AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG012396


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012396 MtrunA17_Chr3g0079841 84.232 241 16 1 17 257 26 244 1.01e-143 404
MsaG012396 MtrunA17_Chr1g0213311 39.799 299 125 7 12 257 15 311 1.26e-53 179
MsaG012396 MtrunA17_Chr3g0143581 49.286 140 69 1 1 138 1 140 1.40e-40 138
MsaG012396 MtrunA17_Chr2g0320431 87.719 57 7 0 159 215 215 271 9.02e-25 99.8
MsaG012396 MtrunA17_Chr7g0214501 33.659 205 75 3 83 257 3 176 9.90e-20 86.7
MsaG012396 MtrunA17_Chr7g0214491 48.052 77 38 1 6 80 9 85 1.35e-16 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012396 AT3G13350.1 43.985 266 102 5 25 257 34 285 2.67e-62 199
MsaG012396 AT1G55650.1 39.683 252 118 7 24 257 27 262 5.78e-53 175
MsaG012396 AT1G04880.1 36.364 297 134 6 16 257 14 310 1.03e-48 167
MsaG012396 AT1G76110.1 36.559 279 131 5 21 257 28 302 1.20e-47 161

Find 69 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGTCTATACCTGTCTTTC+TGG 0.121212 3:+23570628 None:intergenic
TTCGTGATGCTAACCTCTTC+TGG 0.176030 3:-23573466 MsaT012396.1:CDS
GGAGCAATTAGTAGGAAAAT+TGG 0.205100 3:-23570676 MsaT012396.1:CDS
GTTCAGTCTCACGCGGATTT+TGG 0.242316 3:+23573534 None:intergenic
TGTTTCAAGCAATGCATCTA+AGG 0.259440 3:-23570854 MsaT012396.1:CDS
TATCAATGATTCACCTGTTC+AGG 0.286987 3:-23572034 MsaT012396.1:CDS
AGGTAATTGTAGATCGTAAA+TGG 0.317695 3:-23572332 MsaT012396.1:CDS
TGTGTAGGATTCCTACTATA+GGG 0.338046 3:-23572643 MsaT012396.1:intron
AGTGTCTGTGCTGGACTAAT+TGG 0.354657 3:+23570976 None:intergenic
GAGCAATTAGTAGGAAAATT+GGG 0.369568 3:-23570675 MsaT012396.1:CDS
CATAACAAGCGCATCATTCA+TGG 0.386953 3:-23572274 MsaT012396.1:CDS
AAGTCTATACCTGTCTTTCT+GGG 0.390289 3:+23570629 None:intergenic
CGTATTGGTTGTGAAGCTAT+TGG 0.406695 3:+23572068 None:intergenic
TTCATTGACTTACCCTGAAC+AGG 0.413930 3:+23572021 None:intergenic
TTGTGTAGGATTCCTACTAT+AGG 0.432421 3:-23572644 MsaT012396.1:intron
GTGATAAAGCAACGATAGAT+AGG 0.439414 3:+23572242 None:intergenic
TCGTGATGCTAACCTCTTCT+GGG 0.445073 3:-23573465 MsaT012396.1:CDS
CATGAATGATGCGCTTGTTA+TGG 0.445119 3:+23572275 None:intergenic
GAGTAGAGAGCGGTTGGAGG+AGG 0.454942 3:+23573497 None:intergenic
TCTAAGGGTTCTTCTATTGA+AGG 0.459768 3:-23570838 MsaT012396.1:intron
TCCTTGTGGCCTGCAAAATG+AGG 0.463327 3:+23570696 None:intergenic
ACAATTGACATGAAATTTGA+TGG 0.468681 3:-23570934 MsaT012396.1:CDS
ATATATAGTTACGGTGGACC+TGG 0.474943 3:-23570908 MsaT012396.1:CDS
GATAGCAGCACCGTCCGTAT+TGG 0.475279 3:+23572053 None:intergenic
ATCTCGTGGTGGTATTGAAA+AGG 0.485522 3:-23572579 MsaT012396.1:intron
GCAAAATGAGGGCTTTAGCC+TGG 0.485928 3:+23570708 None:intergenic
CTTCACTAACCAGGTGTTGA+GGG 0.490947 3:+23572183 None:intergenic
TCAGATTTGCAAACTATGCT+AGG 0.500294 3:-23570305 None:intergenic
CTCTATCCAGATGCTTTGAG+TGG 0.513745 3:-23572099 MsaT012396.1:intron
CATTGCTTGAAACATGATAC+AGG 0.516873 3:+23570863 None:intergenic
ATCAATGATTCACCTGTTCA+GGG 0.519797 3:-23572033 MsaT012396.1:intron
CCTTGTGGCCTGCAAAATGA+GGG 0.521599 3:+23570697 None:intergenic
TCTGACAGACCCAGAAAGAC+AGG 0.531673 3:-23570638 MsaT012396.1:intron
TTCCTACTAATTGCTCCTTG+TGG 0.533197 3:+23570682 None:intergenic
AGGTCAGAGTAGAGAGCGGT+TGG 0.533695 3:+23573491 None:intergenic
TCAGAGTAGAGAGCGGTTGG+AGG 0.537076 3:+23573494 None:intergenic
GGAAAATTGGGTTTGCGTGG+AGG 0.541228 3:-23570663 MsaT012396.1:CDS
CAATAGCTTCACAACCAATA+CGG 0.543956 3:-23572067 MsaT012396.1:CDS
CAAGTCCCTCCCTCAACACC+TGG 0.544933 3:-23572192 MsaT012396.1:intron
TGATGGCGGATATATAGTTA+CGG 0.545231 3:-23570917 MsaT012396.1:CDS
ATTAGTCCAGCACAGACACT+TGG 0.556813 3:-23570973 MsaT012396.1:CDS
GGCCACAAGGAGCAATTAGT+AGG 0.560286 3:-23570684 MsaT012396.1:CDS
GAAGAACCAAGTGTCTGTGC+TGG 0.560864 3:+23570967 None:intergenic
ATGCGCTTGTTATGGTATCT+CGG 0.562285 3:+23572283 None:intergenic
CTTCAACGAAGAGGTGATGC+AGG 0.562980 3:+23572606 None:intergenic
GTTTCAAGCAATGCATCTAA+GGG 0.563003 3:-23570853 MsaT012396.1:CDS
GTGTAGGATTCCTACTATAG+GGG 0.574437 3:-23572642 MsaT012396.1:intron
TTCGTTGAAGTAACATCTCG+TGG 0.581244 3:-23572593 MsaT012396.1:CDS
TCTTCACTAACCAGGTGTTG+AGG 0.585501 3:+23572182 None:intergenic
CTGGGTTCTGAACAGCTGAA+AGG 0.586271 3:-23570889 MsaT012396.1:CDS
GTAGGAAAATTGGGTTTGCG+TGG 0.592801 3:-23570666 MsaT012396.1:CDS
GAGCGGTTGGAGGAGGACAA+AGG 0.594063 3:+23573504 None:intergenic
CACTAACCAGGTGTTGAGGG+AGG 0.596662 3:+23572186 None:intergenic
AATTGTAGATCGTAAATGGA+AGG 0.598698 3:-23572328 MsaT012396.1:CDS
AAGAGGTGATGCAGGTCTAG+TGG 0.600590 3:+23572614 None:intergenic
ACACTTGGTTCTTCAGTGCG+TGG 0.611516 3:-23570958 MsaT012396.1:CDS
TGTAGATCGTAAATGGAAGG+AGG 0.611934 3:-23572325 MsaT012396.1:CDS
AGAGGTTAGCATCACGAACA+AGG 0.617590 3:+23573471 None:intergenic
ACTAACCAGGTGTTGAGGGA+GGG 0.618972 3:+23572187 None:intergenic
TATATAGTTACGGTGGACCT+GGG 0.620088 3:-23570907 MsaT012396.1:CDS
CTTTCAGCTGTTCAGAACCC+AGG 0.626176 3:+23570890 None:intergenic
AGCTTCACAACCAATACGGA+CGG 0.629115 3:-23572063 MsaT012396.1:CDS
TGTAGGATTCCTACTATAGG+GGG 0.629514 3:-23572641 MsaT012396.1:intron
ATTGACATGAAATTTGATGG+CGG 0.676313 3:-23570931 MsaT012396.1:CDS
AACAAGGTCAGAGTAGAGAG+CGG 0.693390 3:+23573487 None:intergenic
GAGATGTTACTTCAACGAAG+AGG 0.709606 3:+23572597 None:intergenic
TGGCGGATATATAGTTACGG+TGG 0.725652 3:-23570914 MsaT012396.1:CDS
TTTGTGAGTTCAGTCTCACG+CGG 0.743764 3:+23573527 None:intergenic
GTTGAAGTAACATCTCGTGG+TGG 0.754811 3:-23572590 MsaT012396.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 23570306 23573579 23570306 ID=MsaG012396
Chr3 mRNA 23570306 23573579 23570306 ID=MsaT012396.1;Parent=MsaG012396
Chr3 exon 23570306 23570323 23570306 ID=MsaT012396.1.exon7;Parent=MsaT012396.1
Chr3 CDS 23570306 23570323 23570306 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23570639 23570766 23570639 ID=MsaT012396.1.exon6;Parent=MsaT012396.1
Chr3 CDS 23570639 23570766 23570639 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23570839 23571003 23570839 ID=MsaT012396.1.exon5;Parent=MsaT012396.1
Chr3 CDS 23570839 23571003 23570839 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23572034 23572111 23572034 ID=MsaT012396.1.exon4;Parent=MsaT012396.1
Chr3 CDS 23572034 23572111 23572034 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23572193 23572352 23572193 ID=MsaT012396.1.exon3;Parent=MsaT012396.1
Chr3 CDS 23572193 23572352 23572193 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23572580 23572658 23572580 ID=MsaT012396.1.exon2;Parent=MsaT012396.1
Chr3 CDS 23572580 23572658 23572580 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Chr3 exon 23573422 23573579 23573422 ID=MsaT012396.1.exon1;Parent=MsaT012396.1
Chr3 CDS 23573422 23573579 23573422 ID=cds.MsaT012396.1;Parent=MsaT012396.1
Gene Sequence

>MsaT012396.1

ATGACAAGTAACCAGAATCAAAACCAAAATCCGCGTGAGACTGAACTCACAAACCTTTGTCCTCCTCCAACCGCTCTCTACTCTGACCTTGTTCGTGATGCTAACCTCTTCTGGGAAAAACTTCAATCTTTTCATGATTCGCTTGGTATCAAATTAGAGATTCCTACTATAGGGGGTAAGCCACTAGACCTGCATCACCTCTTCGTTGAAGTAACATCTCGTGGTGGTATTGAAAAGGTAATTGTAGATCGTAAATGGAAGGAGGTAATAATGAGCTTCAACTTCCGAGATACCATAACAAGCGCATCATTCATGGTGCGCAAGACCTATCTATCGTTGCTTTATCACTTTGAACAAGCGTATTATTTTTATAAGCAAGTCCCTCCCTCAACACCTGATGCTTTGAGTGGAAACGTTGCCAATAGCTTCACAACCAATACGGACGGTGCTGCTATCAATGATTCACCTGTTCAGGTTAGTCCAATTAGTCCAGCACAGACACTTGGTTCTTCAGTGCGTGGAACAATTGACATGAAATTTGATGGCGGATATATAGTTACGGTGGACCTGGGTTCTGAACAGCTGAAAGGTGTCCTGTATCATGTTTCAAGCAATGCATCTAAGGGTTCTTCTATTGAAGGAGTGGTTACAATTTCTTTTTTTGCTGAGAATTATGCCAGGCTAAAGCCCTCATTTTGCAGGCCACAAGGAGCAATTAGTAGGAAAATTGGGTTTGCGTGGAGGAATCTGACAGACCCAGAAAGACAGATTTGCAAACTATGCTAG

Protein sequence

>MsaT012396.1

MTSNQNQNQNPRETELTNLCPPPTALYSDLVRDANLFWEKLQSFHDSLGIKLEIPTIGGKPLDLHHLFVEVTSRGGIEKVIVDRKWKEVIMSFNFRDTITSASFMVRKTYLSLLYHFEQAYYFYKQVPPSTPDALSGNVANSFTTNTDGAAINDSPVQVSPISPAQTLGSSVRGTIDMKFDGGYIVTVDLGSEQLKGVLYHVSSNASKGSSIEGVVTISFFAENYARLKPSFCRPQGAISRKIGFAWRNLTDPERQICKLC*