AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29680.t1 MTR_5g083110 97.976 247 4 1 1 246 1 247 2.81e-178 489
MS.gene29680.t1 MTR_3g071510 54.800 250 102 6 1 246 1 243 5.12e-82 246
MS.gene29680.t1 MTR_5g072400 46.000 250 101 4 20 238 8 254 7.65e-63 197
MS.gene29680.t1 MTR_3g465550 47.685 216 88 4 38 233 18 228 8.44e-62 194
MS.gene29680.t1 MTR_3g017490 52.381 147 68 2 93 237 114 260 5.84e-48 160
MS.gene29680.t1 MTR_7g090230 52.229 157 72 3 84 237 268 424 7.84e-48 163
MS.gene29680.t1 MTR_8g038440 53.947 152 65 3 91 237 103 254 3.55e-47 157
MS.gene29680.t1 MTR_1g051180 49.057 159 70 2 90 237 205 363 1.29e-44 154
MS.gene29680.t1 MTR_1g090400 48.667 150 75 2 89 237 220 368 1.93e-44 153
MS.gene29680.t1 MTR_7g104720 47.333 150 77 2 89 237 256 404 2.39e-40 143
MS.gene29680.t1 MTR_7g010090 40.887 203 99 3 58 239 231 433 1.53e-36 134
MS.gene29680.t1 MTR_7g106500 44.099 161 75 5 89 237 121 278 1.39e-34 125
MS.gene29680.t1 MTR_6g011640 40.351 171 82 4 89 239 228 398 1.81e-34 127
MS.gene29680.t1 MTR_8g099665 44.025 159 80 4 89 238 210 368 2.11e-33 124
MS.gene29680.t1 MTR_8g106900 45.513 156 78 3 89 237 118 273 9.54e-31 115
MS.gene29680.t1 MTR_3g030520 37.427 171 87 4 89 239 130 300 2.92e-26 103
MS.gene29680.t1 MTR_5g048870 41.935 93 51 1 89 178 64 156 1.01e-14 69.7
MS.gene29680.t1 MTR_1g095960 36.275 102 56 4 137 230 31 131 2.35e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29680.t1 AT5G58530 53.179 173 71 2 76 239 96 267 1.70e-57 184
MS.gene29680.t1 AT5G13810 52.667 150 69 2 90 237 123 272 2.57e-47 158
MS.gene29680.t1 AT2G41330 50.676 148 70 3 93 237 253 400 2.35e-44 154
MS.gene29680.t1 AT3G57070 46.711 152 77 3 90 237 264 415 6.31e-42 148
MS.gene29680.t1 AT5G39865 46.061 165 69 3 93 237 224 388 7.64e-38 136
MS.gene29680.t1 AT1G64500 44.099 161 80 3 89 239 207 367 1.00e-36 133
MS.gene29680.t1 AT5G06470 42.038 157 81 3 89 237 84 238 2.17e-35 126
MS.gene29680.t1 AT3G28850 43.258 178 67 5 93 237 250 426 2.17e-35 130
MS.gene29680.t1 AT4G10630 44.172 163 77 3 89 237 171 333 5.16e-34 125
MS.gene29680.t1 AT5G03870 46.711 152 78 2 89 237 232 383 1.63e-33 125
MS.gene29680.t1 AT3G11773 39.583 144 85 2 95 237 7 149 2.05e-32 116
MS.gene29680.t1 AT5G01420 44.000 150 83 1 89 237 251 400 3.01e-31 119
MS.gene29680.t1 AT1G32760 38.462 221 113 6 26 237 107 313 2.67e-30 115
MS.gene29680.t1 AT3G11773 38.532 109 66 1 129 237 92 199 9.87e-23 92.4

Find 71 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGAATAGTGAAGGAGATTT+TGG 0.249394 5.3:+67341631 None:intergenic
CGGTAATGTGGCCACCAAAT+TGG 0.270785 5.3:-67341795 None:intergenic
GTGTGACGTTCTTGCGGTTC+AGG 0.271638 5.3:+67341356 None:intergenic
TGTTTGGGTTGTAATGTTAA+TGG 0.283205 5.3:-67341124 MS.gene29680:CDS
AGGGAGATTGTTTGTGGTGG+TGG 0.291231 5.3:+67341550 None:intergenic
CTCGGTGAAGCTAACCAATT+TGG 0.309594 5.3:+67341781 None:intergenic
AAACGGATTTAGAAGCTGTT+TGG 0.322439 5.3:-67341140 MS.gene29680:CDS
TGGTGGTGGAGCGGTGGTTC+GGG 0.327903 5.3:+67341564 None:intergenic
AACGGATTTAGAAGCTGTTT+GGG 0.342857 5.3:-67341139 MS.gene29680:CDS
GTGGTGGTGGAGCGGTGGTT+CGG 0.343650 5.3:+67341563 None:intergenic
TCAAAACTAAGCAAACTATC+TGG 0.415443 5.3:+67341057 None:intergenic
GGGAGGGAGATTGTTTGTGG+TGG 0.420392 5.3:+67341547 None:intergenic
GTAATGTTAATGGTTTGATT+AGG 0.422139 5.3:-67341114 MS.gene29680:CDS
CGGAAGTCACAAAGTGTATA+CGG 0.422300 5.3:-67341167 MS.gene29680:CDS
GGTGGTTCGGGAGGCTGATA+AGG 0.427466 5.3:+67341576 None:intergenic
TGAAGTTGATAGAGCGAGTT+CGG 0.441738 5.3:+67341713 None:intergenic
GGAGGGAGGGAGATTGTTTG+TGG 0.455777 5.3:+67341544 None:intergenic
GCAAGAACGTCACACTTCCT+AGG 0.457073 5.3:-67341348 MS.gene29680:CDS
GCGACGGTGGTGGTGAATTA+CGG 0.459130 5.3:+67341752 None:intergenic
TAGAGTTTCAATGTCTTTGA+AGG 0.474062 5.3:+67341681 None:intergenic
GGCTGATAAGGCGCGGAGGA+AGG 0.507767 5.3:+67341588 None:intergenic
AGCTGAATCGTTTGATCGAA+CGG 0.508185 5.3:-67341261 MS.gene29680:CDS
GCGGCGGATTACGCGGAGGC+TGG 0.521946 5.3:+67341489 None:intergenic
GATTGTTTGTGGTGGTGGAG+CGG 0.530639 5.3:+67341555 None:intergenic
CGCGTTCGTCGGTGATGACG+CGG 0.534540 5.3:+67341422 None:intergenic
TGGTGGAGCGGTGGTTCGGG+AGG 0.536147 5.3:+67341567 None:intergenic
CGGTGATGACGCGGAAGTTG+CGG 0.536191 5.3:+67341431 None:intergenic
TAAGGCGCGGAGGAAGGTGG+TGG 0.541659 5.3:+67341594 None:intergenic
CAAGAACGTCACACTTCCTA+GGG 0.546669 5.3:-67341347 MS.gene29680:CDS
GGTGAAGCTAACCAATTTGG+TGG 0.552271 5.3:+67341784 None:intergenic
GGTAGCATGAAGAAACATGC+AGG 0.552753 5.3:+67341088 None:intergenic
AACGGTTGTGATTGCTGTGG+AGG 0.554704 5.3:-67341220 MS.gene29680:CDS
TGATAAGGCGCGGAGGAAGG+TGG 0.566083 5.3:+67341591 None:intergenic
GGTGAATTACGGTGGCGGCT+CGG 0.567412 5.3:+67341763 None:intergenic
CAATGTAACGGTGACGGCGA+CGG 0.571632 5.3:+67341736 None:intergenic
GAGCGAGTTCGGCAATGTAA+CGG 0.572770 5.3:+67341724 None:intergenic
AACGGTGACGGCGACGGTGG+TGG 0.574135 5.3:+67341742 None:intergenic
GATTGAGACATCGCGTTCGT+CGG 0.574663 5.3:+67341411 None:intergenic
CGCGGCAGTCGTTGTATGTG+CGG 0.574917 5.3:+67341470 None:intergenic
TTCGTCGGCGGAGTTTACAT+CGG 0.580690 5.3:-67341322 MS.gene29680:CDS
TGTAACGGTGACGGCGACGG+TGG 0.584819 5.3:+67341739 None:intergenic
TAGGAAGTGTGACGTTCTTG+CGG 0.585484 5.3:+67341350 None:intergenic
CAAACAATCTCCCTCCCTCC+CGG 0.598113 5.3:-67341541 MS.gene29680:CDS
GTTGCGGAGGATTGATCTGA+CGG 0.599374 5.3:+67341447 None:intergenic
CTGATGCGGCGGAATAGTGA+AGG 0.603153 5.3:+67341622 None:intergenic
CAACCGTTCATATTCGACTT+CGG 0.606454 5.3:+67341235 None:intergenic
ACGGTTGTGATTGCTGTGGA+GGG 0.607912 5.3:-67341219 MS.gene29680:CDS
TGTATGTGCGGCGGATTACG+CGG 0.616823 5.3:+67341482 None:intergenic
GGCAGTCGTTGTATGTGCGG+CGG 0.620254 5.3:+67341473 None:intergenic
ACTCCGCCGACGAAAACCCT+AGG 0.629669 5.3:+67341331 None:intergenic
GTCGGCGGAGTTTACATCGG+CGG 0.630455 5.3:-67341319 MS.gene29680:CDS
TGGTGGAGATTCTGATGCGG+CGG 0.632080 5.3:+67341611 None:intergenic
TGATGACGCGGAAGTTGCGG+AGG 0.632748 5.3:+67341434 None:intergenic
GTGGTGGTGAATTACGGTGG+CGG 0.632999 5.3:+67341758 None:intergenic
GTTCGGCAATGTAACGGTGA+CGG 0.636544 5.3:+67341730 None:intergenic
TTCGGGAGGCTGATAAGGCG+CGG 0.636890 5.3:+67341581 None:intergenic
TGTTTGTGGTGGTGGAGCGG+TGG 0.642440 5.3:+67341558 None:intergenic
TTACATCGGCGGCGTTGACG+AGG 0.647643 5.3:-67341308 MS.gene29680:CDS
GTAGCATGAAGAAACATGCA+GGG 0.654005 5.3:+67341089 None:intergenic
GTGAAACAGTTACACGAAAG+CGG 0.662420 5.3:-67341286 MS.gene29680:CDS
GCAAACTATCTGGTGTATCG+CGG 0.678065 5.3:+67341067 None:intergenic
AGGTGGTGGAGATTCTGATG+CGG 0.687798 5.3:+67341608 None:intergenic
TTACCGAAGTCGAATATGAA+CGG 0.689259 5.3:-67341238 MS.gene29680:CDS
GGATTTCGTTGAGTTCGTCG+CGG 0.709368 5.3:+67341377 None:intergenic
ATGTGCGGCGGATTACGCGG+AGG 0.712042 5.3:+67341485 None:intergenic
ATGAACGGTTGTGATTGCTG+TGG 0.715120 5.3:-67341223 MS.gene29680:CDS
ACGGTGGTGGTGAATTACGG+TGG 0.721566 5.3:+67341755 None:intergenic
GGGAGGCTGATAAGGCGCGG+AGG 0.727383 5.3:+67341584 None:intergenic
GTTGTGTGTGATGAGTGTAA+CGG 0.739356 5.3:-67341187 MS.gene29680:CDS
GGAGGATTGATCTGACGGCG+CGG 0.757712 5.3:+67341452 None:intergenic
TGGTGAAGTAAACGACGACG+CGG 0.781889 5.3:+67341509 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGTGTATACGGATAAAAA+CGG - chr5.3:67341705-67341724 MS.gene29680:CDS 25.0%
! GTAATGTTAATGGTTTGATT+AGG - chr5.3:67341748-67341767 MS.gene29680:CDS 25.0%
TAGAGTTTCAATGTCTTTGA+AGG + chr5.3:67341184-67341203 None:intergenic 30.0%
!! AATTTGGTTCAGGTTTTTCT+TGG + chr5.3:67341209-67341228 None:intergenic 30.0%
!! GAAGGAGATTTTGGTAAATT+TGG + chr5.3:67341225-67341244 None:intergenic 30.0%
!! GATTTTGGTAAATTTGGTTC+AGG + chr5.3:67341219-67341238 None:intergenic 30.0%
!! TGTTTGGGTTGTAATGTTAA+TGG - chr5.3:67341738-67341757 MS.gene29680:CDS 30.0%
TTACCGAAGTCGAATATGAA+CGG - chr5.3:67341624-67341643 MS.gene29680:CDS 35.0%
! AAACGGATTTAGAAGCTGTT+TGG - chr5.3:67341722-67341741 MS.gene29680:CDS 35.0%
! AACGGATTTAGAAGCTGTTT+GGG - chr5.3:67341723-67341742 MS.gene29680:CDS 35.0%
AGCTGAATCGTTTGATCGAA+CGG - chr5.3:67341601-67341620 MS.gene29680:CDS 40.0%
CAACCGTTCATATTCGACTT+CGG + chr5.3:67341630-67341649 None:intergenic 40.0%
CGGAAGTCACAAAGTGTATA+CGG - chr5.3:67341695-67341714 MS.gene29680:CDS 40.0%
GTAGCATGAAGAAACATGCA+GGG + chr5.3:67341776-67341795 None:intergenic 40.0%
GTGAAACAGTTACACGAAAG+CGG - chr5.3:67341576-67341595 MS.gene29680:CDS 40.0%
GTTGTGTGTGATGAGTGTAA+CGG - chr5.3:67341675-67341694 MS.gene29680:CDS 40.0%
! CGGAATAGTGAAGGAGATTT+TGG + chr5.3:67341234-67341253 None:intergenic 40.0%
!! TGAAGTTGATAGAGCGAGTT+CGG + chr5.3:67341152-67341171 None:intergenic 40.0%
ATGAACGGTTGTGATTGCTG+TGG - chr5.3:67341639-67341658 MS.gene29680:CDS 45.0%
CAAGAACGTCACACTTCCTA+GGG - chr5.3:67341515-67341534 MS.gene29680:CDS 45.0%
CTCGGTGAAGCTAACCAATT+TGG + chr5.3:67341084-67341103 None:intergenic 45.0%
GGTAGCATGAAGAAACATGC+AGG + chr5.3:67341777-67341796 None:intergenic 45.0%
GGTGAAGCTAACCAATTTGG+TGG + chr5.3:67341081-67341100 None:intergenic 45.0%
! ACACTTCCTAGGGTTTTCGT+CGG - chr5.3:67341525-67341544 MS.gene29680:CDS 45.0%
! TAGGAAGTGTGACGTTCTTG+CGG + chr5.3:67341515-67341534 None:intergenic 45.0%
AACGGTTGTGATTGCTGTGG+AGG - chr5.3:67341642-67341661 MS.gene29680:CDS 50.0%
ACGGTTGTGATTGCTGTGGA+GGG - chr5.3:67341643-67341662 MS.gene29680:CDS 50.0%
AGGGAGATTGTTTGTGGTGG+TGG + chr5.3:67341315-67341334 None:intergenic 50.0%
GAGCGAGTTCGGCAATGTAA+CGG + chr5.3:67341141-67341160 None:intergenic 50.0%
GATTGAGACATCGCGTTCGT+CGG + chr5.3:67341454-67341473 None:intergenic 50.0%
GCAAGAACGTCACACTTCCT+AGG - chr5.3:67341514-67341533 MS.gene29680:CDS 50.0%
GGATTTCGTTGAGTTCGTCG+CGG + chr5.3:67341488-67341507 None:intergenic 50.0%
GTTCGGCAATGTAACGGTGA+CGG + chr5.3:67341135-67341154 None:intergenic 50.0%
GTTGCGGAGGATTGATCTGA+CGG + chr5.3:67341418-67341437 None:intergenic 50.0%
TGGTGAAGTAAACGACGACG+CGG + chr5.3:67341356-67341375 None:intergenic 50.0%
TTCGTCGGCGGAGTTTACAT+CGG - chr5.3:67341540-67341559 MS.gene29680:CDS 50.0%
!! AGGTGGTGGAGATTCTGATG+CGG + chr5.3:67341257-67341276 None:intergenic 50.0%
!! GATTGTTTGTGGTGGTGGAG+CGG + chr5.3:67341310-67341329 None:intergenic 50.0%
CAAACAATCTCCCTCCCTCC+CGG - chr5.3:67341321-67341340 MS.gene29680:CDS 55.0%
CTGATGCGGCGGAATAGTGA+AGG + chr5.3:67341243-67341262 None:intergenic 55.0%
GGAGGGAGGGAGATTGTTTG+TGG + chr5.3:67341321-67341340 None:intergenic 55.0%
GGGAGGGAGATTGTTTGTGG+TGG + chr5.3:67341318-67341337 None:intergenic 55.0%
GTGTGACGTTCTTGCGGTTC+AGG + chr5.3:67341509-67341528 None:intergenic 55.0%
TGGTGGAGATTCTGATGCGG+CGG + chr5.3:67341254-67341273 None:intergenic 55.0%
! AAACGACGACGCGGTTTTCG+AGG + chr5.3:67341347-67341366 None:intergenic 55.0%
! ACGGTGGTGGTGAATTACGG+TGG + chr5.3:67341110-67341129 None:intergenic 55.0%
! CAATGTAACGGTGACGGCGA+CGG + chr5.3:67341129-67341148 None:intergenic 55.0%
! CTTCCTAGGGTTTTCGTCGG+CGG - chr5.3:67341528-67341547 MS.gene29680:CDS 55.0%
! GCGACGGTGGTGGTGAATTA+CGG + chr5.3:67341113-67341132 None:intergenic 55.0%
! GTGGTGGTGAATTACGGTGG+CGG + chr5.3:67341107-67341126 None:intergenic 55.0%
!! TGTATGTGCGGCGGATTACG+CGG + chr5.3:67341383-67341402 None:intergenic 55.0%
ACTCCGCCGACGAAAACCCT+AGG + chr5.3:67341534-67341553 None:intergenic 60.0%
CGCGGCAGTCGTTGTATGTG+CGG + chr5.3:67341395-67341414 None:intergenic 60.0%
GGAGGATTGATCTGACGGCG+CGG + chr5.3:67341413-67341432 None:intergenic 60.0%
GGCAGTCGTTGTATGTGCGG+CGG + chr5.3:67341392-67341411 None:intergenic 60.0%
GTCGGCGGAGTTTACATCGG+CGG - chr5.3:67341543-67341562 MS.gene29680:CDS 60.0%
TGATAAGGCGCGGAGGAAGG+TGG + chr5.3:67341274-67341293 None:intergenic 60.0%
TTCGGGAGGCTGATAAGGCG+CGG + chr5.3:67341284-67341303 None:intergenic 60.0%
! CGGTGATGACGCGGAAGTTG+CGG + chr5.3:67341434-67341453 None:intergenic 60.0%
! GGTGAATTACGGTGGCGGCT+CGG + chr5.3:67341102-67341121 None:intergenic 60.0%
! GGTGGTTCGGGAGGCTGATA+AGG + chr5.3:67341289-67341308 None:intergenic 60.0%
! TGATGACGCGGAAGTTGCGG+AGG + chr5.3:67341431-67341450 None:intergenic 60.0%
!! TGTTTGTGGTGGTGGAGCGG+TGG + chr5.3:67341307-67341326 None:intergenic 60.0%
!! TTACATCGGCGGCGTTGACG+AGG - chr5.3:67341554-67341573 MS.gene29680:CDS 60.0%
GGCTGATAAGGCGCGGAGGA+AGG + chr5.3:67341277-67341296 None:intergenic 65.0%
TAAGGCGCGGAGGAAGGTGG+TGG + chr5.3:67341271-67341290 None:intergenic 65.0%
! CGCGTTCGTCGGTGATGACG+CGG + chr5.3:67341443-67341462 None:intergenic 65.0%
! TGTAACGGTGACGGCGACGG+TGG + chr5.3:67341126-67341145 None:intergenic 65.0%
!! ACGACGCGGTTTTCGAGGCC+GGG + chr5.3:67341342-67341361 None:intergenic 65.0%
!! ATGTGCGGCGGATTACGCGG+AGG + chr5.3:67341380-67341399 None:intergenic 65.0%
!! GACGACGCGGTTTTCGAGGC+CGG + chr5.3:67341343-67341362 None:intergenic 65.0%
!! GTGGTGGTGGAGCGGTGGTT+CGG + chr5.3:67341302-67341321 None:intergenic 65.0%
!! GTTTTCGAGGCCGGGAGGGA+GGG + chr5.3:67341334-67341353 None:intergenic 65.0%
!! TGGTGGTGGAGCGGTGGTTC+GGG + chr5.3:67341301-67341320 None:intergenic 65.0%
GGGAGGCTGATAAGGCGCGG+AGG + chr5.3:67341281-67341300 None:intergenic 70.0%
! AACGGTGACGGCGACGGTGG+TGG + chr5.3:67341123-67341142 None:intergenic 70.0%
! TGGTGGAGCGGTGGTTCGGG+AGG + chr5.3:67341298-67341317 None:intergenic 70.0%
!! ACGCGGTTTTCGAGGCCGGG+AGG + chr5.3:67341339-67341358 None:intergenic 70.0%
!! CGCGGTTTTCGAGGCCGGGA+GGG + chr5.3:67341338-67341357 None:intergenic 70.0%
!! GGTTTTCGAGGCCGGGAGGG+AGG + chr5.3:67341335-67341354 None:intergenic 70.0%
!! GCGGCGGATTACGCGGAGGC+TGG + chr5.3:67341376-67341395 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 67341072 67341812 67341072 ID=MS.gene29680
chr5.3 mRNA 67341072 67341812 67341072 ID=MS.gene29680.t1;Parent=MS.gene29680
chr5.3 exon 67341072 67341812 67341072 ID=MS.gene29680.t1.exon1;Parent=MS.gene29680.t1
chr5.3 CDS 67341072 67341812 67341072 ID=cds.MS.gene29680.t1;Parent=MS.gene29680.t1
Gene Sequence

>MS.gene29680

ATGTGGCCACCAAATTGGTTAGCTTCACCGAGCCGCCACCGTAATTCACCACCACCGTCGCCGTCACCGTTACATTGCCGAACTCGCTCTATCAACTTCACTTGTTCTTCCTTCAAAGACATTGAAACTCTAATCCAAGAAAAACCTGAACCAAATTTACCAAAATCTCCTTCACTATTCCGCCGCATCAGAATCTCCACCACCTTCCTCCGCGCCTTATCAGCCTCCCGAACCACCGCTCCACCACCACAAACAATCTCCCTCCCTCCCGGCCTCGAAAACCGCGTCGTCGTTTACTTCACCAGCCTCCGCGTAATCCGCCGCACATACAACGACTGCCGCGCCGTCAGATCAATCCTCCGCAACTTCCGCGTCATCACCGACGAACGCGATGTCTCAATCGACGATCGATTCCGCGACGAACTCAACGAAATCCTGAACCGCAAGAACGTCACACTTCCTAGGGTTTTCGTCGGCGGAGTTTACATCGGCGGCGTTGACGAGGTGAAACAGTTACACGAAAGCGGTGAGCTGAATCGTTTGATCGAACGGTTACCGAAGTCGAATATGAACGGTTGTGATTGCTGTGGAGGGTTCAGATTTGTTGTGTGTGATGAGTGTAACGGAAGTCACAAAGTGTATACGGATAAAAACGGATTTAGAAGCTGTTTGGGTTGTAATGTTAATGGTTTGATTAGGTGCCCTGCATGTTTCTTCATGCTACCGCGATACACCAGATAG
Protein sequence

>MS.gene29680.t1

MWPPNWLASPSRHRNSPPPSPSPLHCRTRSINFTCSSFKDIETLIQEKPEPNLPKSPSLFRRIRISTTFLRALSASRTTAPPPQTISLPPGLENRVVVYFTSLRVIRRTYNDCRAVRSILRNFRVITDERDVSIDDRFRDELNEILNRKNVTLPRVFVGGVYIGGVDEVKQLHESGELNRLIERLPKSNMNGCDCCGGFRFVVCDECNGSHKVYTDKNGFRSCLGCNVNGLIRCPACFFMLPRYTR