AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG028251


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028251 MtrunA17_Chr5g0435131 93.064 173 6 2 1 173 1 167 4.03e-113 320
MsaG028251 MtrunA17_Chr4g0025901 48.214 168 77 4 6 166 4 168 5.82e-39 132
MsaG028251 MtrunA17_Chr4g0025911 41.667 168 91 4 3 167 1 164 1.92e-32 115
MsaG028251 MtrunA17_Chr1g0177881 59.420 69 28 0 97 165 102 170 3.09e-23 92.0
MsaG028251 MtrunA17_Chr7g0267111 36.207 174 90 4 6 161 4 174 9.20e-23 91.3
MsaG028251 MtrunA17_Chr8g0390531 45.333 75 41 0 88 162 249 323 9.17e-18 80.1
MsaG028251 MtrunA17_Chr3g0141471 50.725 69 34 0 94 162 195 263 1.93e-12 64.7
MsaG028251 MtrunA17_Chr5g0432531 39.189 74 45 0 88 161 177 250 1.53e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028251 AT3G52525.1 60.317 63 25 0 98 160 67 129 8.49e-21 85.5
MsaG028251 AT5G19650.1 53.030 66 31 0 97 162 154 219 9.64e-21 87.0
MsaG028251 AT2G36026.1 60.656 61 24 0 102 162 91 151 1.52e-19 82.8
MsaG028251 AT2G18500.1 48.387 62 32 0 95 156 224 285 3.36e-16 76.3
MsaG028251 AT5G22240.1 45.205 73 40 0 91 163 90 162 2.99e-15 71.6
MsaG028251 AT1G06920.1 40.580 69 41 0 94 162 240 308 9.11e-13 66.6

Find 36 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGAAGAACTGAGGCTATT+AGG 0.218529 5:-59568371 None:intergenic
CCATCACCACAAAGCTTCTT+AGG 0.222603 5:-59568716 None:intergenic
CTCTATACTTCAAATGATAT+TGG 0.278958 5:+59568571 MsaT028251.1:CDS
TGTCATTGTTGAAGCGTTCA+TGG 0.333768 5:+59568673 MsaT028251.1:CDS
TGGAAGAACTGAGGCTATTA+GGG 0.352036 5:-59568370 None:intergenic
GCAACAATAATAATAATTAT+AGG 0.367952 5:+59568468 MsaT028251.1:CDS
AGAGTTTCGAAAATCTTCAT+AGG 0.391478 5:-59568552 None:intergenic
CATACCCACTAGACAAATTC+CGG 0.398561 5:-59570883 None:intergenic
AGAGGGTTCAAGTACGTTAG+AGG 0.399454 5:-59568312 None:intergenic
CCTAAGAAGCTTTGTGGTGA+TGG 0.449802 5:+59568716 MsaT028251.1:CDS
ATATTTCCTAAGAAGCTTTG+TGG 0.453226 5:+59568710 MsaT028251.1:CDS
AGTAAGAATGAGCAAGAATT+CGG 0.482383 5:+59574315 MsaT028251.1:CDS
TTTGTCGTCGGTGTTTGCGT+TGG 0.505988 5:-59568408 None:intergenic
GAGTTTCGAAAATCTTCATA+GGG 0.516842 5:-59568551 None:intergenic
TTCTCATCTAACAAAAGTTG+TGG 0.528866 5:+59568272 MsaT028251.1:CDS
TTGGCAGGATTGAACAATTG+TGG 0.537980 5:+59574282 MsaT028251.1:intron
CGCGCCGGAATTTGTCTAGT+GGG 0.548567 5:+59570879 MsaT028251.1:CDS
ACAAATTCCGGCGCGGTGGT+CGG 0.551859 5:-59570871 None:intergenic
AGATAGCATTGCCGTTGAGA+AGG 0.559747 5:+59568517 MsaT028251.1:CDS
GAGGGTTCAAGTACGTTAGA+GGG 0.563551 5:-59568311 None:intergenic
TGCGTTGGCGTCGTGAGAAG+TGG 0.578810 5:-59568393 None:intergenic
GTTGTCGTTCGAGATGGTTG+TGG 0.580948 5:-59568441 None:intergenic
TGCCGTTGAGAAGGAATCGA+AGG 0.586299 5:+59568526 MsaT028251.1:CDS
GCTGCCGTTGTCGTTCGAGA+TGG 0.592579 5:-59568447 None:intergenic
GTGACAACCGACCACCGCGC+CGG 0.603052 5:+59570864 MsaT028251.1:CDS
CCGCGCCGGAATTTGTCTAG+TGG 0.615316 5:+59570878 MsaT028251.1:CDS
CTCCTTCGATTCCTTCTCAA+CGG 0.620361 5:-59568528 None:intergenic
ACGCTTCAACAATGACATGA+TGG 0.645246 5:-59568667 None:intergenic
GGAAGTGAAATCTTTGTCGT+CGG 0.649275 5:-59568420 None:intergenic
ACAACCATCTCGAACGACAA+CGG 0.654369 5:+59568443 MsaT028251.1:CDS
CTAGACAAATTCCGGCGCGG+TGG 0.658511 5:-59570875 None:intergenic
GTTGGCGTCGTGAGAAGTGG+TGG 0.667857 5:-59568390 None:intergenic
TGGTGATGGTAGACGTGTGA+AGG 0.668871 5:+59568730 MsaT028251.1:CDS
AAGAATGAGCAAGAATTCGG+TGG 0.692590 5:+59574318 MsaT028251.1:CDS
GAGAAGTGGTGGAAGAACTG+AGG 0.698276 5:-59568379 None:intergenic
CCACTAGACAAATTCCGGCG+CGG 0.773703 5:-59570878 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 59568230 59574365 59568230 ID=MsaG028251
Chr5 mRNA 59568230 59574365 59568230 ID=MsaT028251.1;Parent=MsaG028251
Chr5 exon 59568230 59568756 59568230 ID=MsaT028251.1.exon1;Parent=MsaT028251.1
Chr5 CDS 59568230 59568756 59568230 ID=cds.MsaT028251.1;Parent=MsaT028251.1
Chr5 exon 59570854 59570900 59570854 ID=MsaT028251.1.exon2;Parent=MsaT028251.1
Chr5 CDS 59570854 59570900 59570854 ID=cds.MsaT028251.1;Parent=MsaT028251.1
Chr5 exon 59574289 59574365 59574289 ID=MsaT028251.1.exon3;Parent=MsaT028251.1
Chr5 CDS 59574289 59574365 59574289 ID=cds.MsaT028251.1;Parent=MsaT028251.1
Gene Sequence

>MsaT028251.1

ATGTCTTTCAATTTCAACAAGAGAAGCCTCGTCAAAACCCTTTTCTCATCTAACAAAAGTTGTGGTTGCATCAAAATAAAACCCTCTAACGTACTTGAACCCTCTCAAAAACCTAAAATCTCCTTTTGTCAAAACACAAACCCTAATAGCCTCAGTTCTTCCACCACTTCTCACGACGCCAACGCAAACACCGACGACAAAGATTTCACTTCCACAACCATCTCGAACGACAACGGCAGCAACAATAATAATAATTATAGGATTTTAAAGCCGGGTACAAAACTCATAGATAGCATTGCCGTTGAGAAGGAATCGAAGGAGCCCTATGAAGATTTTCGAAACTCTATACTTCAAATGATATTGGAGAGAGAGATTTATTCAGAAAATGATCTTCAAGAATTACTTGAGTGTTTTCTTCAGCTTAATGCAAAGTGTCACCATCATGTCATTGTTGAAGCGTTCATGGAGACATGTGAAGAAATATTTCCTAAGAAGCTTTGTGGTGATGGTAGACGTGTGAAGGACATATCTGGGCACGTGACAACCGACCACCGCGCCGGAATTTGTCTAGTGGGATTGAACAATTGTGGACAAAAGAAGAGTAAGAATGAGCAAGAATTCGGTGGTGCAATGTTAGAAGAAAAGAATTAG

Protein sequence

>MsaT028251.1

MSFNFNKRSLVKTLFSSNKSCGCIKIKPSNVLEPSQKPKISFCQNTNPNSLSSSTTSHDANANTDDKDFTSTTISNDNGSNNNNNYRILKPGTKLIDSIAVEKESKEPYEDFRNSILQMILEREIYSENDLQELLECFLQLNAKCHHHVIVEAFMETCEEIFPKKLCGDGRRVKDISGHVTTDHRAGICLVGLNNCGQKKSKNEQEFGGAMLEEKN*