AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1390480


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1390480 MtrunA17_Chr3g0116971 96.330 109 3 1 1 108 1 109 3.12e-71 207
Msa1390480 MtrunA17_Chr3g0116951 68.908 119 23 6 1 108 6 121 6.17e-42 135
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACCCTCTCAACGATTTC+AGG 0.158944 tig0021354:-34906 None:intergenic
TTGAAGGCCATCTCACCATT+TGG 0.332611 tig0021354:-34819 None:intergenic
GGTTGTGGTGGTGGCGGCCA+TGG 0.367830 tig0021354:-34884 None:intergenic
CCTTCGTGGGTAATGTTGAT+TGG 0.388716 tig0021354:-35009 None:intergenic
CGATTTCAGGGTTGTGGTGG+TGG 0.397034 tig0021354:-34893 None:intergenic
TGAAGGCCATCTCACCATTT+GGG 0.418823 tig0021354:-34818 None:intergenic
CAACCCTCTCAACGATTTCA+GGG 0.425008 tig0021354:-34905 None:intergenic
CCATTTGACCTGTTCCTTCG+TGG 0.432698 tig0021354:-35023 None:intergenic
ATAGACAACCCTCTTGTTGA+AGG 0.438765 tig0021354:-34835 None:intergenic
GTCACTCATGGAATACATTC+AGG 0.444691 tig0021354:+35045 Msa1390480:CDS
CATTTGACCTGTTCCTTCGT+GGG 0.467646 tig0021354:-35022 None:intergenic
CAACAAGAGGGTTGTCTATG+AGG 0.468986 tig0021354:+34839 Msa1390480:CDS
CCCTTCGAACTTCTGAAATG+TGG 0.470828 tig0021354:-34773 None:intergenic
TCTCAACGATTTCAGGGTTG+TGG 0.485866 tig0021354:-34899 None:intergenic
TTTCAGGGTTGTGGTGGTGG+CGG 0.488542 tig0021354:-34890 None:intergenic
CGTTGAGAGGGTTGAAGTGG+TGG 0.489360 tig0021354:+34914 Msa1390480:CDS
AACATTACCCACGAAGGAAC+AGG 0.491085 tig0021354:+35015 Msa1390480:CDS
TATGAGGAGGATGCGATTGA+AGG 0.492172 tig0021354:+34855 Msa1390480:CDS
CCACGAAGGAACAGGTCAAA+TGG 0.498880 tig0021354:+35023 Msa1390480:CDS
GTACCTGAGGTTAGGCCCTA+TGG 0.503566 tig0021354:+34948 Msa1390480:CDS
CCACCATAGGGCCTAACCTC+AGG 0.504816 tig0021354:-34951 None:intergenic
GAATACTCTCGCTACCCAAA+TGG 0.533741 tig0021354:+34804 Msa1390480:CDS
CCTTCGAACTTCTGAAATGT+GGG 0.541962 tig0021354:-34772 None:intergenic
ATGAACGTGTACCTGAGGTT+AGG 0.542173 tig0021354:+34940 Msa1390480:CDS
CCCACATTTCAGAAGTTCGA+AGG 0.543003 tig0021354:+34772 Msa1390480:CDS
ACAGGTCAAATGGTCACTCA+TGG 0.552434 tig0021354:+35033 Msa1390480:CDS
CAACGATTTCAGGGTTGTGG+TGG 0.564097 tig0021354:-34896 None:intergenic
GTAGATCACTTGACCACCAT+AGG 0.569439 tig0021354:-34964 None:intergenic
AATGTGGGTGTGGTAGTCAT+TGG 0.581040 tig0021354:-34757 None:intergenic
GGGTAGCGAGAGTATTCGCT+AGG 0.581864 tig0021354:-34798 None:intergenic
AGTGATCTACGAAGAGGACG+TGG 0.585316 tig0021354:+34977 Msa1390480:CDS
TCGCTACCCAAATGGTGAGA+TGG 0.585879 tig0021354:+34812 Msa1390480:CDS
GTGAGATGGCCTTCAACAAG+AGG 0.602330 tig0021354:+34826 Msa1390480:CDS
TAGATCACTTGACCACCATA+GGG 0.606041 tig0021354:-34963 None:intergenic
GAACTTCTGAAATGTGGGTG+TGG 0.614497 tig0021354:-34767 None:intergenic
CCACATTTCAGAAGTTCGAA+GGG 0.620439 tig0021354:+34773 Msa1390480:CDS
CAACCCTGAAATCGTTGAGA+GGG 0.621410 tig0021354:+34902 Msa1390480:CDS
CCTGAGGTTAGGCCCTATGG+TGG 0.626513 tig0021354:+34951 Msa1390480:CDS
ACAACCCTGAAATCGTTGAG+AGG 0.647655 tig0021354:+34901 Msa1390480:CDS
CAAGAGGGTTGTCTATGAGG+AGG 0.649483 tig0021354:+34842 Msa1390480:CDS
GCGATTGAAGGATCACGCCA+TGG 0.655981 tig0021354:+34867 Msa1390480:CDS
TGAGATGGCCTTCAACAAGA+GGG 0.673455 tig0021354:+34827 Msa1390480:CDS
TGGTCAAGTGATCTACGAAG+AGG 0.694239 tig0021354:+34971 Msa1390480:CDS
AATCGTTGAGAGGGTTGAAG+TGG 0.698905 tig0021354:+34911 Msa1390480:CDS
CCAATCAACATTACCCACGA+AGG 0.702298 tig0021354:+35009 Msa1390480:CDS
GGAATATGAACGTGTACCTG+AGG 0.717370 tig0021354:+34935 Msa1390480:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CCTTCGAACTTCTGAAATGT+GGG - tig0021354:34775-34794 None:intergenic 40.0%
CCACATTTCAGAAGTTCGAA+GGG + tig0021354:34773-34792 Msa1390480:CDS 40.0%
ATAGACAACCCTCTTGTTGA+AGG - tig0021354:34838-34857 None:intergenic 40.0%
TAGATCACTTGACCACCATA+GGG - tig0021354:34966-34985 None:intergenic 40.0%
GTCACTCATGGAATACATTC+AGG + tig0021354:35045-35064 Msa1390480:CDS 40.0%
AATGTGGGTGTGGTAGTCAT+TGG - tig0021354:34760-34779 None:intergenic 45.0%
!! GAACTTCTGAAATGTGGGTG+TGG - tig0021354:34770-34789 None:intergenic 45.0%
CCCACATTTCAGAAGTTCGA+AGG + tig0021354:34772-34791 Msa1390480:CDS 45.0%
!! CCCTTCGAACTTCTGAAATG+TGG - tig0021354:34776-34795 None:intergenic 45.0%
GAATACTCTCGCTACCCAAA+TGG + tig0021354:34804-34823 Msa1390480:CDS 45.0%
TGAAGGCCATCTCACCATTT+GGG - tig0021354:34821-34840 None:intergenic 45.0%
TTGAAGGCCATCTCACCATT+TGG - tig0021354:34822-34841 None:intergenic 45.0%
TGAGATGGCCTTCAACAAGA+GGG + tig0021354:34827-34846 Msa1390480:CDS 45.0%
CAACAAGAGGGTTGTCTATG+AGG + tig0021354:34839-34858 Msa1390480:CDS 45.0%
TATGAGGAGGATGCGATTGA+AGG + tig0021354:34855-34874 Msa1390480:CDS 45.0%
TCTCAACGATTTCAGGGTTG+TGG - tig0021354:34902-34921 None:intergenic 45.0%
ACAACCCTGAAATCGTTGAG+AGG + tig0021354:34901-34920 Msa1390480:CDS 45.0%
CAACCCTGAAATCGTTGAGA+GGG + tig0021354:34902-34921 Msa1390480:CDS 45.0%
CAACCCTCTCAACGATTTCA+GGG - tig0021354:34908-34927 None:intergenic 45.0%
TCAACCCTCTCAACGATTTC+AGG - tig0021354:34909-34928 None:intergenic 45.0%
AATCGTTGAGAGGGTTGAAG+TGG + tig0021354:34911-34930 Msa1390480:CDS 45.0%
GGAATATGAACGTGTACCTG+AGG + tig0021354:34935-34954 Msa1390480:CDS 45.0%
ATGAACGTGTACCTGAGGTT+AGG + tig0021354:34940-34959 Msa1390480:CDS 45.0%
GTAGATCACTTGACCACCAT+AGG - tig0021354:34967-34986 None:intergenic 45.0%
TGGTCAAGTGATCTACGAAG+AGG + tig0021354:34971-34990 Msa1390480:CDS 45.0%
CCTTCGTGGGTAATGTTGAT+TGG - tig0021354:35012-35031 None:intergenic 45.0%
CCAATCAACATTACCCACGA+AGG + tig0021354:35009-35028 Msa1390480:CDS 45.0%
AACATTACCCACGAAGGAAC+AGG + tig0021354:35015-35034 Msa1390480:CDS 45.0%
CATTTGACCTGTTCCTTCGT+GGG - tig0021354:35025-35044 None:intergenic 45.0%
ACAGGTCAAATGGTCACTCA+TGG + tig0021354:35033-35052 Msa1390480:CDS 45.0%
TCGCTACCCAAATGGTGAGA+TGG + tig0021354:34812-34831 Msa1390480:CDS 50.0%
GTGAGATGGCCTTCAACAAG+AGG + tig0021354:34826-34845 Msa1390480:CDS 50.0%
CAAGAGGGTTGTCTATGAGG+AGG + tig0021354:34842-34861 Msa1390480:CDS 50.0%
CAACGATTTCAGGGTTGTGG+TGG - tig0021354:34899-34918 None:intergenic 50.0%
AGTGATCTACGAAGAGGACG+TGG + tig0021354:34977-34996 Msa1390480:CDS 50.0%
CCATTTGACCTGTTCCTTCG+TGG - tig0021354:35026-35045 None:intergenic 50.0%
CCACGAAGGAACAGGTCAAA+TGG + tig0021354:35023-35042 Msa1390480:CDS 50.0%
!! GGGTAGCGAGAGTATTCGCT+AGG - tig0021354:34801-34820 None:intergenic 55.0%
GCGATTGAAGGATCACGCCA+TGG + tig0021354:34867-34886 Msa1390480:CDS 55.0%
!! TTTCAGGGTTGTGGTGGTGG+CGG - tig0021354:34893-34912 None:intergenic 55.0%
CGATTTCAGGGTTGTGGTGG+TGG - tig0021354:34896-34915 None:intergenic 55.0%
CGTTGAGAGGGTTGAAGTGG+TGG + tig0021354:34914-34933 Msa1390480:CDS 55.0%
GTACCTGAGGTTAGGCCCTA+TGG + tig0021354:34948-34967 Msa1390480:CDS 55.0%
CCACCATAGGGCCTAACCTC+AGG - tig0021354:34954-34973 None:intergenic 60.0%
CCTGAGGTTAGGCCCTATGG+TGG + tig0021354:34951-34970 Msa1390480:CDS 60.0%
!! GGTTGTGGTGGTGGCGGCCA+TGG - tig0021354:34887-34906 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0021354 gene 34747 35073 34747 ID=Msa1390480;Name=Msa1390480
tig0021354 mRNA 34747 35073 34747 ID=Msa1390480-mRNA-1;Parent=Msa1390480;Name=Msa1390480-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|108
tig0021354 exon 34747 35073 34747 ID=Msa1390480-mRNA-1:exon:12296;Parent=Msa1390480-mRNA-1
tig0021354 CDS 34747 35073 34747 ID=Msa1390480-mRNA-1:cds;Parent=Msa1390480-mRNA-1
Gene Sequence

>Msa1390480

ATGATGAGATCCAATGACTACCACACCCACATTTCAGAAGTTCGAAGGGAGCCTAGCGAATACTCTCGCTACCCAAATGGTGAGATGGCCTTCAACAAGAGGGTTGTCTATGAGGAGGATGCGATTGAAGGATCACGCCATGGCCGCCACCACCACAACCCTGAAATCGTTGAGAGGGTTGAAGTGGTGGAATATGAACGTGTACCTGAGGTTAGGCCCTATGGTGGTCAAGTGATCTACGAAGAGGACGTGGATGTTGAGACCAATCAACATTACCCACGAAGGAACAGGTCAAATGGTCACTCATGGAATACATTCAGGCCATAA

Protein sequence

>Msa1390480

MMRSNDYHTHISEVRREPSEYSRYPNGEMAFNKRVVYEEDAIEGSRHGRHHHNPEIVERVEVVEYERVPEVRPYGGQVIYEEDVDVETNQHYPRRNRSNGHSWNTFRP*