AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0448310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0448310 MtrunA17_Chr3g0090401 74.863 183 45 1 1 182 1272 1454 3.43e-73 240
Msa0448310 MtrunA17_Chr3g0090141 67.213 183 37 1 1 183 1081 1240 5.22e-68 225
Msa0448310 MtrunA17_Chr3g0090371 65.934 182 39 1 1 182 1080 1238 5.29e-67 223
Msa0448310 MtrunA17_Chr3g0087841 63.736 182 43 1 1 182 986 1144 5.37e-64 214
Msa0448310 MtrunA17_Chr3g0090431 84.821 112 17 0 1 112 952 1063 7.01e-54 185
Msa0448310 MtrunA17_Chr3g0089811 55.738 183 74 3 1 183 1083 1258 1.07e-52 181
Msa0448310 MtrunA17_Chr4g0025391 55.738 183 75 3 1 183 1080 1256 4.56e-52 180
Msa0448310 MtrunA17_Chr3g0089441 55.191 183 75 3 1 183 589 764 4.91e-52 178
Msa0448310 MtrunA17_Chr3g0089921 52.577 194 85 3 1 194 333 519 1.06e-51 174
Msa0448310 MtrunA17_Chr3g0089541 55.491 173 72 2 1 173 1084 1251 4.49e-50 174
Msa0448310 MtrunA17_Chr3g0092261 55.191 183 75 3 1 183 1126 1301 9.39e-50 173
Msa0448310 MtrunA17_Chr3g0091061 55.307 179 55 3 1 179 1080 1233 2.31e-49 172
Msa0448310 MtrunA17_Chr3g0089761 57.471 174 69 3 1 174 1081 1249 3.86e-49 171
Msa0448310 MtrunA17_Chr3g0090691 53.073 179 59 2 1 179 1079 1232 4.52e-48 168
Msa0448310 MtrunA17_Chr3g0089211 54.913 173 73 2 1 173 1128 1295 1.47e-47 167
Msa0448310 MtrunA17_Chr3g0089611 56.395 172 68 3 1 172 29 193 5.01e-47 156
Msa0448310 MtrunA17_Chr3g0089991 55.233 172 72 2 1 172 1066 1232 1.51e-46 164
Msa0448310 MtrunA17_Chr3g0089511 56.395 172 68 3 1 172 144 308 5.98e-46 156
Msa0448310 MtrunA17_Chr3g0089871 49.029 206 75 4 1 183 1070 1268 6.81e-46 162
Msa0448310 MtrunA17_Chr3g0091081 49.479 192 70 3 1 190 1084 1250 1.28e-45 161
Msa0448310 MtrunA17_Chr2g0309721 51.913 183 81 3 1 183 1079 1254 3.04e-45 160
Msa0448310 MtrunA17_Chr3g0089251 54.070 172 74 3 1 172 1111 1277 2.56e-44 157
Msa0448310 MtrunA17_Chr3g0089651 53.757 173 75 2 1 173 1087 1254 3.09e-43 154
Msa0448310 MtrunA17_Chr3g0089421 47.179 195 65 6 1 194 1084 1241 4.61e-35 131
Msa0448310 MtrunA17_Chr8g0348931 52.555 137 60 3 1 137 1086 1217 1.24e-28 112
Msa0448310 MtrunA17_Chr3g0092251 58.427 89 35 1 95 183 1 87 4.55e-26 96.7
Msa0448310 MtrunA17_Chr3g0090661 47.368 114 37 1 77 190 13 103 5.31e-24 91.7
Msa0448310 MtrunA17_Chr3g0085751 35.676 185 85 4 1 181 979 1133 2.34e-20 89.0
Msa0448310 MtrunA17_Chr3g0085091 34.254 181 85 4 7 183 993 1143 1.44e-19 86.7
Msa0448310 MtrunA17_Chr3g0085621 37.415 147 84 3 36 176 7 151 4.68e-19 82.8
Msa0448310 MtrunA17_Chr3g0085621 35.172 145 82 5 1 140 103 240 4.40e-13 66.2
Msa0448310 MtrunA17_Chr3g0085111 36.628 172 75 4 7 174 986 1127 5.59e-19 84.7
Msa0448310 MtrunA17_Chr3g0085521 32.086 187 93 5 1 183 976 1132 9.36e-19 84.0
Msa0448310 MtrunA17_Chr3g0085161 31.959 194 97 5 1 190 845 1007 1.97e-18 83.2
Msa0448310 MtrunA17_Chr1g0164581 34.921 189 94 5 4 190 1056 1217 4.79e-18 82.0
Msa0448310 MtrunA17_Chr3g0082401 35.052 194 90 8 1 190 351 512 2.70e-17 79.7
Msa0448310 MtrunA17_Chr3g0085171 29.947 187 97 4 1 183 972 1128 4.13e-17 79.3
Msa0448310 MtrunA17_Chr3g0085131 40.278 144 75 3 7 146 979 1115 5.34e-17 79.0
Msa0448310 MtrunA17_Chr3g0084031 32.990 194 95 5 1 190 991 1153 6.18e-16 75.9
Msa0448310 MtrunA17_Chr3g0086221 31.841 201 101 6 1 196 975 1144 1.18e-15 75.1
Msa0448310 MtrunA17_Chr3g0085711 41.121 107 59 1 39 141 582 688 2.14e-15 74.3
Msa0448310 MtrunA17_Chr3g0085701 39.286 140 72 4 7 141 794 925 3.11e-15 73.9
Msa0448310 MtrunA17_Chr3g0086161 29.500 200 106 5 1 196 975 1143 3.51e-15 73.6
Msa0448310 MtrunA17_Chr3g0091951 33.505 194 90 8 1 190 170 328 2.20e-14 70.5
Msa0448310 MtrunA17_Chr3g0083751 33.158 190 96 7 1 190 1068 1226 2.33e-14 71.2
Msa0448310 MtrunA17_Chr3g0084081 35.570 149 85 3 1 145 987 1128 3.21e-14 70.9
Msa0448310 MtrunA17_Chr3g0084051 31.351 185 93 4 1 181 983 1137 3.77e-14 70.9
Msa0448310 MtrunA17_Chr3g0085791 31.016 187 96 4 1 183 122 279 5.55e-14 69.3
Msa0448310 MtrunA17_Chr3g0089591 31.579 190 99 7 1 190 1129 1287 9.43e-14 69.7
Msa0448310 MtrunA17_Chr3g0086091 31.383 188 94 5 1 183 787 944 9.75e-14 69.3
Msa0448310 MtrunA17_Chr3g0084821 32.812 192 94 8 1 190 1 159 1.27e-13 66.2
Msa0448310 MtrunA17_Chr3g0080871 31.579 190 100 7 1 190 1048 1207 1.92e-13 68.6
Msa0448310 MtrunA17_Chr3g0113511 36.429 140 85 3 4 143 254 389 1.99e-13 68.2
Msa0448310 MtrunA17_Chr3g0113801 36.429 140 85 2 4 143 290 425 2.03e-13 68.2
Msa0448310 MtrunA17_Chr3g0113741 36.429 140 85 2 4 143 254 389 2.34e-13 68.2
Msa0448310 MtrunA17_Chr4g0008461 31.937 191 97 8 1 190 1044 1202 3.73e-13 67.8
Msa0448310 MtrunA17_Chr3g0087541 42.056 107 55 2 39 141 1028 1131 5.90e-13 67.4
Msa0448310 MtrunA17_Chr3g0085331 30.808 198 101 6 1 193 1087 1253 1.26e-12 66.2
Msa0448310 MtrunA17_Chr3g0083681 32.105 190 98 7 1 190 1038 1196 1.29e-12 66.2
Msa0448310 MtrunA17_Chr3g0084061 38.889 108 62 1 37 140 1017 1124 1.96e-12 65.9
Msa0448310 MtrunA17_Chr3g0087581 30.256 195 100 6 1 190 976 1139 2.07e-12 65.5
Msa0448310 MtrunA17_Chr3g0086621 31.282 195 98 6 1 190 973 1136 3.31e-12 65.1
Msa0448310 MtrunA17_Chr3g0089471 35.862 145 86 5 1 145 1126 1263 1.54e-11 63.2
Msa0448310 MtrunA17_Chr3g0087731 30.189 159 83 3 37 191 748 882 1.76e-11 62.8
Msa0448310 MtrunA17_Chr3g0085651 36.364 143 79 4 1 138 1205 1340 4.83e-11 61.6
Msa0448310 MtrunA17_Chr3g0083591 31.579 190 99 7 1 190 1021 1179 5.69e-11 61.2
Msa0448310 MtrunA17_Chr3g0087701 30.120 166 88 3 36 197 1004 1145 6.41e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAGAAATTGTTTGTAATT+TGG 0.076987 3_3:+27949936 None:intergenic
TCCAAAATGGCGAGTGATTC+TGG 0.182890 3_3:+27949489 None:intergenic
TGGAAACCCCATTCAATTAA+TGG 0.204315 3_3:+27949886 None:intergenic
ATAGAAATTGTTTGTAATTT+GGG 0.220364 3_3:+27949937 None:intergenic
TCCAGAATCACTCGCCATTT+TGG 0.272611 3_3:-27949490 Msa0448310:CDS
CATAGTGCAAACTCTAGTTT+TGG 0.340099 3_3:+27949979 None:intergenic
AATCATTAAAAGAAAGTGTT+TGG 0.342848 3_3:+27949629 None:intergenic
AGATGATAATACCTCCAAAA+TGG 0.345639 3_3:+27949476 None:intergenic
AAAATGAGCGATGGAATAAT+TGG 0.357026 3_3:-27949513 Msa0448310:CDS
TCTGAAATGAAACGCTTAGA+TGG 0.357856 3_3:-27949748 Msa0448310:CDS
ATGAAACGCTTAGATGGAAA+TGG 0.372226 3_3:-27949742 Msa0448310:CDS
TTGTCTGCGGCTTGAGTCCT+TGG 0.405022 3_3:-27949677 Msa0448310:CDS
CTGAAAGAGAAGTAAGGCTT+TGG 0.412175 3_3:+27949866 None:intergenic
GAGGAAGGGAGATTGTCTTC+TGG 0.424750 3_3:+27949586 None:intergenic
GATGCCGCCATTAATTGAAT+GGG 0.433794 3_3:-27949893 Msa0448310:CDS
AGATGCCGCCATTAATTGAA+TGG 0.458622 3_3:-27949894 Msa0448310:CDS
CTCAGCATCTTGAGAGAGGA+AGG 0.458997 3_3:+27949571 None:intergenic
TATTGTTAACACCTTGTTGA+AGG 0.464828 3_3:-27949818 Msa0448310:CDS
GAAAGTGTTTGGAGAGAGCA+AGG 0.470476 3_3:+27949640 None:intergenic
TCTGGCAATGACTCAAGTCT+TGG 0.488155 3_3:+27949604 None:intergenic
TGAAACGCTTAGATGGAAAT+GGG 0.513937 3_3:-27949741 Msa0448310:CDS
ACAATTCTGAAAGAGAAGTA+AGG 0.521898 3_3:+27949860 None:intergenic
GAAATTGTTTGTAATTTGGG+TGG 0.552652 3_3:+27949940 None:intergenic
ATCTATTCCGTTACTAATCG+AGG 0.572256 3_3:-27949457 Msa0448310:CDS
AAATTTATGAAAATGAGCGA+TGG 0.595752 3_3:-27949522 Msa0448310:CDS
AGGTAATTTGATCTCTGCCA+AGG 0.601404 3_3:+27949660 None:intergenic
AAATGATCCTCGATTAGTAA+CGG 0.601952 3_3:+27949450 None:intergenic
CTAGAGTTTGCACTATGCGA+AGG 0.616762 3_3:-27949973 Msa0448310:CDS
ATGCCGCCATTAATTGAATG+GGG 0.619843 3_3:-27949892 Msa0448310:CDS
AAAGCTCAGCATCTTGAGAG+AGG 0.624150 3_3:+27949567 None:intergenic
AAGCAACTGCTCCTTCAACA+AGG 0.631044 3_3:+27949807 None:intergenic
TCAGCATCTTGAGAGAGGAA+GGG 0.656170 3_3:+27949572 None:intergenic
AAACCCCATTCAATTAATGG+CGG 0.677087 3_3:+27949889 None:intergenic
ACAAACTTTCAAGAGCGATG+AGG 0.711189 3_3:+27950016 None:intergenic
TAAGTGTTTCAAGAGATGAG+AGG 0.721101 3_3:+27949710 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAATTGTTTGTAATTT+GGG + chr3_3:27949501-27949520 None:intergenic 15.0%
!! AATAGAAATTGTTTGTAATT+TGG + chr3_3:27949502-27949521 None:intergenic 15.0%
!! ACTTATTGACAAAAACATTA+AGG + chr3_3:27949661-27949680 None:intergenic 20.0%
!!! AATCATTAAAAGAAAGTGTT+TGG + chr3_3:27949809-27949828 None:intergenic 20.0%
!!! CATAAATTTTTTCTAAAGCA+GGG + chr3_3:27949902-27949921 None:intergenic 20.0%
!!! TCATAAATTTTTTCTAAAGC+AGG + chr3_3:27949903-27949922 None:intergenic 20.0%
! GACAAAAACATTAAGGAAAA+GGG + chr3_3:27949654-27949673 None:intergenic 25.0%
! TGACAAAAACATTAAGGAAA+AGG + chr3_3:27949655-27949674 None:intergenic 25.0%
!! TTAGATTTTACAATTGTCTG+CGG - chr3_3:27949745-27949764 Msa0448310:CDS 25.0%
! AAATTTATGAAAATGAGCGA+TGG - chr3_3:27949913-27949932 Msa0448310:CDS 25.0%
GAAATTGTTTGTAATTTGGG+TGG + chr3_3:27949498-27949517 None:intergenic 30.0%
! ACAATTCTGAAAGAGAAGTA+AGG + chr3_3:27949578-27949597 None:intergenic 30.0%
TATTGTTAACACCTTGTTGA+AGG - chr3_3:27949617-27949636 Msa0448310:CDS 30.0%
AAAATGAGCGATGGAATAAT+TGG - chr3_3:27949922-27949941 Msa0448310:CDS 30.0%
AGATGATAATACCTCCAAAA+TGG + chr3_3:27949962-27949981 None:intergenic 30.0%
AAATGATCCTCGATTAGTAA+CGG + chr3_3:27949988-27950007 None:intergenic 30.0%
!!! CAAACTCTAGTTTTGGAAGA+TGG + chr3_3:27949452-27949471 None:intergenic 35.0%
!! CATAGTGCAAACTCTAGTTT+TGG + chr3_3:27949459-27949478 None:intergenic 35.0%
AAACCCCATTCAATTAATGG+CGG + chr3_3:27949549-27949568 None:intergenic 35.0%
TGGAAACCCCATTCAATTAA+TGG + chr3_3:27949552-27949571 None:intergenic 35.0%
! TCTGAAATGAAACGCTTAGA+TGG - chr3_3:27949687-27949706 Msa0448310:CDS 35.0%
ATGAAACGCTTAGATGGAAA+TGG - chr3_3:27949693-27949712 Msa0448310:CDS 35.0%
TGAAACGCTTAGATGGAAAT+GGG - chr3_3:27949694-27949713 Msa0448310:CDS 35.0%
TAAGTGTTTCAAGAGATGAG+AGG + chr3_3:27949728-27949747 None:intergenic 35.0%
ATCTATTCCGTTACTAATCG+AGG - chr3_3:27949978-27949997 Msa0448310:CDS 35.0%
ACAAACTTTCAAGAGCGATG+AGG + chr3_3:27949422-27949441 None:intergenic 40.0%
!!! ACTCTAGTTTTGGAAGATGG+TGG + chr3_3:27949449-27949468 None:intergenic 40.0%
AGATGCCGCCATTAATTGAA+TGG - chr3_3:27949541-27949560 Msa0448310:CDS 40.0%
GATGCCGCCATTAATTGAAT+GGG - chr3_3:27949542-27949561 Msa0448310:CDS 40.0%
ATGCCGCCATTAATTGAATG+GGG - chr3_3:27949543-27949562 Msa0448310:CDS 40.0%
CTGAAAGAGAAGTAAGGCTT+TGG + chr3_3:27949572-27949591 None:intergenic 40.0%
AGGTAATTTGATCTCTGCCA+AGG + chr3_3:27949778-27949797 None:intergenic 40.0%
CTAGAGTTTGCACTATGCGA+AGG - chr3_3:27949462-27949481 Msa0448310:CDS 45.0%
AAGCAACTGCTCCTTCAACA+AGG + chr3_3:27949631-27949650 None:intergenic 45.0%
!! GAAAGTGTTTGGAGAGAGCA+AGG + chr3_3:27949798-27949817 None:intergenic 45.0%
TCTGGCAATGACTCAAGTCT+TGG + chr3_3:27949834-27949853 None:intergenic 45.0%
TCAGCATCTTGAGAGAGGAA+GGG + chr3_3:27949866-27949885 None:intergenic 45.0%
AAAGCTCAGCATCTTGAGAG+AGG + chr3_3:27949871-27949890 None:intergenic 45.0%
! TCCAGAATCACTCGCCATTT+TGG - chr3_3:27949945-27949964 Msa0448310:CDS 45.0%
TCCAAAATGGCGAGTGATTC+TGG + chr3_3:27949949-27949968 None:intergenic 45.0%
!! AGAATCACTCGCCATTTTGG+AGG - chr3_3:27949948-27949967 Msa0448310:CDS 45.0%
GAGGAAGGGAGATTGTCTTC+TGG + chr3_3:27949852-27949871 None:intergenic 50.0%
CTCAGCATCTTGAGAGAGGA+AGG + chr3_3:27949867-27949886 None:intergenic 50.0%
TTGTCTGCGGCTTGAGTCCT+TGG - chr3_3:27949758-27949777 Msa0448310:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 27949411 27950046 27949411 ID=Msa0448310;Name=Msa0448310
chr3_3 mRNA 27949411 27950046 27949411 ID=Msa0448310-mRNA-1;Parent=Msa0448310;Name=Msa0448310-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|211
chr3_3 exon 27949411 27950046 27949411 ID=Msa0448310-mRNA-1:exon:5434;Parent=Msa0448310-mRNA-1
chr3_3 CDS 27949411 27950046 27949411 ID=Msa0448310-mRNA-1:cds;Parent=Msa0448310-mRNA-1
Gene Sequence

>Msa0448310

ATGGACATCCTCATCGCTCTTGAAAGTTTGTATCTCCACCATCTTCCAAAACTAGAGTTTGCACTATGCGAAGGAGTTTTCTTACCACCCAAATTACAAACAATTTCTATTAATTCTTTGAGAATAACAAAGATGCCGCCATTAATTGAATGGGGTTTCCAAAGCCTTACTTCTCTTTCAGAATTGTATATTGAAGATAATGATGATATTGTTAACACCTTGTTGAAGGAGCAGTTGCTTCCCTTTTCCTTAATGTTTTTGTCAATAAGTAATCTATCTGAAATGAAACGCTTAGATGGAAATGGGCTTCGACACCTCTCATCTCTTGAAACACTTAGATTTTACAATTGTCTGCGGCTTGAGTCCTTGGCAGAGATCAAATTACCTTGCTCTCTCCAAACACTTTCTTTTAATGATTGTCCAAGACTTGAGTCATTGCCAGAAGACAATCTCCCTTCCTCTCTCAAGATGCTGAGCTTTTGTAAATGCCCTGCTTTAGAAAAAATTTATGAAAATGAGCGATGGAATAATTGGTCCAGAATCACTCGCCATTTTGGAGGTATTATCATCTATTCCGTTACTAATCGAGGATCATTTCTCAATTTCATGACTGTGATTATTATTATGAGTTACTAG
Protein sequence

>Msa0448310

MDILIALESLYLHHLPKLEFALCEGVFLPPKLQTISINSLRITKMPPLIEWGFQSLTSLSELYIEDNDDIVNTLLKEQLLPFSLMFLSISNLSEMKRLDGNGLRHLSSLETLRFYNCLRLESLAEIKLPCSLQTLSFNDCPRLESLPEDNLPSSLKMLSFCKCPALEKIYENERWNNWSRITRHFGGIIIYSVTNRGSFLNFMTVIIIMSY*