AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene94621

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94621.t1 MTR_2g084510 84.298 242 38 0 5 246 1 242 8.24e-152 422
MS.gene94621.t1 MTR_2g084525 91.358 243 21 0 4 246 1 243 1.80e-150 419
MS.gene94621.t1 MTR_2g084495 60.905 243 82 3 4 246 1 230 2.24e-95 279
MS.gene94621.t1 MTR_2g060540 76.224 143 34 0 3 145 6 148 7.04e-78 232
MS.gene94621.t1 MTR_2g060500 77.143 140 32 0 3 142 6 145 1.10e-77 231
MS.gene94621.t1 MTR_1g062160 38.306 248 100 9 3 245 2 201 3.41e-41 140
MS.gene94621.t1 MTR_7g102790 38.462 247 105 8 1 245 1 202 9.08e-39 134
MS.gene94621.t1 MTR_5g030130 41.573 178 87 5 8 180 36 201 2.74e-37 131
MS.gene94621.t1 MTR_4g078170 46.809 141 65 3 8 148 16 146 1.08e-36 129
MS.gene94621.t1 MTR_5g030130 46.377 138 64 3 8 145 36 163 1.12e-36 128
MS.gene94621.t1 MTR_5g007230 43.972 141 69 3 8 148 22 152 5.23e-34 122
MS.gene94621.t1 MTR_8g066820 45.255 137 65 3 8 144 34 160 1.05e-33 122
MS.gene94621.t1 MTR_4g094680 39.437 142 81 4 9 150 24 160 5.94e-26 101
MS.gene94621.t1 MTR_2g055210 28.740 254 151 10 7 245 101 339 1.40e-23 97.4
MS.gene94621.t1 MTR_4g116300 37.589 141 78 4 8 148 6 136 1.99e-23 95.5
MS.gene94621.t1 MTR_2g083710 63.934 61 22 0 3 63 2 62 4.30e-23 89.4
MS.gene94621.t1 MTR_2g083720 38.843 121 36 2 3 123 2 84 2.02e-16 72.4
MS.gene94621.t1 MTR_2g036170 32.653 147 82 5 9 155 39 168 4.42e-16 75.5
MS.gene94621.t1 MTR_8g105930 30.968 155 90 5 9 150 15 165 1.67e-14 70.9
MS.gene94621.t1 MTR_8g097310 26.108 203 95 8 47 246 4 154 8.18e-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.gene94621.t1 AT1G21000 36.032 247 142 9 3 245 9 243 1.17e-38 135
MS.gene94621.t1 AT1G21000 36.032 247 142 9 3 245 12 246 1.31e-38 135
MS.gene94621.t1 AT1G43000 34.959 246 123 7 3 245 12 223 1.87e-38 134
MS.gene94621.t1 AT1G43000 34.959 246 123 7 3 245 5 216 2.14e-38 133
MS.gene94621.t1 AT1G76590 35.417 240 140 8 8 245 19 245 1.12e-37 132
MS.gene94621.t1 AT4G17900 48.551 138 60 4 8 144 35 162 2.07e-36 129
MS.gene94621.t1 AT4G17900 48.551 138 60 4 8 144 21 148 4.59e-36 127
MS.gene94621.t1 AT1G32700 45.714 140 66 3 9 148 14 143 2.02e-33 120
MS.gene94621.t1 AT2G27930 47.857 140 67 3 9 145 6 142 2.28e-32 116
MS.gene94621.t1 AT2G27930 47.857 140 67 3 9 145 6 142 2.28e-32 116
MS.gene94621.t1 AT2G27930 48.175 137 65 3 9 142 6 139 3.24e-32 117
MS.gene94621.t1 AT2G27930 48.175 137 65 3 9 142 6 139 3.24e-32 117
MS.gene94621.t1 AT1G32700 48.214 112 49 2 37 148 2 104 3.44e-28 105
MS.gene94621.t1 AT5G46710 43.796 137 66 4 9 144 14 140 5.74e-27 103
MS.gene94621.t1 AT5G46710 43.796 137 66 4 9 144 30 156 6.01e-27 104
MS.gene94621.t1 AT5G46710 43.704 135 65 4 9 142 30 154 1.51e-26 101
MS.gene94621.t1 AT2G12646 39.583 144 76 5 5 148 1 133 5.54e-25 99.8
MS.gene94621.t1 AT2G12646 40.000 140 73 5 9 148 8 136 9.81e-25 99.0
MS.gene94621.t1 AT2G12646 40.000 140 73 5 9 148 8 136 9.81e-25 99.0
MS.gene94621.t1 AT1G31040 35.211 142 80 4 9 150 21 150 2.68e-23 95.1
MS.gene94621.t1 AT3G60670 37.500 136 74 5 9 144 9 133 1.70e-19 84.7
MS.gene94621.t1 AT2G01818 29.339 242 135 10 9 246 13 222 1.86e-18 81.6
MS.gene94621.t1 AT2G27930 51.190 84 36 2 62 142 61 142 1.87e-17 78.2
MS.gene94621.t1 AT2G27930 51.190 84 36 2 62 142 61 142 1.87e-17 78.2

Find 39 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTCATTTCTGAACTTGTT+TGG 0.226434 2.4:-14906670 None:intergenic
CCAGTTTGCGTTTATCAAAA+AGG 0.264489 2.4:+14907428 MS.gene94621:intron
CGCAAGAATTGATGAGAAAA+AGG 0.267119 2.4:+14907584 MS.gene94621:CDS
TCCATTTCTTCCATCTCTCT+TGG 0.271024 2.4:-14907471 None:intergenic
TTTCCAATGTTGAACCTCTT+AGG 0.309596 2.4:-14907072 None:intergenic
CCATTTCTTCCATCTCTCTT+GGG 0.325447 2.4:-14907470 None:intergenic
TCTATACAAAATTCACATAA+TGG 0.333459 2.4:-14906724 None:intergenic
CCCAAGAGAGATGGAAGAAA+TGG 0.347606 2.4:+14907470 MS.gene94621:CDS
CATTTCTGAACTTGTTTGGA+TGG 0.368188 2.4:-14906666 None:intergenic
ACCTTGGCTTGTAAACTTGC+TGG 0.395128 2.4:+14906612 MS.gene94621:CDS
GAAGCCGATGAGCGATTAAC+CGG 0.402296 2.4:-14907666 None:intergenic
AATGTTGAACCTCTTAGGTT+GGG 0.418949 2.4:-14907067 None:intergenic
AAAGAAAGGGAATAGCTCAT+AGG 0.424904 2.4:+14907709 MS.gene94621:CDS
TGACAGAGAAAGCATTCTTC+CGG 0.441662 2.4:+14907647 MS.gene94621:CDS
CAAAGGTCATAGAGTAATAC+AGG 0.450961 2.4:+14906756 MS.gene94621:CDS
ATTTCTGAACTTGTTTGGAT+GGG 0.453864 2.4:-14906665 None:intergenic
CAATGTTGAACCTCTTAGGT+TGG 0.472346 2.4:-14907068 None:intergenic
CACATGTTTGTAAATTTCGT+TGG 0.484536 2.4:-14906974 None:intergenic
AAGAAAGGGAATAGCTCATA+GGG 0.490291 2.4:+14907710 MS.gene94621:CDS
GCCAGCAAGTTTACAAGCCA+AGG 0.514131 2.4:-14906613 None:intergenic
GAGCTCATACCCAACCTAAG+AGG 0.539841 2.4:+14907058 MS.gene94621:CDS
AAAAGAGTCCCTATTGTGAC+CGG 0.541668 2.4:-14907097 None:intergenic
ATATCTAGATCAATCAATCA+AGG 0.554194 2.4:+14907497 MS.gene94621:CDS
TACAAACATGTGGATATCCT+CGG 0.556715 2.4:+14906985 MS.gene94621:CDS
AAGAATGCTTTCTCTGTCAT+CGG 0.559247 2.4:-14907643 None:intergenic
CCAAAGAGCAAAAGTAGGTA+GGG 0.559658 2.4:-14907149 None:intergenic
AGGATATGATGAGTGTACCT+TGG 0.561440 2.4:+14906596 MS.gene94621:intron
TTTCGTAAACCCAAGAGAGA+TGG 0.562278 2.4:+14907461 MS.gene94621:CDS
TCTTCCGGTTAATCGCTCAT+CGG 0.573214 2.4:+14907662 MS.gene94621:CDS
TCACGTAGGTTTGAATTCCG+AGG 0.586677 2.4:-14907002 None:intergenic
GCCAAAGAGCAAAAGTAGGT+AGG 0.587378 2.4:-14907150 None:intergenic
AAGAAGATCATCATATAATG+AGG 0.589252 2.4:+14906942 MS.gene94621:CDS
CAACGAAATTTACAAACATG+TGG 0.600716 2.4:+14906975 MS.gene94621:CDS
CAACCTAAGAGGTTCAACAT+TGG 0.614000 2.4:+14907069 MS.gene94621:CDS
GCATGCCAAAGAGCAAAAGT+AGG 0.621061 2.4:-14907154 None:intergenic
TGTATAGAATCTCGTCACAA+AGG 0.625069 2.4:+14906739 MS.gene94621:CDS
AAGATCATCATATAATGAGG+TGG 0.649716 2.4:+14906945 MS.gene94621:CDS
ACTAGAGCTATTAATCACGT+AGG 0.680389 2.4:-14907016 None:intergenic
CAAACAAGTTCAGAAATGAG+CGG 0.722844 2.4:+14906671 MS.gene94621:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAAAATACAAAGAATT+AGG - chr2.4:14906549-14906568 None:intergenic 15.0%
!!! TTTTTCTTAATGCAATTTTT+GGG + chr2.4:14906562-14906581 MS.gene94621:intron 15.0%
!!! TTTTTTCTTAATGCAATTTT+TGG + chr2.4:14906561-14906580 MS.gene94621:intron 15.0%
!! ATTAATAGTAATAAAAGGAG+TGG - chr2.4:14907271-14907290 None:intergenic 20.0%
!! GCTTGACATTATAATTAAAA+TGG - chr2.4:14906527-14906546 None:intergenic 20.0%
!! TCTATACAAAATTCACATAA+TGG - chr2.4:14906727-14906746 None:intergenic 20.0%
!!! ATAATATTTTGCAATGATCT+AGG + chr2.4:14906811-14906830 MS.gene94621:intron 20.0%
!!! ATGTTTTAAACGGTAAAAAA+TGG + chr2.4:14907214-14907233 MS.gene94621:intron 20.0%
!!! TCCTTTTATTACTATTAATC+CGG + chr2.4:14907272-14907291 MS.gene94621:intron 20.0%
! AAGAAGATCATCATATAATG+AGG + chr2.4:14906942-14906961 MS.gene94621:CDS 25.0%
! AAGCCAAATTCAAAAAGAAA+GGG + chr2.4:14907696-14907715 MS.gene94621:CDS 25.0%
! ATATCTAGATCAATCAATCA+AGG + chr2.4:14907497-14907516 MS.gene94621:CDS 25.0%
! TCCGGATTAATAGTAATAAA+AGG - chr2.4:14907276-14907295 None:intergenic 25.0%
!! ATTCCCTTTCTTTTTGAATT+TGG - chr2.4:14907702-14907721 None:intergenic 25.0%
!!! TTAATGCAATTTTTGGGTTT+TGG + chr2.4:14906568-14906587 MS.gene94621:intron 25.0%
!!! TTTTTTGCCTTCTCTTTTTT+AGG - chr2.4:14907528-14907547 None:intergenic 25.0%
AAGATCATCATATAATGAGG+TGG + chr2.4:14906945-14906964 MS.gene94621:CDS 30.0%
AATTGATGAGAAAAAGGAAG+AGG + chr2.4:14907590-14907609 MS.gene94621:CDS 30.0%
ATCAACATGAGTACAATAAC+TGG - chr2.4:14907359-14907378 None:intergenic 30.0%
CAACGAAATTTACAAACATG+TGG + chr2.4:14906975-14906994 MS.gene94621:CDS 30.0%
CAAGCCAAATTCAAAAAGAA+AGG + chr2.4:14907695-14907714 MS.gene94621:CDS 30.0%
CACATGTTTGTAAATTTCGT+TGG - chr2.4:14906977-14906996 None:intergenic 30.0%
TTTGCGTTTATCAAAAAGGA+TGG + chr2.4:14907432-14907451 MS.gene94621:CDS 30.0%
! ACTTTTCTTTCAACCATTAC+CGG + chr2.4:14907329-14907348 MS.gene94621:intron 30.0%
! ATTTCTGAACTTGTTTGGAT+GGG - chr2.4:14906668-14906687 None:intergenic 30.0%
!!! ATTTTTGGGTTTTGGTTCTT+AGG + chr2.4:14906576-14906595 MS.gene94621:intron 30.0%
AAAGAAAGGGAATAGCTCAT+AGG + chr2.4:14907709-14907728 MS.gene94621:CDS 35.0%
AAGAAAGGGAATAGCTCATA+GGG + chr2.4:14907710-14907729 MS.gene94621:CDS 35.0%
AAGAATGCTTTCTCTGTCAT+CGG - chr2.4:14907646-14907665 None:intergenic 35.0%
AATAACTGGTATTCCGGTAA+TGG - chr2.4:14907345-14907364 None:intergenic 35.0%
AATGTTGAACCTCTTAGGTT+GGG - chr2.4:14907070-14907089 None:intergenic 35.0%
ACTAGAGCTATTAATCACGT+AGG - chr2.4:14907019-14907038 None:intergenic 35.0%
ACTATTAATCCGGAGATTGA+AGG + chr2.4:14907282-14907301 MS.gene94621:intron 35.0%
AGGAAGACGTAGAAAAAGAA+AGG + chr2.4:14907610-14907629 MS.gene94621:CDS 35.0%
AGGTTCAACATTGGAAAAAC+CGG + chr2.4:14907078-14907097 MS.gene94621:CDS 35.0%
CAAACAAGTTCAGAAATGAG+CGG + chr2.4:14906671-14906690 MS.gene94621:CDS 35.0%
CAAAGGTCATAGAGTAATAC+AGG + chr2.4:14906756-14906775 MS.gene94621:CDS 35.0%
CCAGTTTGCGTTTATCAAAA+AGG + chr2.4:14907428-14907447 MS.gene94621:intron 35.0%
CGCAAGAATTGATGAGAAAA+AGG + chr2.4:14907584-14907603 MS.gene94621:CDS 35.0%
GAGTACAATAACTGGTATTC+CGG - chr2.4:14907351-14907370 None:intergenic 35.0%
GGAAGACGTAGAAAAAGAAA+GGG + chr2.4:14907611-14907630 MS.gene94621:CDS 35.0%
GTAGAAAAAGAAAGGGAAGA+AGG + chr2.4:14907618-14907637 MS.gene94621:CDS 35.0%
TACAAACATGTGGATATCCT+CGG + chr2.4:14906985-14907004 MS.gene94621:CDS 35.0%
TGTATAGAATCTCGTCACAA+AGG + chr2.4:14906739-14906758 MS.gene94621:CDS 35.0%
TTTCCAATGTTGAACCTCTT+AGG - chr2.4:14907075-14907094 None:intergenic 35.0%
! CATTTCTGAACTTGTTTGGA+TGG - chr2.4:14906669-14906688 None:intergenic 35.0%
! CCTTTTTGATAAACGCAAAC+TGG - chr2.4:14907431-14907450 None:intergenic 35.0%
AAAAGAGTCCCTATTGTGAC+CGG - chr2.4:14907100-14907119 None:intergenic 40.0%
AGGATATGATGAGTGTACCT+TGG + chr2.4:14906596-14906615 MS.gene94621:intron 40.0%
CAACCTAAGAGGTTCAACAT+TGG + chr2.4:14907069-14907088 MS.gene94621:CDS 40.0%
CAATGTTGAACCTCTTAGGT+TGG - chr2.4:14907071-14907090 None:intergenic 40.0%
CATCATATGCCTTCAATCTC+CGG - chr2.4:14907294-14907313 None:intergenic 40.0%
CCAAAGAGCAAAAGTAGGTA+GGG - chr2.4:14907152-14907171 None:intergenic 40.0%
CCATTTCTTCCATCTCTCTT+GGG - chr2.4:14907473-14907492 None:intergenic 40.0%
GCGTTTATCAAAAAGGATGG+TGG + chr2.4:14907435-14907454 MS.gene94621:CDS 40.0%
TCCATTTCTTCCATCTCTCT+TGG - chr2.4:14907474-14907493 None:intergenic 40.0%
TGGAAAAACCGGTCACAATA+GGG + chr2.4:14907089-14907108 MS.gene94621:CDS 40.0%
TTGGAAAAACCGGTCACAAT+AGG + chr2.4:14907088-14907107 MS.gene94621:CDS 40.0%
TTTCGTAAACCCAAGAGAGA+TGG + chr2.4:14907461-14907480 MS.gene94621:CDS 40.0%
! ATGGATTTTCATTGCAGTCG+AGG - chr2.4:14906708-14906727 None:intergenic 40.0%
! CGCTCATTTCTGAACTTGTT+TGG - chr2.4:14906673-14906692 None:intergenic 40.0%
! TGGCATGCAAGGTGAAATTT+TGG + chr2.4:14907169-14907188 MS.gene94621:intron 40.0%
!! TGACAGAGAAAGCATTCTTC+CGG + chr2.4:14907647-14907666 MS.gene94621:CDS 40.0%
CCCAAGAGAGATGGAAGAAA+TGG + chr2.4:14907470-14907489 MS.gene94621:CDS 45.0%
GCATGCCAAAGAGCAAAAGT+AGG - chr2.4:14907157-14907176 None:intergenic 45.0%
GCCAAAGAGCAAAAGTAGGT+AGG - chr2.4:14907153-14907172 None:intergenic 45.0%
GGCATCGCCTAAAAAAGAGA+AGG + chr2.4:14907518-14907537 MS.gene94621:CDS 45.0%
TCACGTAGGTTTGAATTCCG+AGG - chr2.4:14907005-14907024 None:intergenic 45.0%
TCTTCCGGTTAATCGCTCAT+CGG + chr2.4:14907662-14907681 MS.gene94621:CDS 45.0%
! CGGAGATTGAAGGCATATGA+TGG + chr2.4:14907292-14907311 MS.gene94621:intron 45.0%
! CTTTTGCTCTTTGGCATGCA+AGG + chr2.4:14907158-14907177 MS.gene94621:CDS 45.0%
!! ACCTTGGCTTGTAAACTTGC+TGG + chr2.4:14906612-14906631 MS.gene94621:CDS 45.0%
!! CCCTACCTACTTTTGCTCTT+TGG + chr2.4:14907149-14907168 MS.gene94621:CDS 45.0%
!! ACATAATATAAAAATATAAT+AGG - chr2.4:14907198-14907217 None:intergenic 5.0%
!!! TTTTTATATTATGTTTTAAA+CGG + chr2.4:14907204-14907223 MS.gene94621:intron 5.0%
GAAGCCGATGAGCGATTAAC+CGG - chr2.4:14907669-14907688 None:intergenic 50.0%
GAGCTCATACCCAACCTAAG+AGG + chr2.4:14907058-14907077 MS.gene94621:CDS 50.0%
GCCAGCAAGTTTACAAGCCA+AGG - chr2.4:14906616-14906635 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 14906505 14907746 14906505 ID=MS.gene94621
chr2.4 mRNA 14906505 14907746 14906505 ID=MS.gene94621.t1;Parent=MS.gene94621
chr2.4 exon 14906505 14906510 14906505 ID=MS.gene94621.t1.exon1;Parent=MS.gene94621.t1
chr2.4 CDS 14906505 14906510 14906505 ID=cds.MS.gene94621.t1;Parent=MS.gene94621.t1
chr2.4 exon 14906598 14906777 14906598 ID=MS.gene94621.t1.exon2;Parent=MS.gene94621.t1
chr2.4 CDS 14906598 14906777 14906598 ID=cds.MS.gene94621.t1;Parent=MS.gene94621.t1
chr2.4 exon 14906940 14907179 14906940 ID=MS.gene94621.t1.exon3;Parent=MS.gene94621.t1
chr2.4 CDS 14906940 14907179 14906940 ID=cds.MS.gene94621.t1;Parent=MS.gene94621.t1
chr2.4 exon 14907432 14907746 14907432 ID=MS.gene94621.t1.exon4;Parent=MS.gene94621.t1
chr2.4 CDS 14907432 14907746 14907432 ID=cds.MS.gene94621.t1;Parent=MS.gene94621.t1
Gene Sequence

>MS.gene94621

ATGACGGTAATGTGTCTATCCATTTTAATTATAATGTCAAGCCTAATTCTTTGTATTTTTTTCTTAATGCAATTTTTGGGTTTTGGTTCTTAGGATATGATGAGTGTACCTTGGCTTGTAAACTTGCTGGCAATCACTTCGTTTTTTACAACATGTGAAGCCCATCCAAACAAGTTCAGAAATGAGCGGAACAAGTTCTGCCTCGACTGCAATGAAAATCCATTATGTGAATTTTGTATAGAATCTCGTCACAAAGGTCATAGAGTAATACAGGTGAGTGTTGTTTAATTTGATTACTAGATCTGTATAATATTTTGCAATGATCTAGGTATCTGTGTCATATCTATTTCTCTTCGCTTTGTTTTTGTTACACTTAAGCAATTTTAGTTGATTTTTTTTAACTATGTTATGTAAATATTTGCAATGATAAATCAGATAAGAAGATCATCATATAATGAGGTGGTTAAGACCAACGAAATTTACAAACATGTGGATATCCTCGGAATTCAAACCTACGTGATTAATAGCTCTAGTGTTGTATTCTTAAGCAAGAGAGCTCATACCCAACCTAAGAGGTTCAACATTGGAAAAACCGGTCACAATAGGGACTCTTTTTGTAAGAGATGTGATAGAAATCTTGCAGACCCTACCTACTTTTGCTCTTTGGCATGCAAGGTGAAATTTTGGTTTCCTATTATATTTTTATATTATGTTTTAAACGGTAAAAAATGGTTCAATATATGAAAAACTAGTATATTTTATTCCACTCCTTTTATTACTATTAATCCGGAGATTGAAGGCATATGATGGAGATTATAACTTAAACTTTTCTTTCAACCATTACCGGAATACCAGTTATTGTACTCATGTTGATTTTGTTTTCTTTTTGAAAGAATGATTAATTAATGTTGCATTATATGATACCAGTTTGCGTTTATCAAAAAGGATGGTGGCTTTTTCGTAAACCCAAGAGAGATGGAAGAAATGGAAAGATATCTAGATCAATCAATCAAGGCATCGCCTAAAAAAGAGAAGGCAAAAAAATGTTGCAAACAAAATCTGAAACGAAAATTAGAAGACGCAAGAATTGATGAGAAAAAGGAAGAGGAAGACGTAGAAAAAGAAAGGGAAGAAGGCGCCGATGACAGAGAAAGCATTCTTCCGGTTAATCGCTCATCGGCTTCACTTCGCAAGCCAAATTCAAAAAGAAAGGGAATAGCTCATAGGGCACCTTTTTTTTAA
Protein sequence

>MS.gene94621.t1

MTDMMSVPWLVNLLAITSFFTTCEAHPNKFRNERNKFCLDCNENPLCEFCIESRHKGHRVIQIRRSSYNEVVKTNEIYKHVDILGIQTYVINSSSVVFLSKRAHTQPKRFNIGKTGHNRDSFCKRCDRNLADPTYFCSLACKFAFIKKDGGFFVNPREMEEMERYLDQSIKASPKKEKAKKCCKQNLKRKLEDARIDEKKEEEDVEKEREEGADDRESILPVNRSSASLRKPNSKRKGIAHRAPFF