AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009616

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009616 MtrunA17_Chr2g0315381 92.073 164 13 0 1 164 1 164 2.73e-100 293
MsaG009616 MtrunA17_Chr2g0315361 80.357 168 29 3 1 164 1 168 1.91e-81 245
MsaG009616 MtrunA17_Chr2g0315371 64.767 193 54 5 1 187 1 185 1.11e-77 235
MsaG009616 MtrunA17_Chr7g0244971 34.595 185 85 6 11 187 11 167 1.81e-21 89.7
MsaG009616 MtrunA17_Chr7g0244981 34.810 158 82 2 7 164 6 142 1.27e-20 87.4
MsaG009616 MtrunA17_Chr8g0334541 36.054 147 63 3 18 164 8 123 4.81e-18 80.5
MsaG009616 MtrunA17_Chr2g0315391 42.342 111 54 6 8 116 6 108 1.67e-17 75.1
MsaG009616 MtrunA17_Chr2g0315351 42.342 111 54 6 8 116 6 108 6.84e-17 73.6
MsaG009616 MtrunA17_Chr8g0350621 35.484 155 74 7 10 164 3 131 2.09e-16 75.5
MsaG009616 MtrunA17_Chr8g0350641 33.913 115 54 3 56 164 41 139 1.62e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAAGATCTCCAGCAATTA+AGG 0.210019 2:+62438930 None:intergenic
CAACAAGCTTGAGGAGGATT+TGG 0.242987 2:-62438794 MsaT009616.1:CDS
AGCCACATCATTGGAGTCTT+TGG 0.282004 2:+62438858 None:intergenic
ATTGCTTTCTTGCCATTTGT+TGG 0.339828 2:+62439072 None:intergenic
TGACTTATCATCATATGTTA+TGG 0.341599 2:+62438999 None:intergenic
CCAGCAATTAAGGGTAAAAC+TGG 0.365538 2:+62438940 None:intergenic
AGGCGTGGCAGTCTTGCGTC+AGG 0.372828 2:-62433075 MsaT009616.1:CDS
CTGCTTTGGCTTCCAACAAA+TGG 0.408980 2:-62439084 MsaT009616.1:CDS
GGTCATACTTGGAGAAAGTA+TGG 0.428672 2:-62435891 MsaT009616.1:CDS
TAAGGTCAATTTCGCCAACT+TGG 0.434948 2:-62435944 MsaT009616.1:intron
TGATTGATGACGGTCATACT+TGG 0.450773 2:-62435902 MsaT009616.1:CDS
TATTGGAACAGCCACATCAT+TGG 0.456556 2:+62438849 None:intergenic
GGATAATGGAGAATCTGCTT+TGG 0.464816 2:-62439098 None:intergenic
ACAAGATCTCCAGCAATTAA+GGG 0.474137 2:+62438931 None:intergenic
AATGGTGGTCGCGGTCGAAA+TGG 0.493406 2:-62431918 MsaT009616.1:CDS
AAGGTCAATTTCGCCAACTT+GGG 0.514084 2:-62435943 MsaT009616.1:CDS
ATGGAAGAAGAGCTTATAAG+AGG 0.516162 2:-62439051 MsaT009616.1:CDS
ACTGCTGGAAGTTTGCGTCC+AGG 0.533619 2:-62433034 MsaT009616.1:intron
AGTGGTGGCAATGGTGGTCG+CGG 0.543550 2:-62431927 MsaT009616.1:CDS
AGTCAAATATAGAAGTGAAA+GGG 0.551702 2:-62438981 MsaT009616.1:CDS
AAGTCAAATATAGAAGTGAA+AGG 0.557104 2:-62438982 MsaT009616.1:CDS
AAGCTTGAGGAGGATTTGGA+TGG 0.559719 2:-62438790 MsaT009616.1:CDS
TCGCAAATACGAAATACTAC+AGG 0.562971 2:-62435857 MsaT009616.1:intron
ACTTCAATATTGATTGATGA+CGG 0.580045 2:-62435912 MsaT009616.1:CDS
AACGAATTGCAACAAGCTTG+AGG 0.590596 2:-62438803 MsaT009616.1:CDS
GGCGTGGCAGTCTTGCGTCA+GGG 0.590904 2:-62433074 MsaT009616.1:CDS
TTTCTCTTGTTCGACCCTGT+AGG 0.601177 2:+62438730 None:intergenic
AACAAATGGCAAGAAAGCAA+TGG 0.602679 2:-62439070 MsaT009616.1:CDS
CGCCAAAGACTCCAATGATG+TGG 0.609286 2:-62438860 MsaT009616.1:CDS
GCTTATAAGAGGACGTGACA+TGG 0.611904 2:-62439040 MsaT009616.1:CDS
AGAAGTGGCAGTGGTGGCAA+TGG 0.615838 2:-62431936 MsaT009616.1:CDS
TCAATGATTTAAGTACCTCA+CGG 0.616583 2:+62438908 None:intergenic
AGTGGCAGTGGTGGCAATGG+TGG 0.630549 2:-62431933 MsaT009616.1:CDS
GTAGATGCAAGAAGTGGCAG+TGG 0.639668 2:-62431945 MsaT009616.1:intron
TGCTGGAGATCTTGTCCGTG+AGG 0.652783 2:-62438923 MsaT009616.1:CDS
GAATTGCAACAAGCTTGAGG+AGG 0.664236 2:-62438800 MsaT009616.1:CDS
GATGCAAGAAGTGGCAGTGG+TGG 0.664473 2:-62431942 MsaT009616.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 62430679 62439115 62430679 ID=MsaG009616
Chr2 mRNA 62430679 62439115 62430679 ID=MsaT009616.1;Parent=MsaG009616
Chr2 exon 62430679 62430700 62430679 ID=MsaT009616.1.exon5;Parent=MsaT009616.1
Chr2 CDS 62430679 62430700 62430679 ID=cds.MsaT009616.1;Parent=MsaT009616.1
Chr2 exon 62431884 62431963 62431884 ID=MsaT009616.1.exon4;Parent=MsaT009616.1
Chr2 CDS 62431884 62431963 62431884 ID=cds.MsaT009616.1;Parent=MsaT009616.1
Chr2 exon 62433035 62433095 62433035 ID=MsaT009616.1.exon3;Parent=MsaT009616.1
Chr2 CDS 62433035 62433095 62433035 ID=cds.MsaT009616.1;Parent=MsaT009616.1
Chr2 exon 62435858 62435962 62435858 ID=MsaT009616.1.exon2;Parent=MsaT009616.1
Chr2 CDS 62435858 62435962 62435858 ID=cds.MsaT009616.1;Parent=MsaT009616.1
Chr2 exon 62438730 62439115 62438730 ID=MsaT009616.1.exon1;Parent=MsaT009616.1
Chr2 CDS 62438730 62439115 62438730 ID=cds.MsaT009616.1;Parent=MsaT009616.1
Gene Sequence

>MsaT009616.1

ATGGAGAATCTGCTTTGGCTTCCAACAAATGGCAAGAAAGCAATGGAAGAAGAGCTTATAAGAGGACGTGACATGGCAAATCAATTACTTGAAGCCATAACATATGATGATAAGTCAAATATAGAAGTGAAAGGGTCAAACTCAAAATCATCACCAGTTTTACCCTTAATTGCTGGAGATCTTGTCCGTGAGGTACTTAAATCATTGACAAATACACTTTTACTCTTGAATAACGCCAAAGACTCCAATGATGTGGCTGTTCCAATAAGTGTTAGTGATTTTTCTTTCTCAACGAATTGCAACAAGCTTGAGGAGGATTTGGATGGATCTTGCAAGAAACTAAAGACTCTCAACACCAAAAATCCTACAGGGTCGAACAAGAGAAAGTCAATTTCGCCAACTTGGGAAAAAAGCACTTCAATATTGATTGATGACGGTCATACTTGGAGAAAGTATGGACAAAAAAAGATCGCAAATACGAAATACTACAGGCGTGGCAGTCTTGCGTCAGGGCACAAAAAACTGTGTTCACTGCTGGAAGTTTGCGTCCAGATGCAAGAAGTGGCAGTGGTGGCAATGGTGGTCGCGGTCGAAATGGATATTCATGTTCACTTGAAATGTTGTTATCGAAAAAATAAAACGACCACTTTTTAA
Protein sequence

>MsaT009616.1

MENLLWLPTNGKKAMEEELIRGRDMANQLLEAITYDDKSNIEVKGSNSKSSPVLPLIAGDLVREVLKSLTNTLLLLNNAKDSNDVAVPISVSDFSFSTNCNKLEEDLDGSCKKLKTLNTKNPTGSNKRKSISPTWEKSTSILIDDGHTWRKYGQKKIANTKYYRRGSLASGHKKLCSLLEVCVQMQEVAVVAMVVAVEMDIHVHLKCCYRKNKTTTF*