AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0804740


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0804740 MtrunA17_Chr5g0412491 97.006 167 5 0 11 177 1 167 6.88e-116 325
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0804740 AT1G26290.1 42.735 117 58 3 1 116 1 109 8.14e-17 73.6

Find 39 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAAATATATAATTATATT+TGG 0.157980 5_3:+20723675 None:intergenic
TCTTACTATGCCTATTATAT+TGG 0.159642 5_3:-20722948 Msa0804740:three_prime_UTR
CTTACTATGCCTATTATATT+GGG 0.208100 5_3:-20722947 Msa0804740:three_prime_UTR
AGATTTAGAAGAGGAGATTA+AGG 0.230236 5_3:-20723416 Msa0804740:CDS
TAACAAAGAAGCAAATAAAA+AGG 0.238986 5_3:-20723224 Msa0804740:CDS
TCAAGCCCTATTCCTGTAAA+AGG 0.284131 5_3:-20723115 Msa0804740:CDS
AAAATTTACCCCAATATAAT+AGG 0.309509 5_3:+20722938 None:intergenic
CACTTTCTGAGGTGATTATA+AGG 0.320343 5_3:-20723288 Msa0804740:CDS
TTCAACTCCTCTGCTGAAAT+AGG 0.331112 5_3:+20723472 None:intergenic
AAGAAGTGAAGAAGATTGAT+TGG 0.347744 5_3:-20723159 Msa0804740:CDS
GGATAAGAAGCTACTTCAAT+TGG 0.436350 5_3:-20723032 Msa0804740:CDS
TTGATTGGGAGAAGAGTTTG+AGG 0.445900 5_3:-20723144 Msa0804740:CDS
AACGTTATTCATATCCGATC+AGG 0.465153 5_3:+20722915 None:intergenic
AGGAACTAAAATTGAAATCA+AGG 0.471855 5_3:-20723251 Msa0804740:CDS
TTAGAAGAGGAGATTAAGGA+AGG 0.483543 5_3:-20723412 Msa0804740:CDS
GGTGATTATAAGGATGAGAA+TGG 0.489148 5_3:-20723278 Msa0804740:CDS
AAAGGAGAGAGATGCAAAAG+AGG 0.490952 5_3:-20723344 Msa0804740:CDS
TGATTGGGAGAAGAGTTTGA+GGG 0.505362 5_3:-20723143 Msa0804740:CDS
AAAGGATAAGATAATGATGA+GGG 0.511757 5_3:-20723071 Msa0804740:CDS
GCTACTTCAATTGGTGTGGA+AGG 0.513216 5_3:-20723023 Msa0804740:CDS
ATTATAAGGATGAGAATGGA+AGG 0.528677 5_3:-20723274 Msa0804740:CDS
AGAAGTGAAGAAGATTGATT+GGG 0.529976 5_3:-20723158 Msa0804740:CDS
AATAATAACATGGATCATCA+TGG 0.531079 5_3:-20723651 Msa0804740:exon
ATATGTTAGATCAAAGCAAA+AGG 0.536682 5_3:-20723089 Msa0804740:CDS
TTACTATGCCTATTATATTG+GGG 0.540322 5_3:-20722946 Msa0804740:three_prime_UTR
TTGGTGTGGAAGGTTTAAAG+TGG 0.548941 5_3:-20723013 Msa0804740:exon
ATATAATAGGCATAGTAAGA+AGG 0.558419 5_3:+20722951 None:intergenic
CAAAATTAGAGCACTTTCTG+AGG 0.566466 5_3:-20723299 Msa0804740:CDS
GATTGAAAGAGATTTAGAAG+AGG 0.567737 5_3:-20723425 Msa0804740:CDS
GAGGGGAAAGAATGCAAGTG+AGG 0.574468 5_3:-20723053 Msa0804740:CDS
TGAGGTTCCTATTTCAGCAG+AGG 0.574672 5_3:-20723479 Msa0804740:CDS
AGAAGCTACTTCAATTGGTG+TGG 0.577937 5_3:-20723027 Msa0804740:CDS
ATATTTAATTAATAATAACA+TGG 0.583953 5_3:-20723661 Msa0804740:exon
AAAAGGATAAGATAATGATG+AGG 0.592572 5_3:-20723072 Msa0804740:CDS
TGGGAGAAGAGTTTGAGGGC+AGG 0.600710 5_3:-20723139 Msa0804740:CDS
ATAAGGATGAGAATGGAAGG+AGG 0.636221 5_3:-20723271 Msa0804740:CDS
CATCATGGAATGTACACCAA+AGG 0.652781 5_3:-20723636 Msa0804740:intron
AAGGATAAGATAATGATGAG+GGG 0.685809 5_3:-20723070 Msa0804740:CDS
AACTAAAATTGAAATCAAGG+AGG 0.721284 5_3:-20723248 Msa0804740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTCTTGCTTTTTTTAAT+TGG - chr5_3:20723589-20723608 Msa0804740:intron 15.0%
!!! ATTTTCTTGCTTTTTTTAAT+TGG - chr5_3:20723589-20723608 Msa0804740:intron 15.0%
!! TAACAAAGAAGCAAATAAAA+AGG - chr5_3:20723351-20723370 Msa0804740:CDS 20.0%
!! AACAAAGAAGCAAATAAAAA+GGG - chr5_3:20723352-20723371 Msa0804740:CDS 20.0%
!!! ACTTCTTTCAAACATTTTTT+GGG + chr5_3:20723403-20723422 None:intergenic 20.0%
!! AAAATTTACCCCAATATAAT+AGG + chr5_3:20723640-20723659 None:intergenic 20.0%
!! TAACAAAGAAGCAAATAAAA+AGG - chr5_3:20723351-20723370 Msa0804740:CDS 20.0%
!! AACAAAGAAGCAAATAAAAA+GGG - chr5_3:20723352-20723371 Msa0804740:CDS 20.0%
!!! ACTTCTTTCAAACATTTTTT+GGG + chr5_3:20723403-20723422 None:intergenic 20.0%
!! AAAATTTACCCCAATATAAT+AGG + chr5_3:20723640-20723659 None:intergenic 20.0%
! AATAATAACATGGATCATCA+TGG - chr5_3:20722924-20722943 Msa0804740:three_prime_UTR 25.0%
! ATCAACAAAACTATGAAGAA+TGG + chr5_3:20723013-20723032 None:intergenic 25.0%
! GTCAAATAAAAATGTTCTTG+AGG - chr5_3:20723078-20723097 Msa0804740:CDS 25.0%
! AGGAACTAAAATTGAAATCA+AGG - chr5_3:20723324-20723343 Msa0804740:CDS 25.0%
! AACTAAAATTGAAATCAAGG+AGG - chr5_3:20723327-20723346 Msa0804740:CDS 25.0%
!!! CATTTTTTGGGTCTAAAATT+TGG + chr5_3:20723391-20723410 None:intergenic 25.0%
!!! CACTTCTTTCAAACATTTTT+TGG + chr5_3:20723404-20723423 None:intergenic 25.0%
! ATATGTTAGATCAAAGCAAA+AGG - chr5_3:20723486-20723505 Msa0804740:CDS 25.0%
! AAAAGGATAAGATAATGATG+AGG - chr5_3:20723503-20723522 Msa0804740:CDS 25.0%
! AAAGGATAAGATAATGATGA+GGG - chr5_3:20723504-20723523 Msa0804740:CDS 25.0%
! ATATAATAGGCATAGTAAGA+AGG + chr5_3:20723627-20723646 None:intergenic 25.0%
! TCTTACTATGCCTATTATAT+TGG - chr5_3:20723627-20723646 Msa0804740:intron 25.0%
! CTTACTATGCCTATTATATT+GGG - chr5_3:20723628-20723647 Msa0804740:intron 25.0%
! TTACTATGCCTATTATATTG+GGG - chr5_3:20723629-20723648 Msa0804740:intron 25.0%
! AATAATAACATGGATCATCA+TGG - chr5_3:20722924-20722943 Msa0804740:three_prime_UTR 25.0%
! ATCAACAAAACTATGAAGAA+TGG + chr5_3:20723013-20723032 None:intergenic 25.0%
! GTCAAATAAAAATGTTCTTG+AGG - chr5_3:20723078-20723097 Msa0804740:CDS 25.0%
! AGGAACTAAAATTGAAATCA+AGG - chr5_3:20723324-20723343 Msa0804740:CDS 25.0%
! AACTAAAATTGAAATCAAGG+AGG - chr5_3:20723327-20723346 Msa0804740:CDS 25.0%
!!! CATTTTTTGGGTCTAAAATT+TGG + chr5_3:20723391-20723410 None:intergenic 25.0%
!!! CACTTCTTTCAAACATTTTT+TGG + chr5_3:20723404-20723423 None:intergenic 25.0%
! ATATGTTAGATCAAAGCAAA+AGG - chr5_3:20723486-20723505 Msa0804740:CDS 25.0%
! AAAAGGATAAGATAATGATG+AGG - chr5_3:20723503-20723522 Msa0804740:CDS 25.0%
! AAAGGATAAGATAATGATGA+GGG - chr5_3:20723504-20723523 Msa0804740:CDS 25.0%
! ATATAATAGGCATAGTAAGA+AGG + chr5_3:20723627-20723646 None:intergenic 25.0%
! TCTTACTATGCCTATTATAT+TGG - chr5_3:20723627-20723646 Msa0804740:intron 25.0%
! CTTACTATGCCTATTATATT+GGG - chr5_3:20723628-20723647 Msa0804740:intron 25.0%
! TTACTATGCCTATTATATTG+GGG - chr5_3:20723629-20723648 Msa0804740:intron 25.0%
GATTGAAAGAGATTTAGAAG+AGG - chr5_3:20723150-20723169 Msa0804740:CDS 30.0%
AGATTTAGAAGAGGAGATTA+AGG - chr5_3:20723159-20723178 Msa0804740:CDS 30.0%
ATTATAAGGATGAGAATGGA+AGG - chr5_3:20723301-20723320 Msa0804740:CDS 30.0%
AAGAAGTGAAGAAGATTGAT+TGG - chr5_3:20723416-20723435 Msa0804740:CDS 30.0%
AGAAGTGAAGAAGATTGATT+GGG - chr5_3:20723417-20723436 Msa0804740:CDS 30.0%
! ATGATCCTTTTACAGGAATA+GGG + chr5_3:20723468-20723487 None:intergenic 30.0%
! TATGATCCTTTTACAGGAAT+AGG + chr5_3:20723469-20723488 None:intergenic 30.0%
! CTAACATATGATCCTTTTAC+AGG + chr5_3:20723475-20723494 None:intergenic 30.0%
AAGGATAAGATAATGATGAG+GGG - chr5_3:20723505-20723524 Msa0804740:intron 30.0%
GATTGAAAGAGATTTAGAAG+AGG - chr5_3:20723150-20723169 Msa0804740:CDS 30.0%
AGATTTAGAAGAGGAGATTA+AGG - chr5_3:20723159-20723178 Msa0804740:CDS 30.0%
ATTATAAGGATGAGAATGGA+AGG - chr5_3:20723301-20723320 Msa0804740:CDS 30.0%
AAGAAGTGAAGAAGATTGAT+TGG - chr5_3:20723416-20723435 Msa0804740:CDS 30.0%
AGAAGTGAAGAAGATTGATT+GGG - chr5_3:20723417-20723436 Msa0804740:CDS 30.0%
! ATGATCCTTTTACAGGAATA+GGG + chr5_3:20723468-20723487 None:intergenic 30.0%
! TATGATCCTTTTACAGGAAT+AGG + chr5_3:20723469-20723488 None:intergenic 30.0%
! CTAACATATGATCCTTTTAC+AGG + chr5_3:20723475-20723494 None:intergenic 30.0%
AAGGATAAGATAATGATGAG+GGG - chr5_3:20723505-20723524 Msa0804740:intron 30.0%
CTAGAATTTCACTTCACCTT+TGG + chr5_3:20722958-20722977 None:intergenic 35.0%
CAAAGGTGAAGTGAAATTCT+AGG - chr5_3:20722956-20722975 Msa0804740:three_prime_UTR 35.0%
TTAGAAGAGGAGATTAAGGA+AGG - chr5_3:20723163-20723182 Msa0804740:CDS 35.0%
! CAAAATTAGAGCACTTTCTG+AGG - chr5_3:20723276-20723295 Msa0804740:CDS 35.0%
!! CACTTTCTGAGGTGATTATA+AGG - chr5_3:20723287-20723306 Msa0804740:CDS 35.0%
GGTGATTATAAGGATGAGAA+TGG - chr5_3:20723297-20723316 Msa0804740:CDS 35.0%
GGATAAGAAGCTACTTCAAT+TGG - chr5_3:20723543-20723562 Msa0804740:intron 35.0%
! TTGGGGTAAATTTTCCTGAT+CGG - chr5_3:20723646-20723665 Msa0804740:exon 35.0%
AACGTTATTCATATCCGATC+AGG + chr5_3:20723663-20723682 None:intergenic 35.0%
CTAGAATTTCACTTCACCTT+TGG + chr5_3:20722958-20722977 None:intergenic 35.0%
CAAAGGTGAAGTGAAATTCT+AGG - chr5_3:20722956-20722975 Msa0804740:three_prime_UTR 35.0%
TTAGAAGAGGAGATTAAGGA+AGG - chr5_3:20723163-20723182 Msa0804740:CDS 35.0%
! CAAAATTAGAGCACTTTCTG+AGG - chr5_3:20723276-20723295 Msa0804740:CDS 35.0%
!! CACTTTCTGAGGTGATTATA+AGG - chr5_3:20723287-20723306 Msa0804740:CDS 35.0%
GGTGATTATAAGGATGAGAA+TGG - chr5_3:20723297-20723316 Msa0804740:CDS 35.0%
GGATAAGAAGCTACTTCAAT+TGG - chr5_3:20723543-20723562 Msa0804740:intron 35.0%
! TTGGGGTAAATTTTCCTGAT+CGG - chr5_3:20723646-20723665 Msa0804740:exon 35.0%
AACGTTATTCATATCCGATC+AGG + chr5_3:20723663-20723682 None:intergenic 35.0%
CATCATGGAATGTACACCAA+AGG - chr5_3:20722939-20722958 Msa0804740:three_prime_UTR 40.0%
TTCAACTCCTCTGCTGAAAT+AGG + chr5_3:20723106-20723125 None:intergenic 40.0%
CCTTTCTCTGCTGAAAAATC+CGG + chr5_3:20723216-20723235 None:intergenic 40.0%
AAAGGAGAGAGATGCAAAAG+AGG - chr5_3:20723231-20723250 Msa0804740:CDS 40.0%
ATAAGGATGAGAATGGAAGG+AGG - chr5_3:20723304-20723323 Msa0804740:CDS 40.0%
TTGATTGGGAGAAGAGTTTG+AGG - chr5_3:20723431-20723450 Msa0804740:CDS 40.0%
TGATTGGGAGAAGAGTTTGA+GGG - chr5_3:20723432-20723451 Msa0804740:CDS 40.0%
TCAAGCCCTATTCCTGTAAA+AGG - chr5_3:20723460-20723479 Msa0804740:CDS 40.0%
AGAAGCTACTTCAATTGGTG+TGG - chr5_3:20723548-20723567 Msa0804740:intron 40.0%
TTGGTGTGGAAGGTTTAAAG+TGG - chr5_3:20723562-20723581 Msa0804740:intron 40.0%
CATCATGGAATGTACACCAA+AGG - chr5_3:20722939-20722958 Msa0804740:three_prime_UTR 40.0%
TTCAACTCCTCTGCTGAAAT+AGG + chr5_3:20723106-20723125 None:intergenic 40.0%
CCTTTCTCTGCTGAAAAATC+CGG + chr5_3:20723216-20723235 None:intergenic 40.0%
AAAGGAGAGAGATGCAAAAG+AGG - chr5_3:20723231-20723250 Msa0804740:CDS 40.0%
ATAAGGATGAGAATGGAAGG+AGG - chr5_3:20723304-20723323 Msa0804740:CDS 40.0%
TTGATTGGGAGAAGAGTTTG+AGG - chr5_3:20723431-20723450 Msa0804740:CDS 40.0%
TGATTGGGAGAAGAGTTTGA+GGG - chr5_3:20723432-20723451 Msa0804740:CDS 40.0%
TCAAGCCCTATTCCTGTAAA+AGG - chr5_3:20723460-20723479 Msa0804740:CDS 40.0%
AGAAGCTACTTCAATTGGTG+TGG - chr5_3:20723548-20723567 Msa0804740:intron 40.0%
TTGGTGTGGAAGGTTTAAAG+TGG - chr5_3:20723562-20723581 Msa0804740:intron 40.0%
TGAGGTTCCTATTTCAGCAG+AGG - chr5_3:20723096-20723115 Msa0804740:CDS 45.0%
!! ATTTTGCTCGTCGATTGCTC+CGG - chr5_3:20723194-20723213 Msa0804740:CDS 45.0%
!! CCGGATTTTTCAGCAGAGAA+AGG - chr5_3:20723213-20723232 Msa0804740:CDS 45.0%
GCTACTTCAATTGGTGTGGA+AGG - chr5_3:20723552-20723571 Msa0804740:intron 45.0%
TGAGGTTCCTATTTCAGCAG+AGG - chr5_3:20723096-20723115 Msa0804740:CDS 45.0%
!! ATTTTGCTCGTCGATTGCTC+CGG - chr5_3:20723194-20723213 Msa0804740:CDS 45.0%
!! CCGGATTTTTCAGCAGAGAA+AGG - chr5_3:20723213-20723232 Msa0804740:CDS 45.0%
GCTACTTCAATTGGTGTGGA+AGG - chr5_3:20723552-20723571 Msa0804740:intron 45.0%
!! ATATTTAATTAATAATAACA+TGG - chr5_3:20722914-20722933 Msa0804740:three_prime_UTR 5.0%
!! ATATTTAATTAATAATAACA+TGG - chr5_3:20722914-20722933 Msa0804740:three_prime_UTR 5.0%
GAGGGGAAAGAATGCAAGTG+AGG - chr5_3:20723522-20723541 Msa0804740:intron 50.0%
GAGGGGAAAGAATGCAAGTG+AGG - chr5_3:20723522-20723541 Msa0804740:intron 50.0%
TGGGAGAAGAGTTTGAGGGC+AGG - chr5_3:20723436-20723455 Msa0804740:CDS 55.0%
TGGGAGAAGAGTTTGAGGGC+AGG - chr5_3:20723436-20723455 Msa0804740:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 20722902 20723695 20722902 ID=Msa0804740;Name=Msa0804740
chr5_3 mRNA 20722902 20723695 20722902 ID=Msa0804740-mRNA-1;Parent=Msa0804740;Name=Msa0804740-mRNA-1;_AED=0.01;_eAED=0.01;_QI=31|1|1|1|1|1|2|116|177
chr5_3 exon 20722902 20723523 20722902 ID=Msa0804740-mRNA-1:exon:8378;Parent=Msa0804740-mRNA-1
chr5_3 exon 20723637 20723695 20723637 ID=Msa0804740-mRNA-1:exon:8377;Parent=Msa0804740-mRNA-1
chr5_3 five_prime_UTR 20723665 20723695 20723665 ID=Msa0804740-mRNA-1:five_prime_utr;Parent=Msa0804740-mRNA-1
chr5_3 CDS 20723637 20723664 20723637 ID=Msa0804740-mRNA-1:cds;Parent=Msa0804740-mRNA-1
chr5_3 CDS 20723018 20723523 20723018 ID=Msa0804740-mRNA-1:cds;Parent=Msa0804740-mRNA-1
chr5_3 three_prime_UTR 20722902 20723017 20722902 ID=Msa0804740-mRNA-1:three_prime_utr;Parent=Msa0804740-mRNA-1
Gene Sequence

>Msa0804740

ATGGATCATCATGGAATGTACACCAAAGATATGTCAAATAAAAATGTTCTTGAGGTTCCTATTTCAGCAGAGGAGTTGAAGATACGAAGTGAGCTTGCAATGATGATTGAAAGAGATTTAGAAGAGGAGATTAAGGAAGGTTTATACAATTTTGCTCGTCGATTGCTCCGGATTTTTCAGCAGAGAAAGGAGAGAGATGCAAAAGAGGCAGCATTTGATAAAGTAGATAACAAAATTAGAGCACTTTCTGAGGTGATTATAAGGATGAGAATGGAAGGAGGAACTAAAATTGAAATCAAGGAGGTTAACAAAGAAGCAAATAAAAAGGGTTGTGCTTTTACACCAAATTTTAGACCCAAAAAATGTTTGAAAGAAGTGAAGAAGATTGATTGGGAGAAGAGTTTGAGGGCAGGTTCAAGCCCTATTCCTGTAAAAGGATCATATGTTAGATCAAAGCAAAAGGATAAGATAATGATGAGGGGAAAGAATGCAAGTGAGGATAAGAAGCTACTTCAATTGGTGTGGAAGGTTTAA

Protein sequence

>Msa0804740

MDHHGMYTKDMSNKNVLEVPISAEELKIRSELAMMIERDLEEEIKEGLYNFARRLLRIFQQRKERDAKEAAFDKVDNKIRALSEVIIRMRMEGGTKIEIKEVNKEANKKGCAFTPNFRPKKCLKEVKKIDWEKSLRAGSSPIPVKGSYVRSKQKDKIMMRGKNASEDKKLLQLVWKV*