AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG028260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028260 MtrunA17_Chr5g0435021 96.463 311 11 0 1 311 1 311 0.0 625
MsaG028260 MtrunA17_Chr5g0393721 46.957 115 47 2 172 286 192 292 1.96e-25 103
MsaG028260 MtrunA17_Chr1g0207311 50.000 94 41 2 197 286 173 264 1.66e-24 100
MsaG028260 MtrunA17_Chr1g0207301 46.667 120 51 3 167 286 250 356 1.87e-23 99.0
MsaG028260 MtrunA17_Chr3g0134741 58.571 70 29 0 217 286 228 297 1.22e-22 95.9
MsaG028260 MtrunA17_Chr1g0152651 62.903 62 23 0 225 286 281 342 2.12e-22 95.9
MsaG028260 MtrunA17_Chr8g0384141 50.000 80 33 1 201 280 104 176 2.91e-19 85.5
MsaG028260 MtrunA17_Chr3g0134001 62.500 56 21 0 225 280 178 233 2.16e-18 83.2
MsaG028260 MtrunA17_Chr7g0243041 66.038 53 18 0 225 277 33 85 8.18e-18 79.0
MsaG028260 MtrunA17_Chr4g0074161 42.453 106 57 1 180 281 164 269 1.41e-17 82.8
MsaG028260 MtrunA17_Chr1g0190731 50.769 65 32 0 217 281 192 256 1.87e-14 73.2
MsaG028260 MtrunA17_Chr5g0402161 55.696 79 33 1 202 280 123 199 4.32e-11 62.0
MsaG028260 MtrunA17_Chr2g0311101 43.421 76 43 0 205 280 156 231 6.64e-11 62.4
MsaG028260 MtrunA17_Chr1g0193321 49.020 51 26 0 231 281 475 525 9.78e-11 62.8
MsaG028260 MtrunA17_Chr1g0153241 37.805 82 46 1 199 280 71 147 9.80e-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
MsaG028260 AT5G37800.1 53.968 189 65 5 130 311 121 294 1.12e-54 180
MsaG028260 AT1G66470.1 62.585 147 48 2 163 309 147 286 3.47e-51 171
MsaG028260 AT2G14760.1 60.000 70 28 0 217 286 236 305 4.56e-24 100
MsaG028260 AT4G33880.1 60.000 70 28 0 217 286 265 334 8.67e-24 100
MsaG028260 AT1G27740.1 54.430 79 36 0 208 286 157 235 1.76e-23 97.4
MsaG028260 AT5G43175.1 58.442 77 30 1 212 286 124 200 2.07e-23 96.3
MsaG028260 AT2G14760.3 50.602 83 28 1 217 286 236 318 1.37e-20 90.9
MsaG028260 AT5G01305.1 57.576 66 28 0 212 277 31 96 5.23e-20 85.9
MsaG028260 AT2G24260.2 50.000 86 39 1 217 302 34 115 2.18e-19 85.9
MsaG028260 AT2G24260.1 50.000 86 39 1 217 302 137 218 1.24e-18 85.5
MsaG028260 AT4G30980.1 40.678 118 58 3 184 301 104 209 3.03e-18 84.0
MsaG028260 AT4G30980.2 40.678 118 58 3 184 301 152 257 3.97e-18 84.3
MsaG028260 AT4G00120.1 43.820 89 48 2 192 280 88 174 1.03e-16 77.4
MsaG028260 AT5G58010.1 50.000 72 36 0 210 281 91 162 1.14e-16 79.3
MsaG028260 AT3G21330.1 58.929 56 23 0 225 280 276 331 7.33e-16 77.8
MsaG028260 AT3G50330.1 64.179 67 22 1 225 291 126 190 1.50e-11 63.5
MsaG028260 AT5G09750.1 51.250 80 32 1 201 280 109 181 4.26e-11 62.4

Find 41 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGGCAGCTGATGAATTT+TGG 0.276615 5:-59684002 MsaT028260.1:CDS
AGCAACACTTTGAGGATCTT+TGG 0.293258 5:+59684549 None:intergenic
TTGCTGCAAATTATTCTCAT+TGG 0.332794 5:+59685197 None:intergenic
CATGGCTTCTTTGCATTGGC+AGG 0.350562 5:+59684613 None:intergenic
CTTGAAGAAGCGATCTTCTA+TGG 0.360051 5:-59684950 MsaT028260.1:intron
GATGGTTCACAAAGCACTAA+TGG 0.373871 5:-59685420 MsaT028260.1:CDS
CATTTGGCACAAGTTCTTGT+AGG 0.374925 5:+59684392 None:intergenic
AAATCTACCTTGGAACCATT+TGG 0.388020 5:+59684376 None:intergenic
AATGCAAAAGAGAAGCAAAA+TGG 0.391258 5:-59685075 MsaT028260.1:CDS
TCATCATCACAAGGGACATT+TGG 0.398490 5:+59685021 None:intergenic
TTCTTACTTGCAGCTGTGCA+TGG 0.415931 5:+59684595 None:intergenic
TGCTTAGCTTTCAACAGAGC+TGG 0.417572 5:-59685227 MsaT028260.1:CDS
ACCTTGGCAGCAACACTTTG+AGG 0.436246 5:+59684541 None:intergenic
TGTGCATGGCTTCTTTGCAT+TGG 0.456555 5:+59684609 None:intergenic
TCCTCAAAGTGTTGCTGCCA+AGG 0.458152 5:-59684542 MsaT028260.1:intron
CTACAAGAACTTGTGCCAAA+TGG 0.480564 5:-59684391 MsaT028260.1:CDS
GAAACTTCAAGTGGTAGCTA+TGG 0.482106 5:-59685111 MsaT028260.1:CDS
ATGAGAATAATTTGCAGCAA+TGG 0.492330 5:-59685194 MsaT028260.1:CDS
ACAATGTAGAATGTTGTTGT+TGG 0.495112 5:+59685512 None:intergenic
TCTCCTACTCTATGCAGAAA+AGG 0.510749 5:-59685357 MsaT028260.1:CDS
GAGTCTTTGATTAATTTCAA+AGG 0.522051 5:-59685294 MsaT028260.1:CDS
GGTTGATTTGGTTACCATGT+TGG 0.524353 5:-59684199 MsaT028260.1:CDS
ACAAATTTGTGCATGGTGCA+AGG 0.524955 5:-59685147 MsaT028260.1:CDS
ACACTTTGAGGATCTTTGGA+TGG 0.550437 5:+59684553 None:intergenic
GTTTCTTCAGTTGCAAGTGA+AGG 0.554782 5:-59684154 MsaT028260.1:intron
TGATGATAGCTTAATAAAAG+AGG 0.558766 5:-59684992 MsaT028260.1:CDS
GGTGGAAAAGCTCCTGACAT+AGG 0.572595 5:-59683970 MsaT028260.1:CDS
TAGCTTTCAACAGAGCTGGA+TGG 0.582750 5:-59685223 MsaT028260.1:CDS
AGAAGATCGCTTCTTCAAGA+CGG 0.585959 5:+59684954 None:intergenic
CAAAATGGTGAAAGTTCATG+TGG 0.590862 5:-59685060 MsaT028260.1:CDS
ACTAATTGCTTTCTCCAACA+TGG 0.596287 5:+59684185 None:intergenic
AATAGCTTTGAAACTTCAAG+TGG 0.597044 5:-59685120 MsaT028260.1:CDS
ACTTGTGCCAAATGGTTCCA+AGG 0.597324 5:-59684383 MsaT028260.1:intron
AAGTAACACAAATTTGTGCA+TGG 0.601950 5:-59685154 MsaT028260.1:CDS
TCTATGATTGAAGAAGAAGA+TGG 0.607243 5:-59685438 MsaT028260.1:CDS
ATGGTGAAAGTTCATGTGGA+TGG 0.618317 5:-59685056 MsaT028260.1:CDS
GAAGAGAGAGAATAAGTGAG+AGG 0.626364 5:-59684423 MsaT028260.1:CDS
TCATCGTCGTCATCATCACA+AGG 0.632243 5:+59685012 None:intergenic
TATTACAACAATCTCATGCA+AGG 0.641770 5:-59685261 MsaT028260.1:CDS
TGATAGCTTAATAAAAGAGG+CGG 0.653073 5:-59684989 MsaT028260.1:CDS
CATCGTCGTCATCATCACAA+GGG 0.736454 5:+59685013 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 59683924 59685544 59683924 ID=MsaG028260
Chr5 mRNA 59683924 59685544 59683924 ID=MsaT028260.1;Parent=MsaG028260
Chr5 exon 59683924 59684025 59683924 ID=MsaT028260.1.exon5;Parent=MsaT028260.1
Chr5 CDS 59683924 59684025 59683924 ID=cds.MsaT028260.1;Parent=MsaT028260.1
Chr5 exon 59684155 59684220 59684155 ID=MsaT028260.1.exon4;Parent=MsaT028260.1
Chr5 CDS 59684155 59684220 59684155 ID=cds.MsaT028260.1;Parent=MsaT028260.1
Chr5 exon 59684384 59684449 59684384 ID=MsaT028260.1.exon3;Parent=MsaT028260.1
Chr5 CDS 59684384 59684449 59684384 ID=cds.MsaT028260.1;Parent=MsaT028260.1
Chr5 exon 59684543 59684650 59684543 ID=MsaT028260.1.exon2;Parent=MsaT028260.1
Chr5 CDS 59684543 59684650 59684543 ID=cds.MsaT028260.1;Parent=MsaT028260.1
Chr5 exon 59684951 59685544 59684951 ID=MsaT028260.1.exon1;Parent=MsaT028260.1
Chr5 CDS 59684951 59685544 59684951 ID=cds.MsaT028260.1;Parent=MsaT028260.1
Gene Sequence

>MsaT028260.1

ATGGCACTAGCCAACAACAACATTCTACATTGTATTTTTGACGAGACTACTATGGAGATTAACTCTGTAATGTCTCATAAAAAATCTATGATTGAAGAAGAAGATGGTTCACAAAGCACTAATGGATTAAGCAATGATTCAGCTTCAGCTTCTGTCATTACAAATTCTCCTACTCTATGCAGAAAAGGTCATGTTTATAACAACAATACAAGTTATGAACTTGAAGAAGAGTCTTTGATTAATTTCAAAGGCAATGATGAGTATTACAACAATCTCATGCAAGGTAGTGAATCATTGCTTAGCTTTCAACAGAGCTGGATGGTTTCCAATGAGAATAATTTGCAGCAATGGAATCATGCTAGTCCTAAAAGTAACACAAATTTGTGCATGGTGCAAGGTTTCAATAGCTTTGAAACTTCAAGTGGTAGCTATGGATCCATATTCAATAATGCAAAAGAGAAGCAAAATGGTGAAAGTTCATGTGGATGGCTATACTCTGAACCAAATGTCCCTTGTGATGATGACGACGATGATGATAGCTTAATAAAAGAGGCGGAAACACATGAATCCGTCTTGAAGAAGCGATCTTCTATGGGGGGAAACATGCAACCTGCCAATGCAAAGAAGCCATGCACAGCTGCAAGTAAGAAAGAAAAACATAAGTCAAATCCATCCAAAGATCCTCAAAGTGTTGCTGCCAAGAATAGAAGAGAGAGAATAAGTGAGAGGCTCAAGATCCTACAAGAACTTGTGCCAAATGGTTCCAAGGTTGATTTGGTTACCATGTTGGAGAAAGCAATTAGTTATGTGAAGTTTCTTCAGTTGCAAGTGAAGGTGTTGGCAGCTGATGAATTTTGGCCTGTCAATGGTGGAAAAGCTCCTGACATAGGTCAAGTAAAACAAGCAATTGATGCAATTCTTTCATCTCAAAGATGA
Protein sequence

>MsaT028260.1

MALANNNILHCIFDETTMEINSVMSHKKSMIEEEDGSQSTNGLSNDSASASVITNSPTLCRKGHVYNNNTSYELEEESLINFKGNDEYYNNLMQGSESLLSFQQSWMVSNENNLQQWNHASPKSNTNLCMVQGFNSFETSSGSYGSIFNNAKEKQNGESSCGWLYSEPNVPCDDDDDDDSLIKEAETHESVLKKRSSMGGNMQPANAKKPCTAASKKEKHKSNPSKDPQSVAAKNRRERISERLKILQELVPNGSKVDLVTMLEKAISYVKFLQLQVKVLAADEFWPVNGGKAPDIGQVKQAIDAILSSQR*