AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1449380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1449380 MtrunA17_Chr2g0281511 85.246 122 18 0 1 122 1 122 4.02e-75 218
Msa1449380 MtrunA17_Chr2g0309121 81.967 122 21 1 1 122 1 121 7.39e-70 205
Msa1449380 MtrunA17_Chr3g0081891 84.810 79 12 0 1 79 1 79 7.79e-45 140
Msa1449380 MtrunA17_Chr7g0276661 35.115 131 65 4 7 119 38 166 3.86e-21 83.2
Msa1449380 MtrunA17_Chr0c01g0489371 41.758 91 51 1 22 110 224 314 2.78e-17 75.9
Msa1449380 MtrunA17_Chr8g0356961 40.449 89 51 1 24 110 77 165 1.10e-16 71.6
Msa1449380 MtrunA17_Chr8g0372431 29.897 97 68 0 24 120 6 102 1.25e-16 69.7
Msa1449380 MtrunA17_Chr6g0485871 33.721 86 56 1 24 108 214 299 8.65e-13 63.2
Msa1449380 MtrunA17_Chr8g0356951 37.363 91 53 2 24 110 217 307 1.21e-12 62.8
Msa1449380 MtrunA17_Chr5g0434641 34.066 91 58 1 22 110 208 298 1.61e-12 62.4
Msa1449380 MtrunA17_Chr7g0228081 31.250 80 55 0 41 120 13 92 4.05e-12 57.8
Msa1449380 MtrunA17_Chr5g0430431 42.623 61 35 0 56 116 194 254 8.33e-12 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 23 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGTTACTGCTTCTATTT+TGG 0.123735 tig0032542:-4624 Msa1449380:CDS
AAAATTCCGATGTTCATTAT+TGG 0.199581 tig0032542:-4652 Msa1449380:CDS
GAAGTCAATGGTGCTGAATT+AGG 0.200131 tig0032542:-4683 Msa1449380:CDS
TACCAGTTTCTTCATCAAAA+AGG 0.252196 tig0032542:+4433 None:intergenic
TGTATGCTACCGTCGTTAAC+TGG 0.297739 tig0032542:-4266 Msa1449380:CDS
CCTCGACGTGTTGCCGAGAA+TGG 0.307864 tig0032542:-4483 Msa1449380:CDS
CGGTCAATAATCCTCCTAAT+AGG 0.355854 tig0032542:-4290 Msa1449380:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 tig0032542:-4606 Msa1449380:intron
AAGTCAATGGTGCTGAATTA+GGG 0.416476 tig0032542:-4682 Msa1449380:CDS
ACGGTAGCATACATCCTATT+AGG 0.440754 tig0032542:+4276 None:intergenic
ATTGGTATACAAACCATTCT+CGG 0.470714 tig0032542:+4470 None:intergenic
GTATGCTACCGTCGTTAACT+GGG 0.522932 tig0032542:-4265 Msa1449380:CDS
GCATGGATCAGAAATACATA+GGG 0.559318 tig0032542:-4374 Msa1449380:CDS
AGCATGGATCAGAAATACAT+AGG 0.564126 tig0032542:-4375 Msa1449380:CDS
CTTGAAAAGTGCCTAAAAGT+TGG 0.570138 tig0032542:-4330 Msa1449380:CDS
AGAAATACATAGGGAGAGGA+TGG 0.573439 tig0032542:-4365 Msa1449380:CDS
GATCAGAAATACATAGGGAG+AGG 0.587262 tig0032542:-4369 Msa1449380:CDS
TCACACTGCGTCAAGAAGCA+TGG 0.587686 tig0032542:-4391 Msa1449380:CDS
CCATTCTCGGCAACACGTCG+AGG 0.599354 tig0032542:+4483 None:intergenic
GAGATTGGAGTTGAAGTCAA+TGG 0.619642 tig0032542:-4695 Msa1449380:CDS
GTAGCATACATCCTATTAGG+AGG 0.633251 tig0032542:+4279 None:intergenic
ATACTTCCAATAATGAACAT+CGG 0.646998 tig0032542:+4646 None:intergenic
TAATCAGTCCCAGTTAACGA+CGG 0.733495 tig0032542:+4257 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCCGATGTTCATTAT+TGG - tig0032542:4309-4328 Msa1449380:CDS 25.0%
! ATACTTCCAATAATGAACAT+CGG + tig0032542:4318-4337 None:intergenic 25.0%
!! TAATGTTACTGCTTCTATTT+TGG - tig0032542:4337-4356 Msa1449380:CDS 25.0%
!! AAGGAGAATTTTAGATTGAT+TGG + tig0032542:4512-4531 None:intergenic 25.0%
! TTTGGATGGAAACAATGTTT+TGG - tig0032542:4355-4374 Msa1449380:CDS 30.0%
ATTGGTATACAAACCATTCT+CGG + tig0032542:4494-4513 None:intergenic 30.0%
TACCAGTTTCTTCATCAAAA+AGG + tig0032542:4531-4550 None:intergenic 30.0%
! AAACAACATCACCAACTTTT+AGG + tig0032542:4645-4664 None:intergenic 30.0%
! AAGTCAATGGTGCTGAATTA+GGG - tig0032542:4279-4298 Msa1449380:CDS 35.0%
!! GTTACTGCTTCTATTTTGGA+TGG - tig0032542:4341-4360 Msa1449380:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG - tig0032542:4362-4381 Msa1449380:CDS 35.0%
! CTCCTTTTTGATGAAGAAAC+TGG - tig0032542:4526-4545 Msa1449380:intron 35.0%
AGCATGGATCAGAAATACAT+AGG - tig0032542:4586-4605 Msa1449380:intron 35.0%
GCATGGATCAGAAATACATA+GGG - tig0032542:4587-4606 Msa1449380:intron 35.0%
!! CTTGAAAAGTGCCTAAAAGT+TGG - tig0032542:4631-4650 Msa1449380:CDS 35.0%
!!! TGGTGATGTTGTTTTGTTCA+CGG - tig0032542:4651-4670 Msa1449380:CDS 35.0%
GAGATTGGAGTTGAAGTCAA+TGG - tig0032542:4266-4285 Msa1449380:CDS 40.0%
! GAAGTCAATGGTGCTGAATT+AGG - tig0032542:4278-4297 Msa1449380:CDS 40.0%
GATCAGAAATACATAGGGAG+AGG - tig0032542:4592-4611 Msa1449380:intron 40.0%
AGAAATACATAGGGAGAGGA+TGG - tig0032542:4596-4615 Msa1449380:intron 40.0%
CGGTCAATAATCCTCCTAAT+AGG - tig0032542:4671-4690 Msa1449380:CDS 40.0%
GTAGCATACATCCTATTAGG+AGG + tig0032542:4685-4704 None:intergenic 40.0%
ACGGTAGCATACATCCTATT+AGG + tig0032542:4688-4707 None:intergenic 40.0%
TGTATGCTACCGTCGTTAAC+TGG - tig0032542:4695-4714 Msa1449380:CDS 45.0%
GTATGCTACCGTCGTTAACT+GGG - tig0032542:4696-4715 Msa1449380:CDS 45.0%
TCACACTGCGTCAAGAAGCA+TGG - tig0032542:4570-4589 Msa1449380:intron 50.0%
CCATTCTCGGCAACACGTCG+AGG + tig0032542:4481-4500 None:intergenic 60.0%
CCTCGACGTGTTGCCGAGAA+TGG - tig0032542:4478-4497 Msa1449380:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0032542 gene 4260 4723 4260 ID=Msa1449380;Name=Msa1449380
tig0032542 mRNA 4260 4723 4260 ID=Msa1449380-mRNA-1;Parent=Msa1449380;Name=Msa1449380-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|122
tig0032542 exon 4607 4723 4607 ID=Msa1449380-mRNA-1:exon:16915;Parent=Msa1449380-mRNA-1
tig0032542 exon 4260 4511 4260 ID=Msa1449380-mRNA-1:exon:16914;Parent=Msa1449380-mRNA-1
tig0032542 CDS 4607 4723 4607 ID=Msa1449380-mRNA-1:cds;Parent=Msa1449380-mRNA-1
tig0032542 CDS 4260 4511 4260 ID=Msa1449380-mRNA-1:cds;Parent=Msa1449380-mRNA-1
Gene Sequence

>Msa1449380

ATGAATGAGATTGGAGTTGAAGTCAATGGTGCTGAATTAGGGAATCTTCAAAATTCCGATGTTCATTATTGGAAGTATAATGTTACTGCTTCTATTTTGGATGGAAACAATGTTTTGAATTTTCCTCGACGTGTTGCCGAGAATGGTTTGTATACCAATCAATCTAAAATTCTCCTTTTTGATGAAGAAACTGGTAAATCTTATGACTGTGATGTTCACACTGCGTCAAGAAGCATGGATCAGAAATACATAGGGAGAGGATGGTACGACTTTGTTCTTGAAAAGTGCCTAAAAGTTGGTGATGTTGTTTTGTTCACGGTCAATAATCCTCCTAATAGGATGTATGCTACCGTCGTTAACTGGGACTGA
Protein sequence

>Msa1449380

MNEIGVEVNGAELGNLQNSDVHYWKYNVTASILDGNNVLNFPRRVAENGLYTNQSKILLFDEETGKSYDCDVHTASRSMDQKYIGRGWYDFVLEKCLKVGDVVLFTVNNPPNRMYATVVNWD*