AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001072


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001072 MtrunA17_Chr1g0158941 92.282 298 18 1 1 298 1 293 0.0 530
MsaG001072 MtrunA17_Chr3g0126381 64.677 201 45 6 121 297 1 199 5.34e-73 223
MsaG001072 MtrunA17_Chr2g0287761 50.485 206 81 2 92 297 1 185 1.23e-62 196
MsaG001072 MtrunA17_Chr0c01g0489461 37.795 254 135 4 43 295 156 387 2.41e-49 168
MsaG001072 MtrunA17_Chr7g0273081 37.931 232 119 5 66 295 93 301 5.05e-38 136
MsaG001072 MtrunA17_Chr3g0132471 35.391 243 138 4 54 293 79 305 3.63e-37 134
MsaG001072 MtrunA17_Chr1g0191571 38.318 214 102 5 91 296 135 326 1.41e-36 133
MsaG001072 MtrunA17_Chr8g0366551 35.468 203 97 5 91 286 123 298 2.78e-32 121
MsaG001072 MtrunA17_Chr3g0126361 53.846 130 37 7 15 123 5 132 7.15e-30 110
MsaG001072 MtrunA17_Chr5g0426851 30.822 292 152 9 27 295 23 287 2.01e-28 110
MsaG001072 MtrunA17_Chr8g0345871 30.769 273 145 5 40 297 115 358 2.64e-28 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001072 AT5G53210.1 47.429 350 113 7 19 297 14 363 2.14e-86 263
MsaG001072 AT5G53210.2 44.109 331 114 7 19 278 14 344 1.28e-71 225
MsaG001072 AT3G06120.1 46.377 207 95 3 92 297 1 192 3.10e-54 175
MsaG001072 AT3G24140.1 41.048 229 123 2 69 297 177 393 4.85e-49 168
MsaG001072 AT3G24140.2 41.048 229 123 2 69 297 177 393 5.20e-49 168
MsaG001072 AT1G72210.1 34.404 218 97 6 91 295 124 308 1.45e-30 117
MsaG001072 AT1G72210.2 35.000 200 85 5 91 278 124 290 2.21e-29 114
MsaG001072 AT4G01460.1 35.885 209 112 3 90 297 113 300 5.46e-28 110
MsaG001072 AT4G01460.2 35.885 209 112 3 90 297 113 300 5.46e-28 110
MsaG001072 AT1G22490.1 34.300 207 111 4 91 296 114 296 6.30e-27 107
MsaG001072 AT1G22490.2 35.106 188 98 3 91 278 114 277 2.61e-25 103
MsaG001072 AT2G46810.2 33.493 209 106 3 91 297 120 297 5.93e-25 102
MsaG001072 AT2G46810.3 33.493 209 106 3 91 297 180 357 2.36e-24 101
MsaG001072 AT2G46810.1 33.493 209 106 3 91 297 192 369 2.80e-24 101
MsaG001072 AT5G65320.1 33.333 219 120 5 79 295 93 287 2.68e-23 97.4
MsaG001072 AT3G61950.2 31.280 211 107 4 91 297 126 302 1.97e-21 92.4
MsaG001072 AT3G61950.1 31.280 211 107 4 91 297 177 353 3.76e-21 92.4
MsaG001072 AT2G46810.4 32.275 189 96 2 91 278 120 277 1.73e-20 90.1
MsaG001072 AT5G65320.2 33.500 200 109 4 79 278 93 268 3.52e-20 88.6
MsaG001072 AT5G46690.1 33.838 198 129 1 91 286 87 284 5.06e-19 86.3
MsaG001072 AT3G61950.6 31.638 177 85 2 91 265 126 268 7.69e-19 85.1
MsaG001072 AT3G61950.3 31.638 177 85 2 91 265 177 319 1.09e-18 85.5
MsaG001072 AT5G46690.2 56.164 73 30 1 91 161 87 159 2.13e-18 84.0

Find 36 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTTGTTTCTTGGATTCT+AGG 0.149526 1:+14728252 None:intergenic
GCTATACTTGTTCACTATTA+AGG 0.194492 1:-14727880 MsaT001072.1:intron
TATGGAGTTCTTGGACTAAT+TGG 0.233920 1:+14728170 None:intergenic
AACCGTTTCGTCACGAATTC+CGG 0.237314 1:-14727988 MsaT001072.1:CDS
CTCATTGATGTTATCATTGA+TGG 0.240583 1:+14728082 None:intergenic
AGCCATTGATATGGAGTTCT+TGG 0.282669 1:+14728161 None:intergenic
TTTCTTAATAAAATGTTTGC+TGG 0.293141 1:+14727307 None:intergenic
CTAATTGGTAAGATTATTCT+AGG 0.295024 1:+14728185 None:intergenic
CATTGTTGTAGCCATTGATA+TGG 0.334687 1:+14728152 None:intergenic
ATATTCAATGAAACTGAGTT+TGG 0.348570 1:-14728927 MsaT001072.1:CDS
AACAAGGTGTCATGATCTAT+TGG 0.372909 1:+14728960 None:intergenic
ACCGTTTCGTCACGAATTCC+GGG 0.393233 1:-14727987 MsaT001072.1:CDS
TGTGACTTCTTCAATTATAG+AGG 0.399402 1:-14728754 MsaT001072.1:CDS
ATGGAAGAAGCTGAAGAAGT+TGG 0.426375 1:+14728101 None:intergenic
GGACTTAGTGGTAAAGGTCT+TGG 0.429539 1:+14728206 None:intergenic
TTCGTCACGAATTCCGGGGC+AGG 0.440139 1:-14727982 MsaT001072.1:CDS
AAGATTATTCTAGGACTTAG+TGG 0.440624 1:+14728194 None:intergenic
ATTCTAGGACTTAGTGGTAA+AGG 0.492814 1:+14728200 None:intergenic
CCCCGGAATTCGTGACGAAA+CGG 0.495669 1:+14727986 None:intergenic
TGTCGCGAATTCAACATCTT+CGG 0.496233 1:-14728057 MsaT001072.1:CDS
GTACAAAATGGAAACTCAAA+AGG 0.509601 1:-14728985 None:intergenic
CAAGTTCTTCAGCACTGAGT+TGG 0.510419 1:+14727340 None:intergenic
GTCCAAGAACTCCATATCAA+TGG 0.523072 1:-14728163 MsaT001072.1:CDS
ATCTTCGGTTGCTGATGTTG+AGG 0.535328 1:-14728042 MsaT001072.1:CDS
ATAGAGGAACAAAACAATGA+TGG 0.547852 1:-14728738 MsaT001072.1:CDS
TGAAACTGAGTTTGGTTCAG+AGG 0.550414 1:-14728919 MsaT001072.1:CDS
TTGGAGATGGCTCAGATGAA+AGG 0.570619 1:+14728120 None:intergenic
ACATCGTATGTCGCATATCA+CGG 0.587471 1:-14728712 MsaT001072.1:CDS
GATCAAGCATCAATAGTTGA+AGG 0.590664 1:-14728317 MsaT001072.1:CDS
AATAGTGAACAAGTATAGCA+TGG 0.592880 1:+14727884 None:intergenic
GAAGCTGAAGAAGTTGGAGA+TGG 0.605113 1:+14728107 None:intergenic
ATTATTCTAAGAGCCTGCCC+CGG 0.625886 1:+14727969 None:intergenic
CCGTTTCGTCACGAATTCCG+GGG 0.670932 1:-14727986 MsaT001072.1:CDS
CAATGGCTACAACAATGTGG+TGG 0.701552 1:-14728146 MsaT001072.1:CDS
TATCAATGGCTACAACAATG+TGG 0.711948 1:-14728149 MsaT001072.1:CDS
GAATATATCAGATAACAACA+AGG 0.741545 1:+14728944 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 14727311 14729000 14727311 ID=MsaG001072
Chr1 mRNA 14727311 14729000 14727311 ID=MsaT001072.1;Parent=MsaG001072
Chr1 exon 14727311 14727376 14727311 ID=MsaT001072.1.exon3;Parent=MsaT001072.1
Chr1 CDS 14727311 14727376 14727311 ID=cds.MsaT001072.1;Parent=MsaT001072.1
Chr1 exon 14727881 14728342 14727881 ID=MsaT001072.1.exon2;Parent=MsaT001072.1
Chr1 CDS 14727881 14728342 14727881 ID=cds.MsaT001072.1;Parent=MsaT001072.1
Chr1 exon 14728632 14729000 14728632 ID=MsaT001072.1.exon1;Parent=MsaT001072.1
Chr1 CDS 14728632 14729000 14728632 ID=cds.MsaT001072.1;Parent=MsaT001072.1
Gene Sequence

>MsaT001072.1

ATGGAAACTCAAAAGGCTCCAATAGATCATGACACCTTGTTGTTATCTGATATATTCAATGAAACTGAGTTTGGTTCAGAGGATCTATTTTCCATTTTGGAAAACTTCAATAATTTTTCTCCCATTATCAATGACCAAAACTCAAAAACAACATCTTCAAGTGCTCCTCAAGTTTCTGAAAATGAGCATGCTGAGACATCACAGAAATGCAAGAGACAGAAGATTGTGACTTCTTCAATTATAGAGGAACAAAACAATGATGGACAACATCGTATGTCGCATATCACGGTCGAACGCAATCGAAGAAAGCAAATGAATGAGCAGCTATCTATCTTGAAGTCACTTATGCCTTGCTTTTATGTCAAAAGAGGAGATCAAGCATCAATAGTTGAAGGTGTAATTGATTACATCAACGAGTTACATCAACTACTACAATGCCTAGAATCCAAGAAACAAAGAAAAGTTTACAGTGAAGTAACAAGTCCAAGACCTTTACCACTAAGTCCTAGAATAATCTTACCAATTAGTCCAAGAACTCCATATCAATGGCTACAACAATGTGGTGGTTACCTTTCATCTGAGCCATCTCCAACTTCTTCAGCTTCTTCCATCAATGATAACATCAATGAGCTTGTCGCGAATTCAACATCTTCGGTTGCTGATGTTGAGGTTAAGTTTTGTGGTTCACATGTGCTTTTGAAAACCGTTTCGTCACGAATTCCGGGGCAGGCTCTTAGAATAATGTCTGTTCTTGAAGATCTAATGCTTGAGATTGTTCATGTTAGAGTTAATACTGCTGATGAAACCATGCTATACTTGTTCACTATTAAGATTGGAATTGAATGCCAACTCAGTGCTGAAGAACTTGCTCAACAAATCCAGCAAACATTTTATTAA

Protein sequence

>MsaT001072.1

METQKAPIDHDTLLLSDIFNETEFGSEDLFSILENFNNFSPIINDQNSKTTSSSAPQVSENEHAETSQKCKRQKIVTSSIIEEQNNDGQHRMSHITVERNRRKQMNEQLSILKSLMPCFYVKRGDQASIVEGVIDYINELHQLLQCLESKKQRKVYSEVTSPRPLPLSPRIILPISPRTPYQWLQQCGGYLSSEPSPTSSASSINDNINELVANSTSSVADVEVKFCGSHVLLKTVSSRIPGQALRIMSVLEDLMLEIVHVRVNTADETMLYLFTIKIGIECQLSAEELAQQIQQTFY*