AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068490

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068490.t1 MTR_8g038620 85.161 155 15 1 1 147 1 155 1.27e-92 266
MS.gene068490.t1 MTR_6g007460 67.805 205 13 2 1 152 3 207 1.40e-91 265
MS.gene068490.t1 MTR_7g490310 68.790 157 40 1 1 148 1 157 2.02e-77 230
MS.gene068490.t1 MTR_3g015490 73.649 148 27 2 8 146 3 147 1.12e-72 215
MS.gene068490.t1 MTR_3g088630 54.088 159 54 3 9 149 22 179 4.66e-55 173
MS.gene068490.t1 MTR_3g093860 61.069 131 47 2 10 137 19 148 5.38e-52 162
MS.gene068490.t1 MTR_4g106590 58.571 140 57 1 8 146 25 164 3.87e-51 162
MS.gene068490.t1 MTR_5g036480 54.795 146 60 2 8 148 15 159 1.71e-50 161
MS.gene068490.t1 MTR_3g078613 51.724 145 70 0 8 152 22 166 2.63e-50 160
MS.gene068490.t1 MTR_1g049100 58.824 136 54 2 8 141 7 142 4.14e-49 156
MS.gene068490.t1 MTR_3g078613 51.370 146 70 1 8 152 22 167 1.94e-48 155
MS.gene068490.t1 MTR_4g051330 74.242 66 17 0 87 152 77 142 8.64e-31 108
MS.gene068490.t1 MTR_8g024260 29.008 131 84 1 11 141 38 159 4.29e-15 71.6
MS.gene068490.t1 MTR_8g079940 31.159 138 83 3 9 146 29 154 7.93e-15 70.9
MS.gene068490.t1 MTR_4g061360 29.688 128 81 2 11 138 91 209 1.18e-14 70.5
MS.gene068490.t1 MTR_1g067110 28.125 128 83 2 11 138 87 205 1.90e-13 67.0
MS.gene068490.t1 MTR_1g067110 28.125 128 83 2 11 138 87 205 1.92e-13 67.0
MS.gene068490.t1 MTR_7g117705 31.250 144 86 4 7 150 7 137 3.31e-13 66.2
MS.gene068490.t1 MTR_1g013170 29.167 144 88 3 7 150 7 136 5.37e-13 65.5
MS.gene068490.t1 MTR_3g086100 28.676 136 85 2 11 146 19 142 1.30e-12 64.3
MS.gene068490.t1 MTR_1g032570 30.216 139 85 3 9 147 15 141 1.36e-12 64.3
MS.gene068490.t1 MTR_1g013180 31.343 134 80 3 7 140 158 279 1.52e-12 64.3
MS.gene068490.t1 MTR_7g118260 26.562 128 85 1 11 138 16 134 2.83e-11 60.5
MS.gene068490.t1 MTR_7g118260 26.562 128 85 1 11 138 16 134 3.89e-11 60.1
MS.gene068490.t1 MTR_3g092780 26.667 135 88 2 9 142 56 180 6.31e-11 59.7
MS.gene068490.t1 MTR_3g092780 27.481 131 84 2 9 138 56 176 8.03e-11 59.3
MS.gene068490.t1 MTR_3g092780 26.119 134 90 1 9 142 56 180 9.27e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068490.t1 AT3G57040 67.097 155 41 1 1 145 1 155 2.31e-72 217
MS.gene068490.t1 AT3G57040 67.097 155 41 1 1 145 1 155 2.31e-72 217
MS.gene068490.t1 AT2G41310 63.226 155 49 1 1 147 1 155 1.23e-69 209
MS.gene068490.t1 AT1G59940 61.069 131 51 0 8 138 32 162 4.20e-55 173
MS.gene068490.t1 AT1G59940 61.069 131 51 0 8 138 124 254 1.83e-53 172
MS.gene068490.t1 AT1G10470 59.542 131 53 0 8 138 19 149 2.45e-53 169
MS.gene068490.t1 AT1G10470 59.542 131 53 0 8 138 33 163 3.43e-53 169
MS.gene068490.t1 AT3G48100 57.554 139 58 1 2 139 18 156 6.03e-53 166
MS.gene068490.t1 AT5G62920 60.769 130 51 0 9 138 25 154 6.63e-52 163
MS.gene068490.t1 AT3G56380 54.348 138 62 1 4 140 15 152 2.10e-51 161
MS.gene068490.t1 AT1G19050 54.412 136 62 0 8 143 23 158 2.14e-51 162
MS.gene068490.t1 AT1G74890 56.204 137 60 0 8 144 17 153 3.00e-51 162
MS.gene068490.t1 AT2G40670 53.237 139 56 2 8 140 28 163 1.06e-49 157
MS.gene068490.t1 AT3G56380 53.957 139 62 2 4 140 15 153 1.44e-49 156
MS.gene068490.t1 AT2G40670 52.857 140 56 3 8 140 28 164 6.58e-48 152
MS.gene068490.t1 AT2G07440 65.574 61 21 0 87 147 9 69 8.22e-23 87.8
MS.gene068490.t1 AT1G10470 58.491 53 22 0 86 138 35 87 3.50e-16 72.0
MS.gene068490.t1 AT2G25180 31.343 134 80 3 7 140 15 136 4.41e-14 68.9
MS.gene068490.t1 AT5G07210 28.276 145 91 3 7 151 14 145 6.84e-14 68.2
MS.gene068490.t1 AT1G67710 27.338 139 89 2 5 143 7 133 3.69e-13 66.2
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 5.37e-13 65.5
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 5.37e-13 65.5
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 5.37e-13 65.5
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 6.09e-13 65.5
MS.gene068490.t1 AT5G02810 27.344 128 84 2 11 138 80 198 9.85e-13 65.1
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 1.38e-12 64.3
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 1.38e-12 64.3
MS.gene068490.t1 AT5G60100 30.469 128 80 2 11 138 66 184 1.38e-12 64.3
MS.gene068490.t1 AT5G24470 27.941 136 87 2 6 140 47 172 6.41e-12 62.4
MS.gene068490.t1 AT1G49190 29.545 132 81 3 10 141 35 154 7.29e-12 62.4
MS.gene068490.t1 AT3G16857 28.889 135 84 3 9 143 37 159 8.33e-12 62.4
MS.gene068490.t1 AT1G49190 29.545 132 81 3 10 141 35 154 8.89e-12 62.0
MS.gene068490.t1 AT3G16857 28.889 135 84 3 9 143 37 159 8.95e-12 62.0
MS.gene068490.t1 AT2G46790 25.000 144 98 3 9 152 37 170 2.13e-11 60.8
MS.gene068490.t1 AT2G46790 25.000 144 98 3 9 152 37 170 2.42e-11 60.8

Find 25 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTATGTCTTTAAAAGATT+TGG 0.160260 4.2:-58309068 None:intergenic
CTGATTGTTGAACTGGTTTC+AGG 0.173333 4.2:-58309306 None:intergenic
AGAGATTCAGTTCCATGTTT+TGG 0.265763 4.2:+58308182 MS.gene068490:CDS
AGTAAGGCTTTAAAATTTCT+TGG 0.266953 4.2:+58308475 MS.gene068490:CDS
TCTCACCTGCTAATCCTTGA+TGG 0.304860 4.2:-58309118 None:intergenic
GGCTTTAAAATTTCTTGGTT+TGG 0.308229 4.2:+58308480 MS.gene068490:CDS
TTTACATCTGATTGTTGAAC+TGG 0.343425 4.2:-58309313 None:intergenic
TCTTGGTTTGGTTGAGGATG+TGG 0.414547 4.2:+58308492 MS.gene068490:CDS
TTTGATGAAATCAAGAGTTA+AGG 0.416978 4.2:+58309351 MS.gene068490:CDS
TACAATGGACTCTGCTAGTA+AGG 0.427203 4.2:+58308459 MS.gene068490:CDS
TATTGTATGCCAGGGATGAC+TGG 0.449232 4.2:+58308658 MS.gene068490:CDS
AAAATTTCTTGGTTTGGTTG+AGG 0.449963 4.2:+58308486 MS.gene068490:CDS
ACTCTTGATTTCATCAAATG+AGG 0.455768 4.2:-58309346 None:intergenic
ATAACAGATTATTGTATGCC+AGG 0.463952 4.2:+58308649 MS.gene068490:CDS
ATGTTCCATCAAGGATTAGC+AGG 0.504757 4.2:+58309113 MS.gene068490:CDS
TTGATAGAATGTTGATTGAG+AGG 0.516155 4.2:+58308223 MS.gene068490:CDS
GATGTGGCTTCAGAAGTTCA+TGG 0.523538 4.2:+58308508 MS.gene068490:CDS
ATGTGGCTTCAGAAGTTCAT+GGG 0.534908 4.2:+58308509 MS.gene068490:CDS
CTTCAGAGAATGTTCCATCA+AGG 0.539392 4.2:+58309104 MS.gene068490:CDS
AGATCATAGCCAGTCATCCC+TGG 0.546401 4.2:-58308667 None:intergenic
TCTGAAGACATAATCACAAT+CGG 0.548679 4.2:-58309088 None:intergenic
TAACAGATTATTGTATGCCA+GGG 0.564090 4.2:+58308650 MS.gene068490:CDS
TATCATCAACAGCCAAAACA+TGG 0.580138 4.2:-58308194 None:intergenic
TGAAATGATAGTTACTACAA+TGG 0.624009 4.2:+58308444 MS.gene068490:intron
TGTGGCTTCAGAAGTTCATG+GGG 0.695893 4.2:+58308510 MS.gene068490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTCTTAATATTATGA+TGG + chr4.2:58308547-58308566 MS.gene068490:intron 10.0%
!!! ATTATTTTGTTTTTCTATTT+AGG + chr4.2:58308847-58308866 MS.gene068490:intron 10.0%
!!! GATAATTATTATTTATTTTG+TGG + chr4.2:58308413-58308432 MS.gene068490:intron 10.0%
!!! TTTGTTTTCTTTATAATTTT+GGG - chr4.2:58308988-58309007 None:intergenic 10.0%
!!! CTTTGTTTTCTTTATAATTT+TGG - chr4.2:58308989-58309008 None:intergenic 15.0%
!! TTTCTTAAATAGAAGTGATT+TGG + chr4.2:58308895-58308914 MS.gene068490:intron 20.0%
!!! ATATATGAACATAGTTTGTA+TGG + chr4.2:58308336-58308355 MS.gene068490:intron 20.0%
!!! TAACATCAAGTTAACAATTT+TGG - chr4.2:58309018-58309037 None:intergenic 20.0%
!!! TCAATATACTATTTTGTTGA+AGG + chr4.2:58308359-58308378 MS.gene068490:intron 20.0%
! ATTGTAATGATGTAATGTGA+TGG + chr4.2:58308307-58308326 MS.gene068490:intron 25.0%
! TAAACAATTCTTTGATTCTC+AGG + chr4.2:58309042-58309061 MS.gene068490:intron 25.0%
! TGAAAATGAGCACAAAATTA+TGG - chr4.2:58308797-58308816 None:intergenic 25.0%
! TGAAATGATAGTTACTACAA+TGG + chr4.2:58308444-58308463 MS.gene068490:intron 25.0%
! TTGATTCATATTATTCATGC+AGG + chr4.2:58308606-58308625 MS.gene068490:intron 25.0%
! TTGTAATGATGTAATGTGAT+GGG + chr4.2:58308308-58308327 MS.gene068490:intron 25.0%
! TTTGATGAAATCAAGAGTTA+AGG + chr4.2:58309351-58309370 MS.gene068490:CDS 25.0%
!!! AGTAAGGCTTTAAAATTTCT+TGG + chr4.2:58308475-58308494 MS.gene068490:CDS 25.0%
!!! TGATTAGTGATTACTGATTT+GGG + chr4.2:58308957-58308976 MS.gene068490:intron 25.0%
!!! TTTATCAGATGTTTTGAAGA+GGG + chr4.2:58309268-58309287 MS.gene068490:intron 25.0%
!!! TTTTATCAGATGTTTTGAAG+AGG + chr4.2:58309267-58309286 MS.gene068490:intron 25.0%
ACTCTTGATTTCATCAAATG+AGG - chr4.2:58309349-58309368 None:intergenic 30.0%
ATAACAGATTATTGTATGCC+AGG + chr4.2:58308649-58308668 MS.gene068490:CDS 30.0%
ATGTGAAGTCTCACATATTA+TGG + chr4.2:58309229-58309248 MS.gene068490:intron 30.0%
TAACAGATTATTGTATGCCA+GGG + chr4.2:58308650-58308669 MS.gene068490:CDS 30.0%
TCTGAAGACATAATCACAAT+CGG - chr4.2:58309091-58309110 None:intergenic 30.0%
TTTACATCTGATTGTTGAAC+TGG - chr4.2:58309316-58309335 None:intergenic 30.0%
! CATGAAAAGAAGAAGTTTTG+AGG - chr4.2:58308251-58308270 None:intergenic 30.0%
! CGGTATGTCTTTAAAAGATT+TGG - chr4.2:58309071-58309090 None:intergenic 30.0%
! CTCAAAACTTCTTCTTTTCA+TGG + chr4.2:58308249-58308268 MS.gene068490:CDS 30.0%
! CTGATTAGTGATTACTGATT+TGG + chr4.2:58308956-58308975 MS.gene068490:intron 30.0%
! TTGATAGAATGTTGATTGAG+AGG + chr4.2:58308223-58308242 MS.gene068490:CDS 30.0%
!! AAAATTTCTTGGTTTGGTTG+AGG + chr4.2:58308486-58308505 MS.gene068490:CDS 30.0%
!! GGCTTTAAAATTTCTTGGTT+TGG + chr4.2:58308480-58308499 MS.gene068490:CDS 30.0%
TATCATCAACAGCCAAAACA+TGG - chr4.2:58308197-58308216 None:intergenic 35.0%
TGATCTGCTCAGAAAAATCA+AGG + chr4.2:58308684-58308703 MS.gene068490:CDS 35.0%
! AGAGATTCAGTTCCATGTTT+TGG + chr4.2:58308182-58308201 MS.gene068490:CDS 35.0%
ATGTGGCTTCAGAAGTTCAT+GGG + chr4.2:58308509-58308528 MS.gene068490:CDS 40.0%
CTGCTCAGAAAAATCAAGGT+AGG + chr4.2:58308688-58308707 MS.gene068490:intron 40.0%
CTTCAGAGAATGTTCCATCA+AGG + chr4.2:58309104-58309123 MS.gene068490:CDS 40.0%
! ATGTTCCATCAAGGATTAGC+AGG + chr4.2:58309113-58309132 MS.gene068490:CDS 40.0%
! CTGATTGTTGAACTGGTTTC+AGG - chr4.2:58309309-58309328 None:intergenic 40.0%
! TACAATGGACTCTGCTAGTA+AGG + chr4.2:58308459-58308478 MS.gene068490:CDS 40.0%
GATGTGGCTTCAGAAGTTCA+TGG + chr4.2:58308508-58308527 MS.gene068490:CDS 45.0%
TATTGTATGCCAGGGATGAC+TGG + chr4.2:58308658-58308677 MS.gene068490:CDS 45.0%
TCTCACCTGCTAATCCTTGA+TGG - chr4.2:58309121-58309140 None:intergenic 45.0%
TGTGGCTTCAGAAGTTCATG+GGG + chr4.2:58308510-58308529 MS.gene068490:CDS 45.0%
!! TCTTGGTTTGGTTGAGGATG+TGG + chr4.2:58308492-58308511 MS.gene068490:CDS 45.0%
AGATCATAGCCAGTCATCCC+TGG - chr4.2:58308670-58308689 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 58308168 58309405 58308168 ID=MS.gene068490
chr4.2 mRNA 58308168 58309405 58308168 ID=MS.gene068490.t1;Parent=MS.gene068490
chr4.2 exon 58308168 58308270 58308168 ID=MS.gene068490.t1.exon1;Parent=MS.gene068490.t1
chr4.2 CDS 58308168 58308270 58308168 ID=cds.MS.gene068490.t1;Parent=MS.gene068490.t1
chr4.2 exon 58308455 58308531 58308455 ID=MS.gene068490.t1.exon2;Parent=MS.gene068490.t1
chr4.2 CDS 58308455 58308531 58308455 ID=cds.MS.gene068490.t1;Parent=MS.gene068490.t1
chr4.2 exon 58308628 58308705 58308628 ID=MS.gene068490.t1.exon3;Parent=MS.gene068490.t1
chr4.2 CDS 58308628 58308705 58308628 ID=cds.MS.gene068490.t1;Parent=MS.gene068490.t1
chr4.2 exon 58309064 58309134 58309064 ID=MS.gene068490.t1.exon4;Parent=MS.gene068490.t1
chr4.2 CDS 58309064 58309134 58309064 ID=cds.MS.gene068490.t1;Parent=MS.gene068490.t1
chr4.2 exon 58309276 58309405 58309276 ID=MS.gene068490.t1.exon5;Parent=MS.gene068490.t1
chr4.2 CDS 58309276 58309405 58309276 ID=cds.MS.gene068490.t1;Parent=MS.gene068490.t1
Gene Sequence

>MS.gene068490

ATGGGTATGGCTGCAGAGATTCAGTTCCATGTTTTGGCTGTTGATGATAATATTATTGATAGAATGTTGATTGAGAGGCTCCTCAAAACTTCTTCTTTTCATGGTACTTTTCTTGTTTATTTTTTTAATTTTGATTTATATTGTAATGATGTAATGTGATGGGAAAAAATATATGAACATAGTTTGTATGGTCAATATACTATTTTGTTGAAGGTGTGATTTTTTTGTTACTAAGATTGACAAATGATAATTATTATTTATTTTGTGGTTTTGTATTGAAATGATAGTTACTACAATGGACTCTGCTAGTAAGGCTTTAAAATTTCTTGGTTTGGTTGAGGATGTGGCTTCAGAAGTTCATGGGGTAAAATTCTCAAACAATTTTTCTTAATATTATGATGGCTTAGACTATTTTGATGTATAAGTTTGTATTAATATTTGATTCATATTATTCATGCAGGATGTAGATGTAAATCTGATCATAACAGATTATTGTATGCCAGGGATGACTGGCTATGATCTGCTCAGAAAAATCAAGGTAGGTTCTTGAGATATTGCAATACTTTTTTAAATTGATTTTGTCACTTTTTATTTGATTTGTCTATTTTGAATTTCATTAACTTTTTCCATAATTTTGTGCTCATTTTCAAAATTTGAATGTATCAAAAAGTTTTGTGAAATTATTTTGTTTTTCTATTTAGGTAAGAATTTGAAAAATAGTATCATATTTCTTAAATAGAAGTGATTTGGATTTTCGAATCAAAATAATAAAAATCACTTCTGAATCTCTGATTAGTGATTACTGATTTGGGATATTCCCAAAATTATAAAGAAAACAAAGCTCAAACCAAAATTGTTAACTTGATGTTAAAGCTAAACAATTCTTTGATTCTCAGGAATCCAAATCTTTTAAAGACATACCGATTGTGATTATGTCTTCAGAGAATGTTCCATCAAGGATTAGCAGGTGAGAAAATTGTATACATCATTTGTTGAAATCAAGTATCAAATGCAGTTGTGAGCACATGATATCTTATAACACATTACTAATTGTTTGTAAAATGTGAAGTCTCACATATTATGGACTAATTGTTTGTAATTTTATCAGATGTTTTGAAGAGGGAGCTGAAGAATTCTTCCTGAAACCAGTTCAACAATCAGATGTAAACAAGCTGAAGCCTCATTTGATGAAATCAAGAGTTAAGGAAGAGCAAGAACAAACAACCCATCAACAATAA
Protein sequence

>MS.gene068490.t1

MGMAAEIQFHVLAVDDNIIDRMLIERLLKTSSFHVTTMDSASKALKFLGLVEDVASEVHGDVDVNLIITDYCMPGMTGYDLLRKIKESKSFKDIPIVIMSSENVPSRISRCFEEGAEEFFLKPVQQSDVNKLKPHLMKSRVKEEQEQTTHQQ