AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0423220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0423220 MtrunA17_Chr3g0124061 93.970 199 12 0 1 199 1 199 7.28e-141 390
Msa0423220 MtrunA17_Chr3g0124111 88.945 199 22 0 1 199 1 199 7.68e-133 370
Msa0423220 MtrunA17_Chr3g0124141 86.935 199 26 0 1 199 1 199 4.41e-127 356
Msa0423220 MtrunA17_Chr3g0124091 85.075 201 27 2 1 199 1 200 9.55e-122 342
Msa0423220 MtrunA17_Chr3g0124151 84.906 106 16 0 94 199 1 106 1.18e-62 189
Msa0423220 MtrunA17_Chr3g0124131 80.000 50 10 0 1 50 1 50 4.66e-24 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0423220 AT5G65030.1 30.964 197 124 3 11 199 10 202 2.00e-26 100
Msa0423220 AT5G10210.1 32.124 193 109 7 15 196 13 194 2.03e-24 95.5

Find 37 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGCCCCAAAGAATTCT+TGG 0.233772 3_2:+72968635 Msa0423220:CDS
CTACCAAATCAGTACCCTTT+TGG 0.251571 3_2:+72968589 Msa0423220:CDS
ATAAGAGTAGGTTGAATAAT+TGG 0.258714 3_2:+72968904 Msa0423220:CDS
TGCGCTTGGCGCAGCTTTGG+AGG 0.349292 3_2:+72968995 Msa0423220:CDS
TTAATCTCCACTTCTACTTC+CGG 0.353807 3_2:-72968843 None:intergenic
AGCTAAGGCAAAGGAAGATA+TGG 0.356544 3_2:+72968688 Msa0423220:CDS
ATTTGCGCTTGGCGCAGCTT+TGG 0.402289 3_2:+72968992 Msa0423220:CDS
GCTCCAACACTAGGCTTTGT+TGG 0.406615 3_2:-72968668 None:intergenic
AGTGGCTTCGGTTCATGAAA+TGG 0.417821 3_2:+72968872 Msa0423220:CDS
GTCCCAAAAGGGTACTGATT+TGG 0.428896 3_2:-72968592 None:intergenic
GATTCAAGAATCACTTTCCA+TGG 0.437928 3_2:-72968741 None:intergenic
GCAAGGCTGTATCTTCCAAC+AGG 0.447411 3_2:+72968528 Msa0423220:CDS
GATTAAAATAAGAGTGGCTT+CGG 0.448073 3_2:+72968860 Msa0423220:CDS
TGCACCAAGCGCGATGATCA+TGG 0.461361 3_2:-72968950 None:intergenic
GCTAAGGCAAAGGAAGATAT+GGG 0.463318 3_2:+72968689 Msa0423220:CDS
ATTAAATGACTCGTCCCAAA+AGG 0.469911 3_2:-72968604 None:intergenic
TTGGAAAAGGTGAGATTCCA+TGG 0.470388 3_2:+72968724 Msa0423220:CDS
AAAGCCTAGTGTTGGAGCTA+AGG 0.499139 3_2:+72968673 Msa0423220:CDS
TTTGCCTTAGCTCCAACACT+AGG 0.507447 3_2:-72968677 None:intergenic
CAACTGAAGTTTGCATATGC+AGG 0.509989 3_2:-72968444 None:intergenic
GGGTCACAACTTATTGGAAA+AGG 0.523568 3_2:+72968711 Msa0423220:CDS
TTAAATGACTCGTCCCAAAA+GGG 0.547621 3_2:-72968603 None:intergenic
AGTGGAGATTAAAATAAGAG+TGG 0.548596 3_2:+72968854 Msa0423220:CDS
AATGAGTGTGGATGCAAGAA+TGG 0.549203 3_2:+72968927 Msa0423220:CDS
ATGGCCATGATCATCGCGCT+TGG 0.550412 3_2:+72968946 Msa0423220:CDS
GATTGTGATATATTTGCGCT+TGG 0.560902 3_2:+72968981 Msa0423220:CDS
TAACCAACAAAGCCTAGTGT+TGG 0.564525 3_2:+72968665 Msa0423220:CDS
TTGAATAATTGGAATGAGTG+TGG 0.579695 3_2:+72968915 Msa0423220:CDS
GATTCTTGAATCACAAAACA+TGG 0.583125 3_2:+72968752 Msa0423220:CDS
TAGTGTTGGAGCTAAGGCAA+AGG 0.590191 3_2:+72968679 Msa0423220:CDS
CTCAACACCGGAAGTAGAAG+TGG 0.592858 3_2:+72968836 Msa0423220:CDS
AGAGGAAATGTTCTCAACAC+CGG 0.624098 3_2:+72968824 Msa0423220:CDS
TTGAAGATGTATTTAGTGAG+TGG 0.629374 3_2:+72968789 Msa0423220:CDS
GAGTGGAAGTGATTGCAAAG+AGG 0.644927 3_2:+72968806 Msa0423220:CDS
AAACGTTGAATTCATCAAGT+CGG 0.660973 3_2:+72968491 Msa0423220:CDS
CTAAGGCAAAGGAAGATATG+GGG 0.679009 3_2:+72968690 Msa0423220:CDS
TAAGGCAAAGGAAGATATGG+GGG 0.682962 3_2:+72968691 Msa0423220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTTTCCAAGAATTCTTT+GGG - chr3_2:72968645-72968664 None:intergenic 25.0%
!! AAGATTTTCCAAGAATTCTT+TGG - chr3_2:72968646-72968665 None:intergenic 25.0%
! AAAACATGGAGTTGAAAAAA+TGG + chr3_2:72968766-72968785 Msa0423220:CDS 25.0%
! TGGAAAAGAAAAATAAGAGT+AGG + chr3_2:72968892-72968911 Msa0423220:CDS 25.0%
!! ATAAGAGTAGGTTGAATAAT+TGG + chr3_2:72968904-72968923 Msa0423220:CDS 25.0%
AAACGTTGAATTCATCAAGT+CGG + chr3_2:72968491-72968510 Msa0423220:CDS 30.0%
!!! ATACTTTTGTTGTTTCCTGT+TGG - chr3_2:72968546-72968565 None:intergenic 30.0%
! GATTTTCCAAGAATTCTTTG+GGG - chr3_2:72968644-72968663 None:intergenic 30.0%
GATTCTTGAATCACAAAACA+TGG + chr3_2:72968752-72968771 Msa0423220:CDS 30.0%
TTGAAGATGTATTTAGTGAG+TGG + chr3_2:72968789-72968808 Msa0423220:CDS 30.0%
AGTGGAGATTAAAATAAGAG+TGG + chr3_2:72968854-72968873 Msa0423220:CDS 30.0%
GATTAAAATAAGAGTGGCTT+CGG + chr3_2:72968860-72968879 Msa0423220:CDS 30.0%
TTGAATAATTGGAATGAGTG+TGG + chr3_2:72968915-72968934 Msa0423220:CDS 30.0%
! TACCAAATCAGTACCCTTTT+GGG + chr3_2:72968590-72968609 Msa0423220:CDS 35.0%
TTAAATGACTCGTCCCAAAA+GGG - chr3_2:72968606-72968625 None:intergenic 35.0%
ATTAAATGACTCGTCCCAAA+AGG - chr3_2:72968607-72968626 None:intergenic 35.0%
GATTCAAGAATCACTTTCCA+TGG - chr3_2:72968744-72968763 None:intergenic 35.0%
TTAATCTCCACTTCTACTTC+CGG - chr3_2:72968846-72968865 None:intergenic 35.0%
GATTGTGATATATTTGCGCT+TGG + chr3_2:72968981-72969000 Msa0423220:CDS 35.0%
CAACTGAAGTTTGCATATGC+AGG - chr3_2:72968447-72968466 None:intergenic 40.0%
CGGCAAAAAACATGTTTGCA+AGG + chr3_2:72968511-72968530 Msa0423220:CDS 40.0%
! CTACCAAATCAGTACCCTTT+TGG + chr3_2:72968589-72968608 Msa0423220:CDS 40.0%
TTCTTGCCCCAAAGAATTCT+TGG + chr3_2:72968635-72968654 Msa0423220:CDS 40.0%
TAACCAACAAAGCCTAGTGT+TGG + chr3_2:72968665-72968684 Msa0423220:CDS 40.0%
AGCTAAGGCAAAGGAAGATA+TGG + chr3_2:72968688-72968707 Msa0423220:CDS 40.0%
GCTAAGGCAAAGGAAGATAT+GGG + chr3_2:72968689-72968708 Msa0423220:CDS 40.0%
CTAAGGCAAAGGAAGATATG+GGG + chr3_2:72968690-72968709 Msa0423220:CDS 40.0%
TAAGGCAAAGGAAGATATGG+GGG + chr3_2:72968691-72968710 Msa0423220:CDS 40.0%
ATATGGGGGTCACAACTTAT+TGG + chr3_2:72968705-72968724 Msa0423220:CDS 40.0%
GGGTCACAACTTATTGGAAA+AGG + chr3_2:72968711-72968730 Msa0423220:CDS 40.0%
TTGGAAAAGGTGAGATTCCA+TGG + chr3_2:72968724-72968743 Msa0423220:CDS 40.0%
AGAGGAAATGTTCTCAACAC+CGG + chr3_2:72968824-72968843 Msa0423220:CDS 40.0%
AATGAGTGTGGATGCAAGAA+TGG + chr3_2:72968927-72968946 Msa0423220:CDS 40.0%
! GCATATGCAGGTGTTTTCGA+TGG - chr3_2:72968435-72968454 None:intergenic 45.0%
!! GTCCCAAAAGGGTACTGATT+TGG - chr3_2:72968595-72968614 None:intergenic 45.0%
! AAAGCCTAGTGTTGGAGCTA+AGG + chr3_2:72968673-72968692 Msa0423220:CDS 45.0%
TTTGCCTTAGCTCCAACACT+AGG - chr3_2:72968680-72968699 None:intergenic 45.0%
! TAGTGTTGGAGCTAAGGCAA+AGG + chr3_2:72968679-72968698 Msa0423220:CDS 45.0%
GAGTGGAAGTGATTGCAAAG+AGG + chr3_2:72968806-72968825 Msa0423220:CDS 45.0%
AGTGGCTTCGGTTCATGAAA+TGG + chr3_2:72968872-72968891 Msa0423220:CDS 45.0%
GCAAGGCTGTATCTTCCAAC+AGG + chr3_2:72968528-72968547 Msa0423220:CDS 50.0%
! GCTCCAACACTAGGCTTTGT+TGG - chr3_2:72968671-72968690 None:intergenic 50.0%
CTCAACACCGGAAGTAGAAG+TGG + chr3_2:72968836-72968855 Msa0423220:CDS 50.0%
ATGGCCATGATCATCGCGCT+TGG + chr3_2:72968946-72968965 Msa0423220:CDS 55.0%
TGCACCAAGCGCGATGATCA+TGG - chr3_2:72968953-72968972 None:intergenic 55.0%
ATTTGCGCTTGGCGCAGCTT+TGG + chr3_2:72968992-72969011 Msa0423220:CDS 55.0%
! TGCGCTTGGCGCAGCTTTGG+AGG + chr3_2:72968995-72969014 Msa0423220:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 72968426 72969025 72968426 ID=Msa0423220;Name=Msa0423220
chr3_2 mRNA 72968426 72969025 72968426 ID=Msa0423220-mRNA-1;Parent=Msa0423220;Name=Msa0423220-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|199
chr3_2 exon 72968426 72969025 72968426 ID=Msa0423220-mRNA-1:exon:18106;Parent=Msa0423220-mRNA-1
chr3_2 CDS 72968426 72969025 72968426 ID=Msa0423220-mRNA-1:cds;Parent=Msa0423220-mRNA-1
Gene Sequence

>Msa0423220

ATGGATCCATCGAAAACACCTGCATATGCAAACTTCAGTTGTGAACTGAGAATAATACAAGCACGAAACGTTGAATTCATCAAGTCGGCAAAAAACATGTTTGCAAGGCTGTATCTTCCAACAGGAAACAACAAAAGTATTCAACTCAACAGCAAAAAAGTTTCTACCAAATCAGTACCCTTTTGGGACGAGTCATTTAATCTAGATTGTTCTTGCCCCAAAGAATTCTTGGAAAATCTTAACCAACAAAGCCTAGTGTTGGAGCTAAGGCAAAGGAAGATATGGGGGTCACAACTTATTGGAAAAGGTGAGATTCCATGGAAAGTGATTCTTGAATCACAAAACATGGAGTTGAAAAAATGGTTGAAGATGTATTTAGTGAGTGGAAGTGATTGCAAAGAGGAAATGTTCTCAACACCGGAAGTAGAAGTGGAGATTAAAATAAGAGTGGCTTCGGTTCATGAAATGGAAAAGAAAAATAAGAGTAGGTTGAATAATTGGAATGAGTGTGGATGCAAGAATGGCCATGATCATCGCGCTTGGTGCAGCGCTGAAGATTGTGATATATTTGCGCTTGGCGCAGCTTTGGAGGCTTTTTGA

Protein sequence

>Msa0423220

MDPSKTPAYANFSCELRIIQARNVEFIKSAKNMFARLYLPTGNNKSIQLNSKKVSTKSVPFWDESFNLDCSCPKEFLENLNQQSLVLELRQRKIWGSQLIGKGEIPWKVILESQNMELKKWLKMYLVSGSDCKEEMFSTPEVEVEIKIRVASVHEMEKKNKSRLNNWNECGCKNGHDHRAWCSAEDCDIFALGAALEAF*