AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72970.t1 MTR_2g014550 94.787 211 10 1 1 211 1 210 2.32e-148 411
MS.gene72970.t1 MTR_2g014520 84.541 207 32 0 5 211 1 207 3.18e-131 367
MS.gene72970.t1 MTR_4g088335 69.543 197 60 0 15 211 10 206 1.21e-105 303
MS.gene72970.t1 MTR_4g078870 52.356 191 89 2 20 209 14 203 3.47e-73 220
MS.gene72970.t1 MTR_5g044580 41.848 184 102 3 26 205 32 214 1.10e-46 153
MS.gene72970.t1 MTR_2g020850 41.420 169 96 1 42 210 23 188 1.34e-46 152
MS.gene72970.t1 MTR_7g010890 40.000 185 106 3 25 205 31 214 7.83e-44 146
MS.gene72970.t1 MTR_4g118470 40.314 191 100 3 24 210 18 198 4.16e-42 142
MS.gene72970.t1 MTR_4g118480 38.537 205 112 3 10 210 2 196 2.30e-40 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72970.t1 AT5G46090 60.748 214 77 3 1 209 1 212 1.21e-96 280
MS.gene72970.t1 AT4G18425 58.019 212 87 2 1 210 1 212 1.30e-90 265
MS.gene72970.t1 AT4G28485 48.731 197 99 2 15 209 2 198 2.19e-64 198
MS.gene72970.t1 AT3G02430 44.340 212 94 3 22 211 6 215 8.07e-63 194
MS.gene72970.t1 AT4G24310 48.438 192 92 3 23 209 18 207 1.48e-59 186
MS.gene72970.t1 AT3G21550 43.605 172 91 2 37 207 6 172 1.16e-43 144
MS.gene72970.t1 AT1G09157 36.957 184 104 1 34 205 56 239 2.19e-40 138
MS.gene72970.t1 AT5G39650 36.559 186 102 2 34 205 57 240 1.72e-39 135
MS.gene72970.t1 AT3G21520 40.000 160 89 2 49 206 33 187 1.60e-37 129
MS.gene72970.t1 AT4G28485 54.545 99 45 0 111 209 65 163 5.44e-32 114
MS.gene72970.t1 AT5G27370 36.932 176 96 4 45 205 11 186 1.07e-30 112

Find 46 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAGGCTCCTCTCAGCTTC+TGG 0.270180 2.3:+60782275 None:intergenic
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.3:-60782044 MS.gene72970:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.3:-60782043 MS.gene72970:CDS
AAGGGCATGTGGGTTATTGA+TGG 0.393194 2.3:-60782008 MS.gene72970:CDS
ATTTCAGAGCACCGGACATT+TGG 0.394083 2.3:-60782231 MS.gene72970:CDS
TTATGGGTTTGCCACCTTCA+AGG 0.406503 2.3:-60782027 MS.gene72970:CDS
TGCAACTTGAGGTGGAAGTT+TGG 0.409649 2.3:+60781980 None:intergenic
CAATTATTAACTTGTTGAAA+GGG 0.415154 2.3:+60781737 None:intergenic
ATGGCGATGCCTGTGGCAAT+TGG 0.419997 2.3:-60781819 MS.gene72970:CDS
TATGGGTTTGCCACCTTCAA+GGG 0.422703 2.3:-60782026 MS.gene72970:CDS
CCTACTGAGAGACATGGAAT+AGG 0.427667 2.3:-60781765 MS.gene72970:CDS
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.3:+60782258 None:intergenic
GCATGCGGTGATGTCAATTC+TGG 0.434994 2.3:-60781925 MS.gene72970:CDS
AGAACCATCAAAAGAGATAC+AGG 0.448641 2.3:-60781850 MS.gene72970:CDS
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.3:+60782204 None:intergenic
TCAATTATTAACTTGTTGAA+AGG 0.463534 2.3:+60781736 None:intergenic
TGCTATCAGTAAAGTTTAGC+AGG 0.467137 2.3:+60782075 None:intergenic
TTGCCACCTTCAAGGGCATG+TGG 0.474826 2.3:-60782019 MS.gene72970:CDS
TAAGAATAACGATGAACAAA+AGG 0.479910 2.3:-60782324 MS.gene72970:CDS
AATAACCCACATGCCCTTGA+AGG 0.501829 2.3:+60782013 None:intergenic
TAGAAGGTTTGCCAAATGTC+CGG 0.511649 2.3:+60782220 None:intergenic
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.3:-60782212 MS.gene72970:CDS
CTGGAACATCCGCATTCCGC+AGG 0.537897 2.3:+60782294 None:intergenic
TCTGTACTTGTGTCTCTATG+TGG 0.542497 2.3:-60782110 MS.gene72970:CDS
AATTATTAACTTGTTGAAAG+GGG 0.546060 2.3:+60781738 None:intergenic
AGACACAAGTACAGAAGTCA+TGG 0.561323 2.3:+60782118 None:intergenic
TCCAGAAGCTGAGAGGAGCC+TGG 0.563140 2.3:-60782276 MS.gene72970:CDS
CCTATTCCATGTCTCTCAGT+AGG 0.565915 2.3:+60781765 None:intergenic
TGCCACCTTCAAGGGCATGT+GGG 0.570413 2.3:-60782018 MS.gene72970:CDS
AGTTCGACATTTCAGAGCAC+CGG 0.577759 2.3:-60782239 MS.gene72970:CDS
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.3:-60782060 MS.gene72970:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.3:-60781940 MS.gene72970:CDS
AGAGATACAGGAAATTCTCA+TGG 0.587742 2.3:-60781838 MS.gene72970:CDS
ATTATTAACTTGTTGAAAGG+GGG 0.590301 2.3:+60781739 None:intergenic
AATTCTCATGGCGATGCCTG+TGG 0.604206 2.3:-60781826 MS.gene72970:CDS
AACCCACATGCCCTTGAAGG+TGG 0.607741 2.3:+60782016 None:intergenic
AACAAAAGGTTCCACTCCTG+CGG 0.611057 2.3:-60782310 MS.gene72970:CDS
ACATCCGCATTCCGCAGGAG+TGG 0.617607 2.3:+60782299 None:intergenic
GGTTCCACTCCTGCGGAATG+CGG 0.617826 2.3:-60782303 MS.gene72970:CDS
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.3:-60781889 MS.gene72970:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.3:-60782059 MS.gene72970:CDS
GCATTTCCTACTGAGAGACA+TGG 0.643869 2.3:-60781771 MS.gene72970:CDS
CGGATGTTCCAGAAGCTGAG+AGG 0.669051 2.3:-60782283 MS.gene72970:CDS
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.3:+60782197 None:intergenic
TATCAGTAAAGTTTAGCAGG+AGG 0.692885 2.3:+60782078 None:intergenic
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.3:-60782058 MS.gene72970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAGAATAACGATGAACAAA+AGG - chr2.3:60781775-60781794 MS.gene72970:CDS 25.0%
! TTGCCAACATTTGTAAAAAT+CGG + chr2.3:60781941-60781960 None:intergenic 25.0%
GTTTATAGATTTCATGCATG+CGG - chr2.3:60782159-60782178 MS.gene72970:CDS 30.0%
TAAAAATCGGTGACAAAAGT+TGG + chr2.3:60781928-60781947 None:intergenic 30.0%
! ATTTCCTGTATCTCTTTTGA+TGG + chr2.3:60782256-60782275 None:intergenic 30.0%
!!! TCACCGATTTTTACAAATGT+TGG - chr2.3:60781935-60781954 MS.gene72970:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG + chr2.3:60781844-60781863 None:intergenic 35.0%
AGAACCATCAAAAGAGATAC+AGG - chr2.3:60782249-60782268 MS.gene72970:CDS 35.0%
AGAGATACAGGAAATTCTCA+TGG - chr2.3:60782261-60782280 MS.gene72970:CDS 35.0%
TATCAGTAAAGTTTAGCAGG+AGG + chr2.3:60782024-60782043 None:intergenic 35.0%
TGCATTGTTTGATCAGAATG+TGG - chr2.3:60782210-60782229 MS.gene72970:CDS 35.0%
TGCTATCAGTAAAGTTTAGC+AGG + chr2.3:60782027-60782046 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG - chr2.3:60782055-60782074 MS.gene72970:CDS 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG - chr2.3:60782056-60782075 MS.gene72970:CDS 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG + chr2.3:60782250-60782269 None:intergenic 35.0%
AGACACAAGTACAGAAGTCA+TGG + chr2.3:60781984-60782003 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG - chr2.3:60782041-60782060 MS.gene72970:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG - chr2.3:60782040-60782059 MS.gene72970:CDS 40.0%
TAGAAGGTTTGCCAAATGTC+CGG + chr2.3:60781882-60781901 None:intergenic 40.0%
TCTGTACTTGTGTCTCTATG+TGG - chr2.3:60781989-60782008 MS.gene72970:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG - chr2.3:60782039-60782058 MS.gene72970:CDS 40.0%
! CGATATTTTGCTGCAACTTG+AGG + chr2.3:60782133-60782152 None:intergenic 40.0%
! TATTTTGCTGCAACTTGAGG+TGG + chr2.3:60782130-60782149 None:intergenic 40.0%
AACAAAAGGTTCCACTCCTG+CGG - chr2.3:60781789-60781808 MS.gene72970:CDS 45.0%
AATAACCCACATGCCCTTGA+AGG + chr2.3:60782089-60782108 None:intergenic 45.0%
AATGCAAGAACAGTGCCTGT+AGG + chr2.3:60781905-60781924 None:intergenic 45.0%
AGTTCGACATTTCAGAGCAC+CGG - chr2.3:60781860-60781879 MS.gene72970:CDS 45.0%
CAAAAAACGCCAATTGCCAC+AGG + chr2.3:60782292-60782311 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+AGG - chr2.3:60782334-60782353 MS.gene72970:CDS 45.0%
CCTATTCCATGTCTCTCAGT+AGG + chr2.3:60782337-60782356 None:intergenic 45.0%
GCATTTCCTACTGAGAGACA+TGG - chr2.3:60782328-60782347 MS.gene72970:CDS 45.0%
TATGGGTTTGCCACCTTCAA+GGG - chr2.3:60782073-60782092 MS.gene72970:CDS 45.0%
TGCAACTTGAGGTGGAAGTT+TGG + chr2.3:60782122-60782141 None:intergenic 45.0%
TTATGGGTTTGCCACCTTCA+AGG - chr2.3:60782072-60782091 MS.gene72970:CDS 45.0%
TTGGCAAACCTTCTACCTAC+AGG - chr2.3:60781887-60781906 MS.gene72970:CDS 45.0%
! AAGGGCATGTGGGTTATTGA+TGG - chr2.3:60782091-60782110 MS.gene72970:CDS 45.0%
!! ATTTCAGAGCACCGGACATT+TGG - chr2.3:60781868-60781887 MS.gene72970:CDS 45.0%
AATTCTCATGGCGATGCCTG+TGG - chr2.3:60782273-60782292 MS.gene72970:CDS 50.0%
GAACAGTGCCTGTAGGTAGA+AGG + chr2.3:60781898-60781917 None:intergenic 50.0%
GCATGCGGTGATGTCAATTC+TGG - chr2.3:60782174-60782193 MS.gene72970:CDS 50.0%
AACCCACATGCCCTTGAAGG+TGG + chr2.3:60782086-60782105 None:intergenic 55.0%
ATGGCGATGCCTGTGGCAAT+TGG - chr2.3:60782280-60782299 MS.gene72970:CDS 55.0%
CGGATGTTCCAGAAGCTGAG+AGG - chr2.3:60781816-60781835 MS.gene72970:CDS 55.0%
! TGCCACCTTCAAGGGCATGT+GGG - chr2.3:60782081-60782100 MS.gene72970:CDS 55.0%
! TTGCCACCTTCAAGGGCATG+TGG - chr2.3:60782080-60782099 MS.gene72970:CDS 55.0%
ACATCCGCATTCCGCAGGAG+TGG + chr2.3:60781803-60781822 None:intergenic 60.0%
ACCAGGCTCCTCTCAGCTTC+TGG + chr2.3:60781827-60781846 None:intergenic 60.0%
CTGGAACATCCGCATTCCGC+AGG + chr2.3:60781808-60781827 None:intergenic 60.0%
GGTTCCACTCCTGCGGAATG+CGG - chr2.3:60781796-60781815 MS.gene72970:CDS 60.0%
TCCAGAAGCTGAGAGGAGCC+TGG - chr2.3:60781823-60781842 MS.gene72970:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 60781743 60782378 60781743 ID=MS.gene72970
chr2.3 mRNA 60781743 60782378 60781743 ID=MS.gene72970.t1;Parent=MS.gene72970
chr2.3 exon 60781743 60782378 60781743 ID=MS.gene72970.t1.exon1;Parent=MS.gene72970.t1
chr2.3 CDS 60781743 60782378 60781743 ID=cds.MS.gene72970.t1;Parent=MS.gene72970.t1
Gene Sequence

>MS.gene72970

ATGGACATCAATTTAGAAATCGACGATGACTCTAAGAATAACGATGAACAAAAGGTTCCACTCCTGCGGAATGCGGATGTTCCAGAAGCTGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGCACCGGACATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCGATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGTCTCTATGTGGTGCATCATGCCTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAGGGCATGTGGGTTATTGATGGATCAACCAAACTTCCACCTCAAGTTGCAGCAAAATATCGCATAAAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTGGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGTTTTTTTCCAGAACCATCAAAAGAGATACAGGAAATTCTCATGGCGATGCCTGTGGCAATTGGCGTTTTTTGCAGCATGATTTTCGTTGCATTTCCTACTGAGAGACATGGAATAGGCTTCCCCCTTTCAACAAGTTAA
Protein sequence

>MS.gene72970.t1

MDINLEIDDDSKNNDEQKVPLLRNADVPEAERSLVQKAISSTFQSTGHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVSLCGASCLLLNFTDSIRDSKGNICYGFATFKGMWVIDGSTKLPPQVAAKYRIKFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILMAMPVAIGVFCSMIFVAFPTERHGIGFPLSTS