AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060590.t1 MTR_2g076400 98.324 179 2 1 1 179 1 178 1.02e-130 363
MS.gene060590.t1 MTR_2g092950 77.707 157 24 1 1 157 1 146 6.13e-89 258
MS.gene060590.t1 MTR_4g079930 86.508 126 17 0 32 157 27 152 1.68e-83 244
MS.gene060590.t1 MTR_2g016110 69.540 174 53 0 2 175 3 176 1.31e-82 242
MS.gene060590.t1 MTR_4g094428 76.296 135 32 0 31 165 43 177 2.58e-77 231
MS.gene060590.t1 MTR_5g072510 74.074 135 35 0 33 167 36 170 6.73e-76 227
MS.gene060590.t1 MTR_8g086350 81.818 132 24 0 26 157 23 154 2.44e-72 216
MS.gene060590.t1 MTR_1g442860 76.000 125 30 0 34 158 65 189 4.40e-70 211
MS.gene060590.t1 MTR_1g075990 73.611 144 38 0 32 175 51 194 1.08e-68 207
MS.gene060590.t1 MTR_3g031830 74.627 134 34 0 34 167 42 175 4.99e-67 204
MS.gene060590.t1 MTR_7g097030 75.758 132 32 0 33 164 63 194 2.71e-65 199
MS.gene060590.t1 MTR_1g069825 75.573 131 32 0 34 164 52 182 1.36e-64 198
MS.gene060590.t1 MTR_7g115700 66.667 135 40 3 32 163 25 157 4.78e-63 192
MS.gene060590.t1 MTR_1g080210 76.000 125 30 0 34 158 40 164 3.43e-61 188
MS.gene060590.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.gene060590.t1 AT2G42610 85.600 125 18 0 33 157 24 148 8.67e-82 240
MS.gene060590.t1 AT2G42610 85.600 125 18 0 33 157 24 148 8.67e-82 240
MS.gene060590.t1 AT1G78815 72.956 159 40 1 2 157 5 163 2.28e-79 234
MS.gene060590.t1 AT1G07090 77.273 132 30 0 33 164 30 161 1.18e-77 230
MS.gene060590.t1 AT1G16910 67.073 164 38 1 3 166 8 155 3.28e-74 220
MS.gene060590.t1 AT5G58500 77.444 133 29 1 33 164 18 150 4.42e-74 221
MS.gene060590.t1 AT4G18610 69.935 153 40 2 33 179 36 188 3.65e-73 218
MS.gene060590.t1 AT2G31160 75.573 131 32 0 34 164 54 184 2.59e-66 202
MS.gene060590.t1 AT3G23290 78.740 127 27 0 32 158 46 172 5.56e-66 201
MS.gene060590.t1 AT5G28490 75.573 131 32 0 33 163 24 154 6.24e-65 197
MS.gene060590.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 2.2:+17553977 MS.gene060590:CDS
GGAAGCCTTGATGCACTTAT+TGG 0.224973 2.2:+17554088 MS.gene060590:CDS
AGAAGAGATTGGAACACTTT+TGG 0.264015 2.2:+17553884 MS.gene060590:CDS
CTAGCAAAAGGATTAGTTTC+AGG 0.303544 2.2:-17554148 None:intergenic
AGAGCTGCTTATGAAGAAAA+TGG 0.368567 2.2:+17554118 MS.gene060590:CDS
CAAATTGATCCAAGTACCTT+AGG 0.370819 2.2:-17553976 None:intergenic
TCTTGAATTCCTAAGGTACT+TGG 0.381797 2.2:+17553967 MS.gene060590:CDS
CTCACGAAGATAGATTCTTA+TGG 0.388339 2.2:-17554176 None:intergenic
TTGTCCTCTAAAACAAGCTT+GGG 0.400385 2.2:+17554066 MS.gene060590:CDS
AAAGGAAAAGACATAGTAGA+AGG 0.430124 2.2:+17553776 MS.gene060590:CDS
CTACAATTTGAAAGTGCAAC+TGG 0.465538 2.2:-17553932 None:intergenic
AGTACATGGTCCAGGTGGTT+CGG 0.478835 2.2:-17554044 None:intergenic
CTTGTCCTCTAAAACAAGCT+TGG 0.483002 2.2:+17554065 MS.gene060590:CDS
GGATCATCAAGATCTTCAAT+AGG 0.489614 2.2:+17553797 MS.gene060590:CDS
CTTATGGAACCACTAGCAAA+AGG 0.491890 2.2:-17554160 None:intergenic
TTACTGCATAGGCAAATTTG+AGG 0.494659 2.2:-17554284 None:intergenic
AGTCACAAAAGAGAAGAGAT+TGG 0.497858 2.2:+17553873 MS.gene060590:CDS
ACCATGTTCTTGAATTCCTA+AGG 0.512890 2.2:+17553960 MS.gene060590:CDS
TTCGGACAAACCGAACCACC+TGG 0.517016 2.2:+17554034 MS.gene060590:CDS
TGTGACTCGTATCGACTAAG+TGG 0.527013 2.2:-17553857 None:intergenic
ATCTTCCAATAAGTGCATCA+AGG 0.536647 2.2:-17554093 None:intergenic
AGAGGACAAGTACATGGTCC+AGG 0.536991 2.2:-17554052 None:intergenic
AATGATAAACTTTACTGCAT+AGG 0.539721 2.2:-17554295 None:intergenic
AAAACAAAAGTGCACTTACA+AGG 0.545619 2.2:+17554001 MS.gene060590:CDS
ACCTTAGGAATTCAAGAACA+TGG 0.577239 2.2:-17553961 None:intergenic
GGTGAGAGATTCTCAAGCTA+AGG 0.580040 2.2:+17554198 MS.gene060590:CDS
GATTCTCAAGCTAAGGCTAG+AGG 0.580908 2.2:+17554205 MS.gene060590:CDS
AGGGTTGCAATTAAACATAA+CGG 0.590674 2.2:+17554256 MS.gene060590:CDS
TCAAGATCTTCAATAGGTGA+TGG 0.598004 2.2:+17553803 MS.gene060590:CDS
AAAGAAGATATGTCCAACAA+AGG 0.618073 2.2:+17553758 None:intergenic
GCTGCTTATGAAGAAAATGG+TGG 0.637680 2.2:+17554121 MS.gene060590:CDS
CATAAGAATCTATCTTCGTG+AGG 0.662614 2.2:+17554177 MS.gene060590:CDS
CAATTTGAAAGTGCAACTGG+TGG 0.691757 2.2:-17553929 None:intergenic
GGACAAGTACATGGTCCAGG+TGG 0.718126 2.2:-17554049 None:intergenic
TGTCCTCTAAAACAAGCTTG+GGG 0.721618 2.2:+17554067 MS.gene060590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTCTTTTTCTTCTTGTA+AGG - chr2.2:17554235-17554254 None:intergenic 25.0%
!!! TTACAAGGTTGTTTGTTTTT+CGG + chr2.2:17554016-17554035 MS.gene060590:CDS 25.0%
AAAGGAAAAGACATAGTAGA+AGG + chr2.2:17553776-17553795 MS.gene060590:CDS 30.0%
ACAAGAAGAAAAAGAAGAAG+AGG + chr2.2:17554236-17554255 MS.gene060590:CDS 30.0%
AGGGTTGCAATTAAACATAA+CGG + chr2.2:17554256-17554275 MS.gene060590:CDS 30.0%
CAAGAAGAAAAAGAAGAAGA+GGG + chr2.2:17554237-17554256 MS.gene060590:CDS 30.0%
! AAAACAAAAGTGCACTTACA+AGG + chr2.2:17554001-17554020 MS.gene060590:CDS 30.0%
! ACACTTTTGGACAATACTTA+AGG + chr2.2:17553897-17553916 MS.gene060590:CDS 30.0%
! TACTATGTCTTTTCCTTTGT+TGG - chr2.2:17553774-17553793 None:intergenic 30.0%
ACCATGTTCTTGAATTCCTA+AGG + chr2.2:17553960-17553979 MS.gene060590:CDS 35.0%
ACCTTAGGAATTCAAGAACA+TGG - chr2.2:17553964-17553983 None:intergenic 35.0%
AGAGCTGCTTATGAAGAAAA+TGG + chr2.2:17554118-17554137 MS.gene060590:CDS 35.0%
AGTCACAAAAGAGAAGAGAT+TGG + chr2.2:17553873-17553892 MS.gene060590:CDS 35.0%
ATCTTCCAATAAGTGCATCA+AGG - chr2.2:17554096-17554115 None:intergenic 35.0%
CAAATTGATCCAAGTACCTT+AGG - chr2.2:17553979-17553998 None:intergenic 35.0%
CATAAGAATCTATCTTCGTG+AGG + chr2.2:17554177-17554196 MS.gene060590:CDS 35.0%
CTCACGAAGATAGATTCTTA+TGG - chr2.2:17554179-17554198 None:intergenic 35.0%
GGATCATCAAGATCTTCAAT+AGG + chr2.2:17553797-17553816 MS.gene060590:CDS 35.0%
TCAAGATCTTCAATAGGTGA+TGG + chr2.2:17553803-17553822 MS.gene060590:CDS 35.0%
TTACTGCATAGGCAAATTTG+AGG - chr2.2:17554287-17554306 None:intergenic 35.0%
! AGAAGAGATTGGAACACTTT+TGG + chr2.2:17553884-17553903 MS.gene060590:CDS 35.0%
! CTAAGGTACTTGGATCAATT+TGG + chr2.2:17553977-17553996 MS.gene060590:CDS 35.0%
! CTACAATTTGAAAGTGCAAC+TGG - chr2.2:17553935-17553954 None:intergenic 35.0%
! GAAACTAATCCTTTTGCTAG+TGG + chr2.2:17554151-17554170 MS.gene060590:CDS 35.0%
! TCTTGAATTCCTAAGGTACT+TGG + chr2.2:17553967-17553986 MS.gene060590:CDS 35.0%
!! CTAGCAAAAGGATTAGTTTC+AGG - chr2.2:17554151-17554170 None:intergenic 35.0%
!! TTGTCCTCTAAAACAAGCTT+GGG + chr2.2:17554066-17554085 MS.gene060590:CDS 35.0%
!!! TGTTTTAGAGGACAAGTACA+TGG - chr2.2:17554061-17554080 None:intergenic 35.0%
CTTATGGAACCACTAGCAAA+AGG - chr2.2:17554163-17554182 None:intergenic 40.0%
GCTGCTTATGAAGAAAATGG+TGG + chr2.2:17554121-17554140 MS.gene060590:CDS 40.0%
! CAATTTGAAAGTGCAACTGG+TGG - chr2.2:17553932-17553951 None:intergenic 40.0%
!! CTTGTCCTCTAAAACAAGCT+TGG + chr2.2:17554065-17554084 MS.gene060590:CDS 40.0%
!! TGTCCTCTAAAACAAGCTTG+GGG + chr2.2:17554067-17554086 MS.gene060590:CDS 40.0%
GATTCTCAAGCTAAGGCTAG+AGG + chr2.2:17554205-17554224 MS.gene060590:CDS 45.0%
GGAAGCCTTGATGCACTTAT+TGG + chr2.2:17554088-17554107 MS.gene060590:CDS 45.0%
GGTGAGAGATTCTCAAGCTA+AGG + chr2.2:17554198-17554217 MS.gene060590:CDS 45.0%
!! TGTGACTCGTATCGACTAAG+TGG - chr2.2:17553860-17553879 None:intergenic 45.0%
!!! CTTCCCCAAGCTTGTTTTAG+AGG - chr2.2:17554073-17554092 None:intergenic 45.0%
AGAGGACAAGTACATGGTCC+AGG - chr2.2:17554055-17554074 None:intergenic 50.0%
AGTACATGGTCCAGGTGGTT+CGG - chr2.2:17554047-17554066 None:intergenic 50.0%
GGACAAGTACATGGTCCAGG+TGG - chr2.2:17554052-17554071 None:intergenic 55.0%
TTCGGACAAACCGAACCACC+TGG + chr2.2:17554034-17554053 MS.gene060590:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 17553767 17554306 17553767 ID=MS.gene060590
chr2.2 mRNA 17553767 17554306 17553767 ID=MS.gene060590.t1;Parent=MS.gene060590
chr2.2 exon 17553767 17554306 17553767 ID=MS.gene060590.t1.exon1;Parent=MS.gene060590.t1
chr2.2 CDS 17553767 17554306 17553767 ID=cds.MS.gene060590.t1;Parent=MS.gene060590.t1
Gene Sequence

>MS.gene060590

ATGTCCAACAAAGGAAAAGACATAGTAGAAGGATCATCAAGATCTTCAATAGGTGATGGTGATCAAAATCAGCAGCATCAACAACAAATTCCACTTAGTCGATACGAGTCACAAAAGAGAAGAGATTGGAACACTTTTGGACAATACTTAAGGAATCAAAGACCACCAGTTGCACTTTCAAATTGTAGTTCAAACCATGTTCTTGAATTCCTAAGGTACTTGGATCAATTTGGAAAAACAAAAGTGCACTTACAAGGTTGTTTGTTTTTCGGACAAACCGAACCACCTGGACCATGTACTTGTCCTCTAAAACAAGCTTGGGGAAGCCTTGATGCACTTATTGGAAGATTAAGAGCTGCTTATGAAGAAAATGGTGGATTACCTGAAACTAATCCTTTTGCTAGTGGTTCCATAAGAATCTATCTTCGTGAGGTGAGAGATTCTCAAGCTAAGGCTAGAGGAATTCCTTACAAGAAGAAAAAGAAGAAGAGGGTTGCAATTAAACATAACGGAGATACCTCAAATTTGCCTATGCAGTAA
Protein sequence

>MS.gene060590.t1

MSNKGKDIVEGSSRSSIGDGDQNQQHQQQIPLSRYESQKRRDWNTFGQYLRNQRPPVALSNCSSNHVLEFLRYLDQFGKTKVHLQGCLFFGQTEPPGPCTCPLKQAWGSLDALIGRLRAAYEENGGLPETNPFASGSIRIYLREVRDSQAKARGIPYKKKKKKRVAIKHNGDTSNLPMQ