
CAAATTGATCCAAGTACCTT+AGG 0.370819 2.3:-20658706 None:intergenic
TCTTGAATTCCTAAGGTACT+TGG 0.381797 2.3:+20658697 MS.gene060189:CDS
CTCACGAAGATAGATTCTTA+TGG 0.388339 2.3:-20658906 None:intergenic
TTGTCCTCTAAAACAAGCTT+GGG 0.400385 2.3:+20658796 MS.gene060189:CDS
AAAGGAAAAGACATAGTAGA+AGG 0.430124 2.3:+20658506 MS.gene060189:CDS
TTCGGACAAACCGAACCTCC+TGG 0.459277 2.3:+20658764 MS.gene060189:CDS
CTACAATTTGAAAGTGCAAC+TGG 0.465538 2.3:-20658662 None:intergenic
AGTACATGGTCCAGGAGGTT+CGG 0.480855 2.3:-20658774 None:intergenic
CTTGTCCTCTAAAACAAGCT+TGG 0.483002 2.3:+20658795 MS.gene060189:CDS
GGATCATCAAGATCTTCAAT+AGG 0.489614 2.3:+20658527 MS.gene060189:CDS
CTTATGGAACCACTAGCAAA+AGG 0.491890 2.3:-20658890 None:intergenic
TTACTGCATAGGCAAATTTG+AGG 0.494659 2.3:-20659014 None:intergenic
AGTCACAAAAGAGAAGAGAT+TGG 0.497858 2.3:+20658603 MS.gene060189:CDS
ACCATGTTCTTGAATTCCTA+AGG 0.512890 2.3:+20658690 MS.gene060189:CDS
TGTGACTCGTATCGACTAAG+TGG 0.527013 2.3:-20658587 None:intergenic
AGAGGACAAGTACATGGTCC+AGG 0.528522 2.3:-20658782 None:intergenic
ATCTTCCAATAAGTGCATCA+AGG 0.536647 2.3:-20658823 None:intergenic
AATGATAAACTTTACTGCAT+AGG 0.539721 2.3:-20659025 None:intergenic
AAAACAAAAGTGCACTTACA+AGG 0.545619 2.3:+20658731 MS.gene060189:CDS
ACCTTAGGAATTCAAGAACA+TGG 0.577239 2.3:-20658691 None:intergenic
GGTGAGAGATTCTCAAGCTA+AGG 0.580040 2.3:+20658928 MS.gene060189:CDS
GATTCTCAAGCTAAGGCTAG+AGG 0.580908 2.3:+20658935 MS.gene060189:CDS
AGGGTTGCAATTAAACATAA+CGG 0.590674 2.3:+20658986 MS.gene060189:CDS
TCAAGATCTTCAATAGGTGA+TGG 0.598004 2.3:+20658533 MS.gene060189:CDS
AAAGAAGATATGTCCAACAA+AGG 0.618073 2.3:+20658488 None:intergenic
GCTGCTTATGAAGAAAATGG+TGG 0.637680 2.3:+20658851 MS.gene060189:CDS
CATAAGAATCTATCTTCGTG+AGG 0.662614 2.3:+20658907 MS.gene060189:CDS
CAATTTGAAAGTGCAACTGG+TGG 0.691757 2.3:-20658659 None:intergenic
TGTCCTCTAAAACAAGCTTG+GGG 0.721618 2.3:+20658797 MS.gene060189:CDS
GGACAAGTACATGGTCCAGG+AGG 0.722613 2.3:-20658779 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTCTTTTTCTTCTTGTA+AGG - chr2.3:20658965-20658984 None:intergenic 25.0%
!!! TTACAAGGTTGTTTGTTTTT+CGG + chr2.3:20658746-20658765 MS.gene060189:CDS 25.0%
AAAGGAAAAGACATAGTAGA+AGG + chr2.3:20658506-20658525 MS.gene060189:CDS 30.0%
ACAAGAAGAAAAAGAAGAAG+AGG + chr2.3:20658966-20658985 MS.gene060189:CDS 30.0%
AGGGTTGCAATTAAACATAA+CGG + chr2.3:20658986-20659005 MS.gene060189:CDS 30.0%
CAAGAAGAAAAAGAAGAAGA+GGG + chr2.3:20658967-20658986 MS.gene060189:CDS 30.0%
! AAAACAAAAGTGCACTTACA+AGG + chr2.3:20658731-20658750 MS.gene060189:CDS 30.0%
! ACACTTTTGGACAATACTTA+AGG + chr2.3:20658627-20658646 MS.gene060189:CDS 30.0%
! TACTATGTCTTTTCCTTTGT+TGG - chr2.3:20658504-20658523 None:intergenic 30.0%
ACCATGTTCTTGAATTCCTA+AGG + chr2.3:20658690-20658709 MS.gene060189:CDS 35.0%
ACCTTAGGAATTCAAGAACA+TGG - chr2.3:20658694-20658713 None:intergenic 35.0%
AGAGCTGCTTATGAAGAAAA+TGG + chr2.3:20658848-20658867 MS.gene060189:CDS 35.0%
AGTCACAAAAGAGAAGAGAT+TGG + chr2.3:20658603-20658622 MS.gene060189:CDS 35.0%
ATCTTCCAATAAGTGCATCA+AGG - chr2.3:20658826-20658845 None:intergenic 35.0%
CAAATTGATCCAAGTACCTT+AGG - chr2.3:20658709-20658728 None:intergenic 35.0%
CATAAGAATCTATCTTCGTG+AGG + chr2.3:20658907-20658926 MS.gene060189:CDS 35.0%
CTCACGAAGATAGATTCTTA+TGG - chr2.3:20658909-20658928 None:intergenic 35.0%
GGATCATCAAGATCTTCAAT+AGG + chr2.3:20658527-20658546 MS.gene060189:CDS 35.0%
TCAAGATCTTCAATAGGTGA+TGG + chr2.3:20658533-20658552 MS.gene060189:CDS 35.0%
TTACTGCATAGGCAAATTTG+AGG - chr2.3:20659017-20659036 None:intergenic 35.0%
! AGAAGAGATTGGAACACTTT+TGG + chr2.3:20658614-20658633 MS.gene060189:CDS 35.0%
! CTAAGGTACTTGGATCAATT+TGG + chr2.3:20658707-20658726 MS.gene060189:CDS 35.0%
! CTACAATTTGAAAGTGCAAC+TGG - chr2.3:20658665-20658684 None:intergenic 35.0%
! GAAACTAATCCTTTTGCTAG+TGG + chr2.3:20658881-20658900 MS.gene060189:CDS 35.0%
! TCTTGAATTCCTAAGGTACT+TGG + chr2.3:20658697-20658716 MS.gene060189:CDS 35.0%
!! CTAGCAAAAGGATTAGTTTC+AGG - chr2.3:20658881-20658900 None:intergenic 35.0%
!! TTGTCCTCTAAAACAAGCTT+GGG + chr2.3:20658796-20658815 MS.gene060189:CDS 35.0%
!!! TGTTTTAGAGGACAAGTACA+TGG - chr2.3:20658791-20658810 None:intergenic 35.0%
CTTATGGAACCACTAGCAAA+AGG - chr2.3:20658893-20658912 None:intergenic 40.0%
GCTGCTTATGAAGAAAATGG+TGG + chr2.3:20658851-20658870 MS.gene060189:CDS 40.0%
! CAATTTGAAAGTGCAACTGG+TGG - chr2.3:20658662-20658681 None:intergenic 40.0%
!! CTTGTCCTCTAAAACAAGCT+TGG + chr2.3:20658795-20658814 MS.gene060189:CDS 40.0%
!! TGTCCTCTAAAACAAGCTTG+GGG + chr2.3:20658797-20658816 MS.gene060189:CDS 40.0%
GATTCTCAAGCTAAGGCTAG+AGG + chr2.3:20658935-20658954 MS.gene060189:CDS 45.0%
GGAAGCCTTGATGCACTTAT+TGG + chr2.3:20658818-20658837 MS.gene060189:CDS 45.0%
GGTGAGAGATTCTCAAGCTA+AGG + chr2.3:20658928-20658947 MS.gene060189:CDS 45.0%
!! TGTGACTCGTATCGACTAAG+TGG - chr2.3:20658590-20658609 None:intergenic 45.0%
!!! CTTCCCCAAGCTTGTTTTAG+AGG - chr2.3:20658803-20658822 None:intergenic 45.0%
AGAGGACAAGTACATGGTCC+AGG - chr2.3:20658785-20658804 None:intergenic 50.0%
AGTACATGGTCCAGGAGGTT+CGG - chr2.3:20658777-20658796 None:intergenic 50.0%
GGACAAGTACATGGTCCAGG+AGG - chr2.3:20658782-20658801 None:intergenic 55.0%
TTCGGACAAACCGAACCTCC+TGG + chr2.3:20658764-20658783 MS.gene060189:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 20658497 20659036 20658497 ID=MS.gene060189
chr2.3 mRNA 20658497 20659036 20658497 ID=MS.gene060189.t1;Parent=MS.gene060189
chr2.3 exon 20658497 20659036 20658497 ID=MS.gene060189.t1.exon1;Parent=MS.gene060189.t1
chr2.3 CDS 20658497 20659036 20658497 ID=cds.MS.gene060189.t1;Parent=MS.gene060189.t1
Gene Sequence

>MS.gene060189

ATGTCCAACAAAGGAAAAGACATAGTAGAAGGATCATCAAGATCTTCAATAGGTGATGGTGATCAAAATCAGCAGCATCAACAACAAATTCCACTTAGTCGATACGAGTCACAAAAGAGAAGAGATTGGAACACTTTTGGACAATACTTAAGGAATCAAAGACCACCAGTTGCACTTTCAAATTGTAGTTCAAACCATGTTCTTGAATTCCTAAGGTACTTGGATCAATTTGGAAAAACAAAAGTGCACTTACAAGGTTGTTTGTTTTTCGGACAAACCGAACCTCCTGGACCATGTACTTGTCCTCTAAAACAAGCTTGGGGAAGCCTTGATGCACTTATTGGAAGATTAAGAGCTGCTTATGAAGAAAATGGTGGATTACCTGAAACTAATCCTTTTGCTAGTGGTTCCATAAGAATCTATCTTCGTGAGGTGAGAGATTCTCAAGCTAAGGCTAGAGGAATTCCTTACAAGAAGAAAAAGAAGAAGAGGGTTGCAATTAAACATAACGGAGATACCTCAAATTTGCCTATGCAGTAA
Protein sequence

>MS.gene060189.t1

MSNKGKDIVEGSSRSSIGDGDQNQQHQQQIPLSRYESQKRRDWNTFGQYLRNQRPPVALSNCSSNHVLEFLRYLDQFGKTKVHLQGCLFFGQTEPPGPCTCPLKQAWGSLDALIGRLRAAYEENGGLPETNPFASGSIRIYLREVRDSQAKARGIPYKKKKKKRVAIKHNGDTSNLPMQ