AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0374040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0374040 MtrunA17_Chr3g0124061 93.970 199 12 0 1 199 1 199 7.28e-141 390
Msa0374040 MtrunA17_Chr3g0124111 88.945 199 22 0 1 199 1 199 7.68e-133 370
Msa0374040 MtrunA17_Chr3g0124141 86.935 199 26 0 1 199 1 199 4.41e-127 356
Msa0374040 MtrunA17_Chr3g0124091 85.075 201 27 2 1 199 1 200 9.55e-122 342
Msa0374040 MtrunA17_Chr3g0124151 84.906 106 16 0 94 199 1 106 1.18e-62 189
Msa0374040 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
Msa0374040 AT5G65030.1 30.964 197 124 3 11 199 10 202 2.00e-26 100
Msa0374040 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_1:+73154647 Msa0374040:CDS
CTACCAAATCAGTACCCTTT+TGG 0.251571 3_1:+73154601 Msa0374040:CDS
ATAAGAGTAGGTTGAATAAT+TGG 0.258714 3_1:+73154916 Msa0374040:CDS
TGCGCTTGGCGCAGCTTTGG+AGG 0.349292 3_1:+73155007 Msa0374040:CDS
TTAATCTCCACTTCTACTTC+CGG 0.353807 3_1:-73154855 None:intergenic
AGCTAAGGCAAAGGAAGATA+TGG 0.356544 3_1:+73154700 Msa0374040:CDS
ATTTGCGCTTGGCGCAGCTT+TGG 0.402289 3_1:+73155004 Msa0374040:CDS
GCTCCAACACTAGGCTTTGT+TGG 0.406615 3_1:-73154680 None:intergenic
AGTGGCTTCGGTTCATGAAA+TGG 0.417821 3_1:+73154884 Msa0374040:CDS
GTCCCAAAAGGGTACTGATT+TGG 0.428896 3_1:-73154604 None:intergenic
GATTCAAGAATCACTTTCCA+TGG 0.437928 3_1:-73154753 None:intergenic
GCAAGGCTGTATCTTCCAAC+AGG 0.447411 3_1:+73154540 Msa0374040:CDS
GATTAAAATAAGAGTGGCTT+CGG 0.448073 3_1:+73154872 Msa0374040:CDS
TGCACCAAGCGCGATGATCA+TGG 0.461361 3_1:-73154962 None:intergenic
GCTAAGGCAAAGGAAGATAT+GGG 0.463318 3_1:+73154701 Msa0374040:CDS
ATTAAATGACTCGTCCCAAA+AGG 0.469911 3_1:-73154616 None:intergenic
TTGGAAAAGGTGAGATTCCA+TGG 0.470388 3_1:+73154736 Msa0374040:CDS
AAAGCCTAGTGTTGGAGCTA+AGG 0.499139 3_1:+73154685 Msa0374040:CDS
TTTGCCTTAGCTCCAACACT+AGG 0.507447 3_1:-73154689 None:intergenic
CAACTGAAGTTTGCATATGC+AGG 0.509989 3_1:-73154456 None:intergenic
GGGTCACAACTTATTGGAAA+AGG 0.523568 3_1:+73154723 Msa0374040:CDS
TTAAATGACTCGTCCCAAAA+GGG 0.547621 3_1:-73154615 None:intergenic
AGTGGAGATTAAAATAAGAG+TGG 0.548596 3_1:+73154866 Msa0374040:CDS
AATGAGTGTGGATGCAAGAA+TGG 0.549203 3_1:+73154939 Msa0374040:CDS
ATGGCCATGATCATCGCGCT+TGG 0.550412 3_1:+73154958 Msa0374040:CDS
GATTGTGATATATTTGCGCT+TGG 0.560902 3_1:+73154993 Msa0374040:CDS
TAACCAACAAAGCCTAGTGT+TGG 0.564525 3_1:+73154677 Msa0374040:CDS
TTGAATAATTGGAATGAGTG+TGG 0.579695 3_1:+73154927 Msa0374040:CDS
GATTCTTGAATCACAAAACA+TGG 0.583125 3_1:+73154764 Msa0374040:CDS
TAGTGTTGGAGCTAAGGCAA+AGG 0.590191 3_1:+73154691 Msa0374040:CDS
CTCAACACCGGAAGTAGAAG+TGG 0.592858 3_1:+73154848 Msa0374040:CDS
AGAGGAAATGTTCTCAACAC+CGG 0.624098 3_1:+73154836 Msa0374040:CDS
TTGAAGATGTATTTAGTGAG+TGG 0.629374 3_1:+73154801 Msa0374040:CDS
GAGTGGAAGTGATTGCAAAG+AGG 0.644927 3_1:+73154818 Msa0374040:CDS
AAACGTTGAATTCATCAAGT+CGG 0.660973 3_1:+73154503 Msa0374040:CDS
CTAAGGCAAAGGAAGATATG+GGG 0.679009 3_1:+73154702 Msa0374040:CDS
TAAGGCAAAGGAAGATATGG+GGG 0.682962 3_1:+73154703 Msa0374040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTTTCCAAGAATTCTTT+GGG - chr3_1:73154657-73154676 None:intergenic 25.0%
!! AAGATTTTCCAAGAATTCTT+TGG - chr3_1:73154658-73154677 None:intergenic 25.0%
! AAAACATGGAGTTGAAAAAA+TGG + chr3_1:73154778-73154797 Msa0374040:CDS 25.0%
! TGGAAAAGAAAAATAAGAGT+AGG + chr3_1:73154904-73154923 Msa0374040:CDS 25.0%
!! ATAAGAGTAGGTTGAATAAT+TGG + chr3_1:73154916-73154935 Msa0374040:CDS 25.0%
AAACGTTGAATTCATCAAGT+CGG + chr3_1:73154503-73154522 Msa0374040:CDS 30.0%
!!! ATACTTTTGTTGTTTCCTGT+TGG - chr3_1:73154558-73154577 None:intergenic 30.0%
! GATTTTCCAAGAATTCTTTG+GGG - chr3_1:73154656-73154675 None:intergenic 30.0%
GATTCTTGAATCACAAAACA+TGG + chr3_1:73154764-73154783 Msa0374040:CDS 30.0%
TTGAAGATGTATTTAGTGAG+TGG + chr3_1:73154801-73154820 Msa0374040:CDS 30.0%
AGTGGAGATTAAAATAAGAG+TGG + chr3_1:73154866-73154885 Msa0374040:CDS 30.0%
GATTAAAATAAGAGTGGCTT+CGG + chr3_1:73154872-73154891 Msa0374040:CDS 30.0%
TTGAATAATTGGAATGAGTG+TGG + chr3_1:73154927-73154946 Msa0374040:CDS 30.0%
! TACCAAATCAGTACCCTTTT+GGG + chr3_1:73154602-73154621 Msa0374040:CDS 35.0%
TTAAATGACTCGTCCCAAAA+GGG - chr3_1:73154618-73154637 None:intergenic 35.0%
ATTAAATGACTCGTCCCAAA+AGG - chr3_1:73154619-73154638 None:intergenic 35.0%
GATTCAAGAATCACTTTCCA+TGG - chr3_1:73154756-73154775 None:intergenic 35.0%
TTAATCTCCACTTCTACTTC+CGG - chr3_1:73154858-73154877 None:intergenic 35.0%
GATTGTGATATATTTGCGCT+TGG + chr3_1:73154993-73155012 Msa0374040:CDS 35.0%
CAACTGAAGTTTGCATATGC+AGG - chr3_1:73154459-73154478 None:intergenic 40.0%
CGGCAAAAAACATGTTTGCA+AGG + chr3_1:73154523-73154542 Msa0374040:CDS 40.0%
! CTACCAAATCAGTACCCTTT+TGG + chr3_1:73154601-73154620 Msa0374040:CDS 40.0%
TTCTTGCCCCAAAGAATTCT+TGG + chr3_1:73154647-73154666 Msa0374040:CDS 40.0%
TAACCAACAAAGCCTAGTGT+TGG + chr3_1:73154677-73154696 Msa0374040:CDS 40.0%
AGCTAAGGCAAAGGAAGATA+TGG + chr3_1:73154700-73154719 Msa0374040:CDS 40.0%
GCTAAGGCAAAGGAAGATAT+GGG + chr3_1:73154701-73154720 Msa0374040:CDS 40.0%
CTAAGGCAAAGGAAGATATG+GGG + chr3_1:73154702-73154721 Msa0374040:CDS 40.0%
TAAGGCAAAGGAAGATATGG+GGG + chr3_1:73154703-73154722 Msa0374040:CDS 40.0%
ATATGGGGGTCACAACTTAT+TGG + chr3_1:73154717-73154736 Msa0374040:CDS 40.0%
GGGTCACAACTTATTGGAAA+AGG + chr3_1:73154723-73154742 Msa0374040:CDS 40.0%
TTGGAAAAGGTGAGATTCCA+TGG + chr3_1:73154736-73154755 Msa0374040:CDS 40.0%
AGAGGAAATGTTCTCAACAC+CGG + chr3_1:73154836-73154855 Msa0374040:CDS 40.0%
AATGAGTGTGGATGCAAGAA+TGG + chr3_1:73154939-73154958 Msa0374040:CDS 40.0%
! GCATATGCAGGTGTTTTCGA+TGG - chr3_1:73154447-73154466 None:intergenic 45.0%
!! GTCCCAAAAGGGTACTGATT+TGG - chr3_1:73154607-73154626 None:intergenic 45.0%
! AAAGCCTAGTGTTGGAGCTA+AGG + chr3_1:73154685-73154704 Msa0374040:CDS 45.0%
TTTGCCTTAGCTCCAACACT+AGG - chr3_1:73154692-73154711 None:intergenic 45.0%
! TAGTGTTGGAGCTAAGGCAA+AGG + chr3_1:73154691-73154710 Msa0374040:CDS 45.0%
GAGTGGAAGTGATTGCAAAG+AGG + chr3_1:73154818-73154837 Msa0374040:CDS 45.0%
AGTGGCTTCGGTTCATGAAA+TGG + chr3_1:73154884-73154903 Msa0374040:CDS 45.0%
GCAAGGCTGTATCTTCCAAC+AGG + chr3_1:73154540-73154559 Msa0374040:CDS 50.0%
! GCTCCAACACTAGGCTTTGT+TGG - chr3_1:73154683-73154702 None:intergenic 50.0%
CTCAACACCGGAAGTAGAAG+TGG + chr3_1:73154848-73154867 Msa0374040:CDS 50.0%
ATGGCCATGATCATCGCGCT+TGG + chr3_1:73154958-73154977 Msa0374040:CDS 55.0%
TGCACCAAGCGCGATGATCA+TGG - chr3_1:73154965-73154984 None:intergenic 55.0%
ATTTGCGCTTGGCGCAGCTT+TGG + chr3_1:73155004-73155023 Msa0374040:CDS 55.0%
! TGCGCTTGGCGCAGCTTTGG+AGG + chr3_1:73155007-73155026 Msa0374040:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 73154438 73155037 73154438 ID=Msa0374040;Name=Msa0374040
chr3_1 mRNA 73154438 73155037 73154438 ID=Msa0374040-mRNA-1;Parent=Msa0374040;Name=Msa0374040-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|199
chr3_1 exon 73154438 73155037 73154438 ID=Msa0374040-mRNA-1:exon:16618;Parent=Msa0374040-mRNA-1
chr3_1 CDS 73154438 73155037 73154438 ID=Msa0374040-mRNA-1:cds;Parent=Msa0374040-mRNA-1
Gene Sequence

>Msa0374040

ATGGATCCATCGAAAACACCTGCATATGCAAACTTCAGTTGTGAACTGAGAATAATACAAGCACGAAACGTTGAATTCATCAAGTCGGCAAAAAACATGTTTGCAAGGCTGTATCTTCCAACAGGAAACAACAAAAGTATTCAACTCAACAGCAAAAAAGTTTCTACCAAATCAGTACCCTTTTGGGACGAGTCATTTAATCTAGATTGTTCTTGCCCCAAAGAATTCTTGGAAAATCTTAACCAACAAAGCCTAGTGTTGGAGCTAAGGCAAAGGAAGATATGGGGGTCACAACTTATTGGAAAAGGTGAGATTCCATGGAAAGTGATTCTTGAATCACAAAACATGGAGTTGAAAAAATGGTTGAAGATGTATTTAGTGAGTGGAAGTGATTGCAAAGAGGAAATGTTCTCAACACCGGAAGTAGAAGTGGAGATTAAAATAAGAGTGGCTTCGGTTCATGAAATGGAAAAGAAAAATAAGAGTAGGTTGAATAATTGGAATGAGTGTGGATGCAAGAATGGCCATGATCATCGCGCTTGGTGCAGCGCTGAAGATTGTGATATATTTGCGCTTGGCGCAGCTTTGGAGGCTTTTTGA

Protein sequence

>Msa0374040

MDPSKTPAYANFSCELRIIQARNVEFIKSAKNMFARLYLPTGNNKSIQLNSKKVSTKSVPFWDESFNLDCSCPKEFLENLNQQSLVLELRQRKIWGSQLIGKGEIPWKVILESQNMELKKWLKMYLVSGSDCKEEMFSTPEVEVEIKIRVASVHEMEKKNKSRLNNWNECGCKNGHDHRAWCSAEDCDIFALGAALEAF*